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  • International Union of Crystallography (IUCr)
  • 1995-1999  (4,021)
  • 1999  (2,258)
  • 1995  (1,763)
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Years
  • 1995-1999  (4,021)
Year
  • 1
    Electronic Resource
    Electronic Resource
    A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 140-144 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is often found in the crystallization of enzyme–inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A2 (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010024
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  • 2
    Electronic Resource
    Electronic Resource
    Crystallization of the NAD(P)-dependent glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 240-242 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NAD(P)-dependent glutamate dehydrogenase from Pyrococcus furiosus has been crystallized by the hanging-drop method of vapour diffusion using lithium sulfate as the precipitant. The crystals belong to the tetragonal system and are in space group P42212 with unit-cell dimensions of a = b = 167.2, c = 172.9 Å. Consideration of the values of Vm and possible packing of the molecules within the cell suggest that the asymmetric unit contains a trimer. P. furiosus belongs to the family of Archaea and is one of the most thermostable organisms known, having an optimal growth temperature of 376 K. The glutamate dehydrogenase isolated from this organism has a half-life of 12 h at 373 K and, therefore, the determination of the structure of this enzyme will be important in advancing our understanding of how proteins are adapted to enable them to survive at such extreme temperatures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994012862
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  • 3
    Electronic Resource
    Electronic Resource
    Shaped protein single crystals (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 278-281 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The formation of protein single crystals grown with the shape controlled by the geometry of the capillary used as a growth cell is presented. The shaped crystals show strong birefringence under crossed nicols and diffract as single crystals up to 1.74 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994013065
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  • 4
    Electronic Resource
    Electronic Resource
    NMR – this other method for protein and nucleic acid structure determination (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 249-270 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: For a quarter of a century X-ray diffraction in single crystals was unique in its ability to solve three-dimensional structures of proteins and nucleic acids at atomic resolution. The situation changed in 1984 with the completion of a protein structure determination by nuclear magnetic resonance (NMR) spectroscopy in solution, and today NMR is a second widely used method for biomacromolecular structure determination. This review describes the method of NMR structure determination of biological macromolecules, and attempts to place NMR structure determination in perspective with X-ray crystallography. NMR is most powerful for studies of relatively small systems with molecular weights up to about 30000, but these structures can be obtained in near-physiological milieus. The two techniques have widely different time scales which afford different insights into internal molecular mobility as well as different views of protein or nucleic acid molecular surfaces and hydration. Generally, in addition to information on the average three-dimensional structure, NMR provides information on a wide array of short-lived transient conformational states. Combining information from the two methods can yield a more detailed insight into the structural basis of protein and nucleic acid functions, and thus provide a more reliable platform for rational drug design and the engineering of novel protein functions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010188
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  • 5
    Electronic Resource
    Electronic Resource
    X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 190-198 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of the B-DNA dodecamer d(CGCGTTAACGCG) duplex (T2A2), with the inverted tetranucleotide core from the duplex d(CGCGAATTCGCG) [A2T2, Dickerson & Drew (1981). J. Mol. Biol. 149, 761–768], and its netropsin complex (T2A2–N) have been determined at 2.3 Å resolution. The crystals are orthorhombic, space group P212121, unit-cell dimensions of a = 25.7, b = 40.5 and c = 67.0 Å, for T2A2 and a = 25.49, b = 40.87, c = 67.02 Å for T2A2–N and are isomorphous with A2T2. The native T2A2 structure, with 70 water molecules had a final R value of 0.15 for 1522 reflections (F 〉 2σ), while for the netropsin complex, with 87 water molecules, the R value was 0.16 for 2420 reflections. In T2A2, a discontinuous string of zigzagging water molecules hydrate the narrow A·T minor groove. In T2A2–N, netropsin binds in one orientation in the minor groove, covering the TTAA central region, by displacing the string of waters, forming the majority of hydrogen bonds with DNA atoms in one strand, and causing very little perturbation of the native structure. The helical twist angle in T2A2 is largest at the duplex center, corresponding to the cleavage site by the restriction enzymes HpaI and HincII. The sequence inversion AATT→TTAA of the tetranucleotide at the center of the molecule results in a different path for the local helix axis in T2A2 and A2T2 but the overall bending is similar in both cases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010759
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  • 6
    Electronic Resource
    Electronic Resource
    Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochrome c' from two bacterial species (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 282-289 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of cytochrome c′ from two bacterial species, Alcaligenes sp and Alcaligenes denitrificans, have been determined from X-ray diffraction data to 3.0 Å resolution using the anomalous scattering of the single Fe atom in each to identify and refine a weak molecular-replacement solution. Molecular-replacement studies, with the program AMORE, used two isomorphous data sets (from the two species), two independent search models (the cytochromes c′ from Rhodospirillum molischianum and Rhodospirillum rubrum), both with and without side chains, and two different resolution ranges (10.0–4.0 and 15.0–3.5Å) to generate a large number of potential solutions. No single solution stood out and none appeared consistently. The Fe-atom position in each structure was then determined from its anomalous-scattering contribution and all molecular- replacement solutions were discarded which did not (i) place the Fe atom correctly and (ii) orient the molecule such that a crystallographic twofold axis generated a dimer like those of the two search models. Finally, electron-density maps phased solely by the Fe-atom anomalous scattering were calculated. As these were combined and subjected to solvent flattening and histogram matching (with the program SQUASH), correlation with the remaining molecular-replacement solutions identified one as correct and enabled it to be improved and subjected to preliminary refinement. The correctness of the solution is confirmed by parallel isomorphous-replacement studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994012874
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  • 7
    Electronic Resource
    Electronic Resource
    Using sampling techniques in protein crystallization (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 305-310 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystallization of homogeneous or highly purified macromolecules depends on many variables such as precipitant, pH, choice of buffer, protein concentration, temperature, the participation of different mono- and divalent ions, as well as the presence of minute amounts of detergent and organic molecules. Finding the best combination among these many parameters is a multi-variable optimization problem. This kind of problem can be treated mathematically by sampling techniques. We have used this technique for protein crystallization. The iterative procedure starts with random sampling, followed by quantitative evaluation and cycles with weighted sampling. A simple procedure, derived from this concept and called MON48, has been successfully applied to many protein crystallization problems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994011728
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  • 8
    Electronic Resource
    Electronic Resource
    Characterization of lysozyme crystals with unusually low solvent content (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 390-392 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Studies on the low-humidity (88%) forms of tetragonal and monoclinic lysozyme, resulting from water-mediated transformations, have provided a wealth of information on the variability in protein hydration, its structural consequences and the water structure associated with proteins, in addition to facilitating the delineation of the rigid and the flexible regions in the protein molecule and the invariant features in its hydration shell. Surprisingly, monoclinic lysozyme continues to diffract even when the environmental humidity is drastically reduced, thus permitting the structural study of the enzyme at different levels of hydration. As part of a study in this direction, three very low humidity forms, two of them occurring at a nominal relative humidity of 38% and the other at 5% relative humidity, have been characterized. These have unprecedented low solvent contents of 16.9, 17.6 and 9.4%, respectively, as determined by the Matthews method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994009790
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  • 9
    Electronic Resource
    Electronic Resource
    Structure of anionic salmon trypsin in a second crystal form (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 725-730 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 Å, resolution. The crystals are orthorhombic and belong to space group P21212 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 Å. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b = 84.33 and c = 39.11 Å [Smalås & Hordvik (1993). Acta Cryst. D49, 318–330]. The presence of a sulfate group involved in several hydrogen bonds to active-site residues, and the location of an additional benzamidine site in the crystal lattice, are the most striking differences between the present and the previous structure. Superposition of main-chain atoms in the two structures give an overall r.m.s. difference of 0.26 Å, with the main differences located to areas with different molecular packing. The overall coordinate error is estimated to be between 0.20 and 0.25 Å, by the method of Luzzati.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995000333
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  • 10
    Electronic Resource
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    The direct rotation function: Patterson correlation search applied to molecular replacement (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 740-748 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Most rotation functions try to achieve maximal correlation between two Patterson functions by systematically rotating one and computing the overlap with the other. In contrast, the direct rotation function rotates a search model relative to the crystal unit cell and evaluates the linear correlation coefficient (Patterson correlation, PC) between squared normalized structure-factor amplitudes of the observed and calculated diffraction data. Structure factors are calculated from the rotated search model in a P1 unit cell identical to that of the target crystal. PC makes use of all self-Patterson vectors of the search model. A comparison of the direct rotation function, a real-space rotation function, and a fast rotation function suggests that the direct rotation function provides a considerable enhancement of the signal-to-noise ratio compared to other two. Combined with PC refinement, the direct rotation function was successful in solving multidomain macromolecular crystal structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995001284
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  • 11
    Electronic Resource
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    Phase refinement and extension by means of non-crystallographic symmetry averaging using parallel computers (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 749-759 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Electron-density averaging, fast Fourier synthesis and fast Fourier analysis programs have been adapted for parallel-computing systems. These have been linked to perform iterative phase improvement and extension utilizing non-crystallographic symmetry and solvent flattening. Various strategies for parallel algorithms have been tested on a variety of computers as a function of the number of computer nodes. Some experimental timing results are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995001399
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  • 12
    Electronic Resource
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    X-ray structure determination of a dimeric hemoglobin from Caudina arenicola (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 760-766 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of a dimeric, cyanomet-liganded hemoglobin D-chain (Hb-D) from Caudina arenicola has been determined by the molecular-replacement method. The search model was a concatenated model of three hemoglobin structures superimposed on the backbone of monomeric, hemichrome hemoglobin C-chain (Hb-C) from the same organism. Hb-D crystallizes in space group P41212 with cell constants a = b = 77.0 and c =61.5 Å with one subunit in the asymmetric unit. The dimer twofold axis corresponds to a crystallographic twofold along one of the body diagonals of the unit cell. Rotation and translation searches as well as model refinement were carried out in X-PLOR with the final model having an R value of 0.19 using the data from 5.0 to 2.9 Å resolution (R = 0.26 for 10.0 to 2.9 Å resolution). The homodimeric structure of Caudina Hb-D features close heme–heme contacts with an Fe—Fe distance of 19.0 Å. The subunit-subunit interface involves both the E and F helices from each subunit with the E helices oriented antiparallel at 50° with respect to one another, similar to the quaternary structure observed for the homodimeric hemoglobin from Scapharca inaequivalvis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995001491
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  • 13
    Electronic Resource
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    Non-ideality of aqueous solutions of polyethylene glycol: consequences for its use as a macromolecular crystallizing agent in vapor-diffusion experiments (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 772-779 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Microisopiestic measurements of the concentrations of polyethylene glycol (PEG 8000) paired with the salts sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been made in a sitting-drop arrangement with PEG in the droplet and salt in the reservoir. Resulting graphs of the concentrations of PEG and salt that are equivalent with respect to the vapor pressure of water are non-linear, do not intersect their origins, and demonstrate that relatively low (mM) salt concentrations are equivalent to relatively high PEG concentrations. The consequences of each of these observations for macromolecular crystallization by the vapor-diffusion technique when PEG is employed as the crystallizing agent are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995000436
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  • 14
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    Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 767-771 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of bovine ribonuclease A cocrystallized with the dinucleotide deoxycytidylyl-3′,5′-guanosine has been determined at 1.9 Å resolution and refined by restrained least squares to R = 0.218 for 7807 reflections. The structure established that the recently observed retrobound mode of attachment of substrate analogues cytidylyl-2′,5′-guanosine and deoxycytidylyl-3′,5′-guanosine found in soaked RNase A crystals is also present in the cocrystallized complex. Retrobinding is thus unlikely to be the result of restrictions imposed by the crystalline environment as the ligands soak into the lattice but rather a phenomenon specific to small nucleotides containing guanine.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995001570
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  • 15
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    Structure of native pancreatic elastase from North Atlantic salmon at 1.61 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 925-937 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of native salmon pancreatic elastase (SPE) has been solved by molecular-replacement methods, and refined by conventional conjugate-gradient methods and simulated-annealing techniques. The final R value is 17.2% for 21 389 reflections between 8.0 and 1.61 Å, and the corresponding free R value is 23.9%. The overall tertiary structure of SPE is remarkably similar to that of porcine pancreatic elastase I (PPE), to which it shows about 67% sequence identity. The primary structure of SPE is determined from the electron-density maps, and only about 15 side chains are somewhat uncertain. Interesting differences between SPE and PPE, are one sequence deletion assigned to position 186, the residue 192 at the entrance of the specificity pocket is substituted from a Gln in PPE to Asn in SPE, and one of the calcium ligands is different. Furthermore, electron density is missing in SPE for the last three residues of the C-terminal helix. A comparison of the present amino-acid sequence of SPE with other sequences available indicates that SPE belongs to the class 1 pancreatic elastases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995004835
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  • 16
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    Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 805-813 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Liver alcohol dehydrogenase (LADH) is a ZnII-dependent dimeric enzyme. LADH with the active-site ZnII substituted by CuII resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure of the active site CuII-substituted LADH complex with NADH and dimethyl sulfoxide (DMSO). The structure was solved by molecular replacement. The space group is P21 with cell dimensions a = 44.4, b = 180.6, c = 50.8 Å and β = 108°. There is one dimer of the enzyme in the asymmetric unit. The refinement was carried out to a crystallographic R-factor of 16.1% for 41 119 unique reflections in the resolution range 12.0 to 2.1 Å. The coordination geometry of CuII in LADH is compared with the active-site metal coordination in the Zn–LADH–NADH–DMSO complex and blue-copper proteins. The distances from the metal to the protein ligands (Cys46, His67 and Cys174) are similar for the ZnII and CuII ions. The distances of the O atom of the inhibitor DMSO to the CuII ion in the two subunits of the dimer are 3.19 and 3.45 Å. These are considerably longer than the corresponding distances for the ZnII enzyme, 2.19 and 2.15 Å. The CuII ion is positioned nearly in the plane of the three protein ligands (NS2) with a geometry similar to the trigonal arrangement of the three strongly bound ligands (N2S) in blue-copper proteins. This coordination probably accounts for the similarity of the spectral characteristics of CuII–LADH and type I copper proteins.
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    URL: http://dx.doi.org/10.1107/S090744499500045X
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  • 17
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    Phasing with mercury at 1 Å wavelength (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 814-818 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Synchrotron sources provide a continuously tunable X-ray beam which makes it possible to optimize the anomalous contribution to phase determination using heavy-atom replacement. This method was used to solve two protein structures, those of Dictyostelium discoideum nucleoside diphosphate kinase and of lobster enolase. The first had 17 kDa of protein in the asymmetric unit, the second, 47 kDa. In both cases, a single mercury derivative yielded single isomorphous replacement with anomalous-scattering phases from which an interpretable electron-density map was derived by solvent flattening. The efficient solution of the X-ray structure was largely due to the large anomalous scattering of mercury at a wavelength shorter than the LIII absorption edge.
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    URL: http://dx.doi.org/10.1107/S0907444995000655
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  • 18
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    Determination of hemihedral twinning and initial structural analysis of crystals of the procarboxypeptidase A ternary complex (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 819-823 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The initial structural analysis of the ternary complex of procarboxypeptidase A from hemihedrally twinned crystals diffracting up to 2.8 Å is described. Detection of twinning by different techniques is presented, including biochemical and intensity statistics approaches. The structure was initially solved using Patterson-search techniques, and the three positioned search models were used to effectively deconvolute the twinned data.
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    URL: http://dx.doi.org/10.1107/S0907444995000643
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  • 19
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    Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 Å resolution X-ray fibre diffraction data (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 792-804 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of α-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous α-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the α-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 Å resolution X-ray diffraction data.
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    URL: http://dx.doi.org/10.1107/S0907444995003027
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  • 20
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    Crystallization and preliminary X-ray diffraction analysis of glutathione peroxidase from human plasma (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 824-826 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The extracellular form of glutathione peroxidase from human plasma has been crystallized by the sitting-drop vapour-diffusion method. The crystals belong to tetragonal space group I41 with cell dimensions of a = b = 83.1 and c = 131.0 Å. They diffract beyond 2.9 Å resolution and have one dimer in the asymmetric unit. A self-rotation function analysis shows the possible (222) symmetry for the tetramers of this enzyme.
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    Crystallization and preliminary X-ray crystallographic analysis of carbamoyl phosphate synthetase from Escherichia coli (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 827-829 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Carbamoyl Phosphate synthetase catalyzes the formation of carbamoyl phosphate, a high-energy intermediate used in several biosynthetic pathways. The enzyme from Escherichia coli has been crystallized at pH 8 in the presence of L-ornithine, MnCl2 and ADP, using PEG 8000 in combination with NEt4Cl and KCl. The crystals (apparently) belong to the orthorhombic space group P212121 with unit-cell dimensions of a = 154.4, b = 166.5 and c = 338.7 Å. The crystals are relatively sensitive to radiation damage, but show diffraction to beyond 2.8 Å resolution. A low-resolution (3.5 Å) native data set has been recorded and conditions for flash cooling the crystal have been established.
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    Additional crystal forms of the E. coli class II fructose-1,6-bisphosphate aldolase (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 833-834 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: We have obtained two additional crystal forms of the metal-dependent class II fructose-1,6-bisphosphate aldolase from Escherichia coli. Crystals in the shape of elongated plates have unit-cell dimensions a = 73.4, b = 120.0, c = 190.1 Å, orthorhombic space group P212121. Monoclinic prisms have unit-cell dimensions a = 67.7, b = 104.3, c = 52.8 Å, β = 105°, space group P21. Diffraction to slightly better than 3.0 Å, has been observed for both forms using in-house and synchrotron facilities. These crystal forms may aid the structure solution of this enzyme by presenting additional forms for heavy-atom derivatization. These forms have multiple copies of the enzyme in the asymmetric unit and averaging methods might also be useful in the analysis.
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    Crystallization and preliminary X-ray crystallographic studies of glutamic acid-specific proteinase from Bacillus licheniformis complex with Z-Leu-Glu-CH2Cl (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 835-836 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A glutamic acid specific proteinase from Bacillus licheniformis has been crystallized as a complex with the inhibitor Z-Leu-Glu-CH2Cl. Crystals were grown by the vapor-diffusion method using sodium formate as a precipitant. The crystals diffracted to about 2.0 Å resolution and belonged to the trigonal space group P3121 (P3221) with unit-cell parameters a = b = 134.3, c = 109.7 Å. A total of 26 964 independent reflections were obtained up to 2.2 Å resolution, the merging R-factor being 0.05 for 42 614 measurements.
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    Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 511-521 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase activity of calcineurin. Rapamycin (sirolimus), which is itself an immunosuppressant by a different mechanism, completes with FK506 for binding to FKBP12 and thereby acts as an antagonist of calcineurin inhibition. We have solved the X-ray structure of unliganded FKBP12 and of FKBP12 in complex with FK506 and with rapamycin; these structures show localized differences in conformation and mobility in those regions of the protein that are known, by site-directed mutagenesis, to be involved in calcineurin inhibition. A comparison of 16 additional X-ray structures of FKBP12 in complex with FKBP12-binding ligands, where those structures were determined from different crystal forms with distinct packing arrangements, lends significance to the observed structural variability and suggests that it represents an intrinsic functional characteristic of the protein. Similar differences have been observed for FKBP12 before, but were considered artifacts of crystal-packing interactions. We suggest that immunosuppressive ligands express their differential effects in part by modulating the conformation of FKBP12, in agreement with mutagenesis experiments on the protein, and not simply through differences in the ligand structures themselves.
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    Crystallization and preliminary characterization of human recombinant N-acetylgalactosamine-4-sulfatase (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1082-1083 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of human recombinant N-acetylgalactosamine-4-sulfatase have been grown using vapour diffusion. The protein contains approximately 13%(w/w) carbohydrate. The crystals belong to the tetragonal space group P41212 or its enantiomorph P43212 with a = b = 108.0 and c = 145.5 Å. The crystals diffract to 2.7 Å resolution.
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    Crystallization and preliminary X-ray analysis of pyruvate kinase type I from Escherichia coli (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1089-1091 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the fructose-l,6-bisphosphate-dependent pyruvate kinase from Escherichia coli have been grown using the hanging-drop vapour-diffusion technique. The space group was found to be C2221 with cell dimensions a = 76.8, b = 247.5, c = 132.6 Å. Diffraction data to 3.0 Å resolution have been recorded and the enzyme molecular symmetry analysed through inspection of the self-rotation function. The crystallized protein is in the allosterically inactive T state.
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    Crystallography made crystal clear. A guide for users of macromolecular models by G. Rhodes (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1103-1103 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Crystal structure analysis for chemists and biologists by J. P. Glusker, M. Lewis and M. Rossi (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1103-1103 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Active-site mimetic inhibition of thrombin (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 550-559 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structures of two mimetic inhibitor complexes of human α-thrombin have been determined by X-ray crystallography. One mimics a β-turn with a bicyclic ring system; the other mimics two different active-site binding modes. The β-turn mimetic is used to approximate a turn found in the conformation of fibrinopeptide A, which is catalytically released by thrombin in the activation of fibrinogen to fibrin. The binding of the second mimetic is a hybrid between normal substrate and the abnormal binding of the potent natural leech inhibitor hirudin. The binding of the β-turn mimetic is tenuous, because it is like a substrate, while that of the substrate–hirudin hybrid is that of a tenacious inhibitor (which it is). Structurally retrospect modifications for rational design and improvement of both mimetic inhibitors are proposed.
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    Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 560-566 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Several empirical modeling protocols are evaluated allowing a quantification of the interaction between an enzyme and a series of inhibitors. The evaluation and optimization of the modeling protocols used a database of 35 non-covalently bound inhibitors of human thrombin. Intermolecular interaction energies were calculated with CHARMm after energy minimization of the modeled complexes using various dielectric functions and constraining strategies. These calculated binding energies were correlated with the experimentally obtained binding constants of the inhibitors. The best protocols resulted in linear correlations with correlation coefficients 〉 0.80. In the best protocols the enzyme was fully constrained, the ligand was allowed to move freely and electrostatics were scaled down drastically or fully neglected during the energy minimization. For the interaction energy evaluation step, a distance-dependent dielectric function ε = R proved to be optimal. This simple empirical protocol, that neglects solvation or entropy effects, can be implemented readily in other force field packages and may be applied on various enzyme–inhibitor complexes, providing a tool for the evaluation and rank-ordering of newly designed inhibitors.
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    Molecular dynamics and structure-based drug design for predicting non-natural nonapeptide binding to a class I MHC protein (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 541-549 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Starting from the known three-dimensional structure of the class I major histocompatibility complex-encoded HLA-B*2705 protein, three non-natural nonapeptides were designed to fit optimally the HLA-B*2705-binding groove. The optimization was performed using structure-based drug design methods and the fact that all the possible interactions of the secondary anchor residue (position 3) with its human leukocyte antigen-binding pocket (pocket D) in nature are not entirely utilized. 150 ps molecular-dynamics (MD) simulation in water was employed to study the stability of the bimolecular complexes with three non-natural peptides (P3 = homophenylalanine, β-naphthylalanine, α-naphthylalanine) as well as with the two natural homologues (P3 = Gly, Leu). Various structural and dynamical properties (atomic fluctuations, solvent-accessible surface areas, peptide Cα-atom positions) of the simulated bimolecular complexes were used to compare the three non-natural with the two natural ligands. Since the various molecular properties have been shown previously to be related to the binding affinity of nonapeptide ligands to the major histocompatibility complex (MHC) HLA-B*2705 protein, the MD data predict a rather higher stability of MHC–ligand complexes with the three non-natural peptides, suggesting that the unnatural peptides studied show an enhanced binding affinity to the HLA-B*2705 protein. These results are in agreement with the experimental values of a semi-quantitative in vitro assembly assay, performed on the five nonapeptides (P3 = Gly, Leu, homophenylalanine, β-naphthylalanine, α-naphthylalanine), which shows their ability to stabilize the native conformation of the HLA-B*2705 heavy chain and also shows that the three non-natural ligands bind with higher affinity (0.5 µM) to the MHC protein than the two natural homologues (40 µM). Thus, this study demonstrates that structural information combined with rational design and molecular-dynamics simulations can illustrate and predict MHC binding and potential T-cell epitope properties as well as contribute to the design of new non-peptidic MHC inhibitors that may be useful for the selective immunotherapy of autoimmune diseases to which HLA alleles are directly associated.
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    Deposition of structure factors at the Protein Data Bank (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 4-4 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Improving the diffraction quality of MTCP-1 crystals by post-crystallization soaking (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 5-7 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Significant improvement in the resolution and quality of the X-ray diffraction of crystals of MTCP-1 protein was observed on post-crystallization soaking. The MTCP-1 crystals grown from 1.5 M ammonium sulfate diffracted to only 3.0 Å resolution with some disorder in the diffraction. After post-crystallization soaking in a solution containing 2.0 M ammonium sulfate, the disorder was eliminated and diffraction extended to better than 2.0 Å resolution. Both native and selenomethionine-enriched crystals demonstrated better diffraction after soaking for several months. This simple technique may be useful to improve the diffraction quality of protein crystals generally.
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    Structure of the bifunctional inhibitor of trypsin and α-amylase from ragi seeds at 2.9 Å resolution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 25-30 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of a bifunctional inhibitor of α-amylase and trypsin from the seeds of ragi (Indian finger millet, Eleusine coracana Gaertneri) has been determined by an X-ray diffraction method. The inhibitor consists of 122 amino acids with five disulfide bridges and belongs to the plant α-amylase/trypsin-inhibitor family. This is the first crystal structure determination of a member of this family. The protein, purified from the seeds of ragi, has a molecular mass of 13300 Da with a pI of 10.3. Crystals were grown by a microdialysis method using ammonium sulfate as precipitant. The improved purification protocol and the modified crystallization conditions enabled reproducible growth of the crystals. The cell parameters are a = 41.2, b = 47.4, c = 55.9 Å. The intensity data were collected to 2.9 Å resolution, and the crystal structure was determined using the molecular-replacement method. The structure was refined using the X-PLOR and CCP4 program packages to a conventional R factor of 21%. The structure contains four α-helices between residues 19–29, 37–51, 56–65 and 90–95, and two short antiparallel β-strands between residues 67–70 and 73–75.
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    The structure of carbamoyl phosphate synthetase determined to 2.1 Å resolution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 8-24 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As isolated from Escherichia coli, the enzyme is an \alpha,β-heterodimer consisting of a small subunit that hydrolyzes glutamine and a large subunit that catalyzes the two required phosphorylation events. Here the three-dimensional structure of carbamoyl phosphate synthetase from E. coli refined to 2.1 Å resolution with an R factor of 17.9% is described. The small subunit is distinctly bilobal with a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. As observed in those enzymes belonging to the \alpha/\beta-hydrolase family, the active-site nucleophile, Cys269, is perched at the top of a tight turn. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain. Both the carboxyphosphate and carbamoyl phosphate synthetic components bind Mn2+ADP. In the carboxyphosphate synthetic component, the two observed Mn2+ ions are both octahedrally coordinated by oxygen-containing ligands and are bridged by the carboxylate side chain of Glu299. Glu215 plays a key allosteric role by coordinating to the physiologically important potassium ion and hydrogen bonding to the ribose hydroxyl groups of ADP. In the carbamoyl phosphate synthetic component, the single observed Mn2+ ion is also octahedrally coordinated by oxygen-containing ligands and Glu761 plays a similar role to that of Glu215. The carboxyphosphate and carbamoyl phosphate synthetic components, while topologically equivalent, are structurally different, as would be expected in light of their separate biochemical functions.
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    Structure analysis of bovine heart cytochrome c oxidase at 2.8 Å resolution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 31-45 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of bovine heart cytochrome c oxidase has been determined at 2.8 Å resolution by the multiple isomorphous replacement (MIR) method with three heavy-atom derivatives. An asymmetric unit of the crystal has a molecular weight of 422 kDa. Eight heavy atoms as main sites of a CH3HgCl derivative were clearly located by solving the difference Patterson function. The electron density obtained by the MIR method was refined by density modification, consisting of solvent flattening, histogram matching and non-crystallographic symmetry averaging. The enzyme exhibits a dimeric structure in the crystal. Out of 3606 amino-acid residues in 26 subunits in the dimer, 3560 residues were located in the electron-density map. The structure was refined by X-PLOR. The final R factor and the free R factor were 0.199 and 0.252 at 2.8 Å resolution, respectively. One monomer in the dimeric structure with a stronger packing interaction has a lower averaged temperature factor than the other, by 16 Å2. The region \pm12 Å from the centre of the transmembrane part is almost 100% \alpha-helix, despite the glycine residue content being as high as 7.1% in the transmembrane region. The residues around haem a of animals have evolved away from those of bacteria in contrast with the residues of the haem a3. The hierarchy of the structural organization of the enzyme complex has been proposed on the basis of intersubunit interactions.
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    High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 46-50 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of recombinant bovine pancreatic phospholipase A2 (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Å resolution. The crystal belongs to the space group P212121 with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Å similar to the native enzyme reported previously by Dijkstra et al. [J. Mol. Biol. (1981), 147, 97–123]. The refinement converged to an R value of 18.4% (Rfree = 22.8%) for 16 374 reflections between 10.0 and 1.5 Å resolution. The surface-loop residues (60–70) are ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis. The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion. In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.
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    Structural studies on the binding of 4-methylumbelliferone glycosides of chitin to rainbow trout lysozyme (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 60-66 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two complexes between rainbow trout lysozyme (RBTL) and 4-methylumbelliferyl chitobioside, 4MeU-(GlcNAc)2, and chitotrioside, 4MeU-(GlcNAc)3, were produced by co-crystallization and soaking, respectively, and the crystal structures were solved at 2.0 Å resolution. The results show that 4-MeU-(GlcNAc)3 binds in subsites A–D and that 4-MeU-(GlcNAc)2 binds in subsites B–D in the active-site cleft of RBTL. This agrees well with earlier crystallographic studies on the binding of oligosaccharides of chitin to RBTL, which showed that (GlcNAc)3 binds to sites B–D in RBTL and not to A–C as seen in the human and turkey egg-white lysozymes. For both complexes the 4-MeU moiety in site D has diffuse electron density and is flexible, as it is only bound to water molecules and not to the protein. Since no electron density was observed in site E, the solved structures give views of nonproductive enzyme–substrate complexes.
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    A MAD experiment performed at the white line of the iridium LIII absorption edge in lysozyme (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 67-76 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A multiple-wavelength anomalous diffraction (MAD) experiment was performed on an iridium derivative of hen egg-white lysozyme. Diffraction data were measured at five wavelengths on the X31 EMBL beamline on the DORIS III storage ring and at two further wavelengths on the X11 beamline. Four iridium-binding sites were located from the dispersive anomalous differences between two wavelengths at the rising and falling inflection points of the Ir LIII-edge white line using direct methods. All other attempts to determine the heavy-atom positions failed. The results demonstrate an experimental method whereby systematic error in MAD data due to sample absorption can be reduced where a white line is present in the absorption spectrum of a heavy atom.
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    Oligonucleotides with 1,5-anhydrohexitol nucleoside building blocks: crystallization and preliminary X-ray studies of h(GTGTACAC) (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 279-280 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Hexitol nucleic acids are oligonucleotides built up from natural nucleobases and a phosphorylated 1,5-anhydrohexitol backbone. The anhydrohexitol oligonucleotide h(GTGTACAC) was synthesized using phosphoramidite chemistry and standard protecting groups. Crystals of h(GTGTACAC) were obtained at either 279 or 289 K by the hanging-drop vapour-diffusion technique using a 24-matrix screen for nucleic acid fragments. The crystals diffract beyond 2.0 Å resolution and belong to the hexagonal space group P6222 (or P6422) with unit-cell parameters a = 36.42 and c = 63.33 Å.
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    Crystallization and preliminary X-ray analysis of the bacterial ATP-binding-cassette (ABC) protein MalK (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 285-286 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The ATP-binding protein, MalK, of the bacterial ABC (ATP-binding-cassette) transport complex MalFGK2 provides the energy for the translocation of maltose and maltodextrins across the cytoplasmic membrane. The MalK protein from Salmonella typhimurium was overexpressed in Escherichia coli and crystallized by the hanging-drop method using (NH4)2SO4 as a precipitant. The crystals belong to space group P6x22 (most probably x = 1 or 5) with cell dimensions a = 181.8 and c = 182.5 Å, corresponding to three or four molecules per asymmetric unit. They diffract to a resolution of about 3 Å on a synchrotron X-ray source and are suitable for structure determination.
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    Cloning, expression and crystallization of pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 287-290 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pyrimidine nucleoside phosphorylase (PYNP) from B. stearothermophilus has been cloned and purified for crystallization. Crystals of a potential protein–inhibitor complex have been prepared by co-crystallization techniques using the substrate analog pseudouridine. These crystals provide good-quality diffraction images to 2.7 Å and belong to space group P21. The asymmetric unit contains the dimer structure of PYNP with unit-cell parameters a = 53.9, b = 71.9, c = 123.3 Å and β = 96.9°.
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    Purification, crystallization and preliminary X-ray diffraction analysis of the yeast phosphorelay protein YPD1 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 291-293 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: YPD1 is a yeast osmoregulatory protein that functions in a phosphorelay signal-transduction pathway. YPD1 has been expressed in Escherichia coli, purified to homogeneity and crystallized. The crystals were obtained by hanging-drop vapor-diffusion using PEG 4000 as a precipitant. Preliminary X-ray diffraction analysis indicates that the crystals belong to tetragonal space group P43212 or P41212 with unit-cell dimensions a = b = 52.71, c = 244.02 Å. X-ray data to 2.7 and 3.0 Å have been collected from native crystals and a heavy-atom derivative, respectively. Positions for two Hg atoms have been located by analysis of difference Patterson maps.
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    Crystallization of the dimerization-initiation site of genomic HIV-1 RNA: preliminary crystallographic results (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 281-284 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The genomic RNA of all retroviruses is encapsidated in virions as a dimer of single-stranded chains held together near their 5′-end. For HIV-1, the initial site of dimerization has been shown to be a hairpin with a nine-residue loop containing a self-complementary sequence of six residues. This structure is proposed to promote dimerization by loop–loop interaction and formation of a so-called `kissing complex'. A 23-nucleotide RNA strand containing the loop enclosed by a seven base-pair stem has been synthesized. This oligomer was crystallized by the vapour-diffusion method at 310 K, pH 6.5, with methyl-pentanediol as the precipitant agent in the presence of MgCl2, KCl and spermine. Quasi-complete diffraction data were obtained at 2.7 Å resolution with a conventional X-ray source and at 2.3 Å resolution on a synchrotron beamline. The space group is P3121 or its enantiomorph P3221, with cell parameters a = b = 60.1, c = 65.9 Å at ambient temperature, or a = b = 59.0, c = 64.3 Å in a nitrogen-gas stream. There are two oligomers per asymmetric unit as determined from absorbance measurements of a dissolved crystal whose volume was carefully determined. In some cases, either perfectly or partially twinned crystals were obtained. Perfect twinning is detected by an apparent hexagonal symmetry and yields unusable crystallographic data, whilst partial twinning yields usable data after adequate processing. Structure solution is under way by searching for heavy-atom derivatives and systematically substituting bromo- or iodo-uridines for uridines.
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    A thermostable xylose isomerase from Thermus caldophilus: biochemical characterization, crystallization and preliminary X-ray analysis (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 294-296 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A highly thermostable xylose isomerase from Thermus caldophilus has been expressed in Escherichia coli. The purified enzyme has an optimum temperature of 363 K. It has been crystallized at room temperature using ammonium sulfate as a precipitant. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 84.35, b = 123.60, c = 140.24 Å. The presence of one molecule of tetrameric xylose isomerase in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.1 Å3 Da−1 and a solvent content of 41% by volume. The crystals initially showed diffraction to 1.7 Å Bragg spacing with synchrotron X-rays, and a set of native data extending to 2.3 Å resolution has been collected.
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    The incorporation of a non-natural amino acid (aza-tryptophan) may help to crystallize a protein and to solve its crystal structure. Application to bacteriophage λ lysozyme. (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 430-435 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Until now, wild-type bacteriophage λ lysozyme had been impossible to crystallize. This difficulty could be overcome by the replacement of the four tryptophan residues by aza-tryptophans. Analysis of the intermolecular and intramolecular contacts in this modification allows understanding of the differences in behaviour between the native and modified molecules. Furthermore, this mutation was very useful for the creation of new heavy-atom binding sites and for the solution of the non-crystallographic symmetry, which is extremely important for phase improvement. This procedure seems to be generally applicable, at least in the search for new possibilities for heavy-atom binding sites.
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    Dimorphism of polyglycine I: structural models for crystal modifications (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 436-442 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Re-examination of the known data on crystalline forms of polyglycine reveals that the crystal modification `polyglycine I' has two different three-dimensional structures depending on the molecular weight. Structural models for both low molecular weight (LMW) and high molecular weight (HMW) polyglycine I crystals are described. In the LMW crystal model, the molecules have an unusual extended conformation generated by alternation of two mirror-symmetrical residual conformations along the chain. The molecules are parallel and each chain forms interpeptide hydrogen bonds with four adjacent chains. The structural model for the HMW crystal represents a composition of twinning crystallites. The crystallites themselves consist of antiparallel enantiomorphous chains united by hydrogen bonds to form rippled sheets. Calculations of the diffraction patterns and packing energy show that these polyglycine I structures have a higher level of conformity with the experimental data than previously suggested models. New insight into the structure of the polyglycine associates opens up the possibility of designing improved silk-like and nylon materials.
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    Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 443-447 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 Å resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.
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    Isomorphous replacement combined with anomalous dispersion in the linear equations: application to a crystal containing four nonapeptide conformers (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 448-457 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The investigation of the structure of the four conformers of the nonapeptide described here has an additional purpose: to illustrate a method for combining isomorphous replacement information with anomalous dispersion information within the linear equations that have found use in the analysis of multiple-wavelength anomalous dispersion data. In the present application, isomorphous replacement data were obtained from the replacement of naturally occurring S atoms in the nonapeptide with Se atoms. Only one wavelength was used for the analysis: Cu Kα radiation. Details of the analysis are presented, as well as the structural results obtained. It was found that the four independent molecules in the structure have similar, but not identical, conformations. The backbones fold into predominantly α-helices with one or two 310-type hydrogen bonds and have extended side chains. Three to four water molecules are associated with each of the four head-to-tail regions between the peptides. Optimal packing between hydrophobic surfaces may account for the existence of four molecules in an asymmetric unit.
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    Envelope skeletonization as a means to determine monomer masks and non-crystallographic symmetry relationships: application in the solution of the structure of fibrinogen fragment D (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 458-463 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An algorithm is described which utilizes the solvent mask generated by the solvent-flattening technique to calculate a monomer molecular envelope. In the case where non-crystallographic symmetry (NCS) is present in the crystal and self-rotation angles are known from a self-rotation function, the resultant monomer envelopes can be used to search for the translation component of the NCS element by a three-dimensional search in real space. In the absence of self-rotation angles, the monomer envelope may be used to derive the NCS operators by reciprocal-space techniques. Thus, an automatic procedure for averaging directly from the solvent-flattening stage can be implemented. The procedure was instrumental in the structure solution of fibrinogen fragment D, which is presented as an example.
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    Real-space molecular-dynamics structure refinement (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 464-468 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.
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    Reliability of atomic displacement parameters in protein crystal structures (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 473-478 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases – an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.
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    PBR: a heavy-atom refinement and phasing procedure to reduce phase bias when heavy-atom derivatives contain common sites (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 469-472 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A procedure, called PBR (phase-bias reduction), has been developed to properly refine heavy-atom derivatives and to generate less biased heavy-atom phases when these derivatives contain common heavy-atom sites. Two independent events are obtained by splitting the refinement and phasing calculations into two stages, the first in which one of the derivatives having common sites is used together with the native amplitudes and the second in which both derivatives with common sites are used simultaneously, with one of them being used as the native data set. Improved centroid phases and the corresponding figures of merit are obtained by phase combination. This procedure has been used in the structure determination of the iron-cluster-containing protein pyruvate–ferredoxin oxidoreductase. When the common heavy-atom sites are properly treated by the PBR procedure, the resulting calculated centroid phases are improved with respect to classical heavy-atom refinement centroid phases where all derivatives are refined together. This leads to improved electron-density distributions, since anomalous difference Fourier maps calculated with the PBR-refined centroid phases and corresponding figures of merit show more clearly the positions of the iron sites.
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    Crystallogenesis studies on yeast aspartyl-tRNA synthetase: use of phase diagram to improve crystal quality (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 149-156 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Aspartyl-tRNA synthetase (AspRS) extracted from yeast is heterogeneous owing to proteolysis of its positively charged N-terminus; its crystals are of poor quality. To overcome this drawback, a rational strategy was developed to grow crystals of sufficient quality for structure determination. The strategy is based on improvement of the protein homogeneity and optimization of crystallization, taking advantage of predictions from crystal-growth theories. An active mutant lacking the first 70 residues was produced and initial crystallization conditions searched. The shape and habit of initial crystals were improved by establishing a phase diagram of protein versus crystallizing-agent concentrations. Growth of large well faceted crystals takes place at low supersaturations near the isochronic supersolubility curve. Further refinement led to reproducible growth of two crystalline forms of bipyramidal (I) or prismatic (II) habit. Both diffract X-rays better than crystals previously obtained with native AspRS. Complete data sets were collected at 3 Å resolution for form I (space group P41212) and form II (space group P3221) and molecular-replacement solutions were found in both space groups.
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    On the application of phase relationships to complex structures. XXXVI: some experiments with a small protein without heavy atoms (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 168-172 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program MULTAN88 has been applied to a known protein, ribonuclease (RNAP1), containing 808 non-H atoms, including five S atoms, plus 83 ordered solvent water molecules. Phase sets with mean phase errors between 69 and 75° were selected by modified figures of merit for trials with the full data at 1.17 Å resolution and also with restricted data at 1.25 and 1.5 Å resolution. These figures of merit had previously only been applied to protein structures containing heavy atoms, and this is the first demonstration of their usefulness with no heavy atom present. An initial set of 1091 phases from a 1.17 Å trial was developed by an objective procedure to give the full structure with a residual of 0.21, which agrees well with the published structure.
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    Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 157-167 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A previous article [Fourme et al. (1995). J. Synchrotron Rad. 2, 36–48] presented the theoretical foundations of MASC, a new contrast-variation method using multiwavelength anomalous scattering, and reported the first experimental results. New experiments have been conducted both at the ESRF (Grenoble, France) and at LURE-DCI (Orsay, France), using cryocooled crystals of three proteins of known structures and very different molecular weights. Amplitudes of \{\Gamma_T({\bf h})\}, the `normal' structure factors of the anomalously scattering part of the crystal including the solvent zone and the ordered anomalous scattering sites (if any), have been extracted from multiwavelength data. In the very low resolution range (d \ge 20 Å), the agreement between experimental \{|\Gamma_T({\bf h})|\} and model values calculated from the bulk solvent is all the more satisfactory since the molecular weight of the protein is high. For spacings between 10 and 20 Å, the agreement between experimental \{|\Gamma_T({\bf h})|\} and model values is also satisfactory if one takes into account ordered anomalous scatterer sites. Such sites have been found in the three cases.
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    Refinement and structural analysis of barnase at 1.5 Å resolution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 386-398 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extracellular 110-residue enzyme initially solved at 2.0 Å resolution, has been refined at 1.5 Å using synchrotron radiation and an imaging-plate scanner. Refinement with anisotropic atomic displacement parameters resulted in increased accuracy of the structure. The final model has a crystallographic R factor of 11.5% and an Rfree of 17.4%. The three independent molecules in the asymmetric unit, referred to as A, B and C, allowed detailed analysis of this final model and meaningful comparison with structures of barnase complexed either with nucleotide inhibitors or with its natural intracellular inhibitor, barstar. The analysis of the overall solvent structure revealed a similar number of water molecules associated with each barnase molecule; among these were 16 equivalent buried solvent molecules, the locations of which are discussed in detail and classified on the basis of their structural role. The importance of the water molecules' contribution to the barnase–barstar interaction is also highlighted. The high accuracy of the present analysis revealed the presence of a Zn2+ ion mediating the contacts between pairs of symmetry-related A, B or C molecules; such an ion had previously only been identified for pairs of C molecules.
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    Structure of recombinant human lactoferrin expressed in Aspergillus awamori (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 403-407 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human lactoferrin (hLf) has considerable potential as a therapeutic agent. Overexpression of hLf in the fungus Aspergillus awamori has resulted in the availability of very large quantities of this protein. Here, the three-dimensional structure of the recombinant hLf has been determined by X-ray crystallography at a resolution of 2.2 Å. The final model, comprising 5339 protein atoms (residues 1–691, 294 solvent molecules, two Fe3+and two CO_3^{2-} ions), gives an R factor of 0.181 (free R = 0.274) after refinement against 32231 reflections in the resolution range 10–2.2 Å. Superposition of the recombinant hLf structure onto the native milk hLf structure shows a very high level of correspondence; the main-chain atoms for the entire polypeptide can be superimposed with an r.m.s. deviation of only 0.3 Å and there are no significant differences in side-chain conformations or in the iron-binding sites. Dynamic properties, as measured by B-value distributions or iron-release kinetics, also agree closely. This shows that the structure of the protein is not affected by the mode of expression, the use of strain-improvement procedures or the changes in glycosylation due to the fungal system.
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    The structure of plastocyanin from the cyanobacterium Phormidium laminosum (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 414-421 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the `blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 Å X-ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 Å and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity). The molecule of P. laminosum plastocyanin has 105 amino-acid residues. The single Cu atom is coordinated by the same residues – two histidines, a cysteine and a methionine – as in other plastocyanins. In the crystal structure, the three molecules of the asymmetric unit are related by a non-crystallographic threefold axis. A Zn atom lies between each pair of neighbouring molecules in this ensemble, being coordinated by a surface histidine residue of one molecule and by two aspartates of the other.
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    Expression, crystallization and preliminary X-ray diffraction studies of N-carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 694-695 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Agrobacterium radiobacter CCRC 14924 N-carbamyl-D-amino-acid amidohydrolase, the enzyme used for production of D-amino acids, was overexpressed in Escherichia coli JM109. The expressed protein was crystallized by vapour diffusion using lithium sulfate as precipitant. It crystallizes in space group P21 with unit-cell parameters a = 69.8, b = 67.9 and c = 137.8 Å and β = 96.4°. There are four molecules per asymmetric unit. Crystals diffract to 2.8 Å resolution using a rotating-anode source at cryogenic (113 K) temperatures.
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    Crystallization and preliminary X-ray diffraction studies of the lipopolysaccharide core biosynthetic enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12A preliminary report of this work was presented at the American Society for Biochemistry and Molecular Biology Meeting, San Francisco, California, August 24–29, 1997. (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 685-688 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: ADP-L-glycero-D-mannoheptose 6-epimerase is a 240 kDa NAD-dependent nucleotide diphosphosugar epimerase from Escherichia coli K12 which catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose. ADP-L-glycero-D-mannoheptose is a required intermediate for lipopolysaccharide inner-core and outer-membrane biosynthesis in several genera of pathogenic and non-pathogenic Gram-negative bacteria. ADP-L-glycero-D-mannoheptose 6-epimerase was overexpressed in E. coli and purified to apparent homogeneity by chromatographic methods. Three crystal forms of the epimerase were obtained by a hanging-drop vapor-diffusion method. A native data set for crystal form III was collected in-house on a Rigaku R-AXIS-IIC image plate at 3.0 Å resolution. The form III crystals belong to the monoclinic space group P21. The unit-cell parameters are a = 98.94, b = 110.53, c = 180.68 Å and β = 90.94°. Our recent results show that these crystals diffract to 2.0 Å resolution at the Cornell High Energy Synchrotron Source. The crystal probably contains six 40 kDa monomers per asymmetric unit, with a corresponding volume per protein mass (Vm) of 4.11 Å3 Da−1 and a solvent fraction of 70%.
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    The high-resolution structure of DNA-binding protein HU from Bacillus stearothermophilus (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 801-809 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Protein HU is a ubiquitous prokaryotic protein which controls the architecture of genomic DNA. It binds DNA non-specifically and promotes the bending and supercoiling of the double helical structure. HU is involved in many DNA-associated cellular processes, including replication, transcription and the packaging of DNA into chromosome-like structures. Originally determined at medium resolution, the crystal structure of HU has now been refined at 2.0 Å resolution. The high-resolution structure shows that the dimeric molecule is essentially a compact platform for two flexible and basic arms which wrap around the DNA molecule. To maximize the protein's stability, non-secondary structural regions are reduced to a minimum, there is an extensive aromatic hydrophobic core and several salt bridges and hydrogen-bonded water molecules knit together crucial regions. Based on the original medium-resolution structure of HU, several proposals were made concerning the structural basis of HU's ability to bind, bend and supercoil DNA. Each of these proposals is fully supported by the high-resolution structure. Most notably, the surfaces of the molecule which appear to mediate protein–DNA and protein–protein interactions have the ideal shapes and physicochemical properties to perform these functions.
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    Influence of packing interactions on the average conformation of B-DNA in crystalline structures (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 810-819 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end-to-end interactions. Phosphate–phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end-to-end interactions and the average conformation of DNA. Dodecamers must have a B-form average conformation with 10 ± 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7–10.6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.
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    Ab initio structure determination of a small protein, rubredoxin, by direct methods (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 820-825 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program SAYTAN has been applied successfully to a known protein, rubredoxin, which contains 52 amino-acid residues including an FeS4 unit, a sulfate ion and 102 solvent water molecules. Starting with initially random phases, useful sets can be obtained from multiple trials and selected by figures of merit at different resolutions. Phase extension followed by weighted Fourier recycling reveals a recognizable structure of rubredoxin. The model is refined against 1 Å resolution data to an R factor of 14.5% using the program SHELXL93.
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    Solution of the structure of tetrameric human glucose 6-phosphate dehydrogenase by molecular replacement (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 826-834 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant human glucose 6-phosphate dehydrogenase (G6PD) has been crystallized and its structure solved by molecular replacement. Crystals of the natural mutant R459L grow under similar conditions in space groups P212121 and C2221 with eight or four 515-residue molecules in the asymmetric unit, respectively. A non-crystallographic 222 tetramer was found in the C2221 crystal form using a 4 Å resolution data set and a dimer of the large β + α domains of the Leuconostoc mesenteroides enzyme as a search model. This tetramer was the only successful search model for the P212121 crystal form using data to 3 Å. Crystals of the deletion mutant ΔG6PD grow in space group F222 with a monomer in the asymmetric unit; 2.5 Å resolution data have been collected. Comparison of the packing of tetramers in the three space groups suggests that the N-terminal tail of the enzyme prevents crystallization with exact 222 molecular symmetry.
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    Ab initio phasing using molecular envelope from solution X-ray scattering (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 243-246 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Solving the phase problem is the crucial and quite often the most difficult and time-consuming step in crystallographic structure determination. The traditional methods of isomorphous replacement (MIR or SIR) and molecular replacement require the availability of an isomorphous heavy-atom derivative or the structure of a homologous protein, respectively. Here, a method is presented which utilizes the low-resolution molecular shape determined from solution X-ray scattering data for the molecular search. The molecular shape of a protein is an important structural property and can be determined directly by the small-angle scattering technique. The idea of locating this molecular shape in the crystallographic unit cell has been tested with experimental diffraction data from nitrite reductase (NiR). The conventional Patterson search proved to be unsuccessful, as the intra-envelope vectors are uniformly distributed and do not match those of intra-molecular (atom-to-atom) vectors. A direct real-space search for orientation and translation was then performed. A self-rotation function using 2.8 Å crystallographic data yielded the polar angles of the non-crystallographic threefold axis. Knowledge of the orientation of this axis reduces the potential six-dimensional search to four (Eulerian angle γ and three translational parameters). The direct four-dimensional search within the unit cell produced a clear solution. The electron-density map based on this solution agrees well with the known structure, and the phase error calculated from the map was 61° within 20 Å resolution. It is anticipated that the low-resolution envelope can be used as a starting model for phase extension by the maximum-entropy and density-modification method.
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    Preliminary X-ray crystallographic analysis of the complex between the DNAase domain of colicin E9 and its cognate immunity protein (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 256-259 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: We have crystallized and performed preliminary X-ray characterization of the complex between the DNAase domain of the E9 colicin and its cognate immunity protein Im9. The dissociation constant for this complex, Kd = 1 × 10−16 M, reveals it to be one of the highest affinity protein–protein interactions known. Single crystals of the 1:1 complex were grown from microseeding experiments using PEG 4K as precipitant. The space group is P212121 with one molecule of complex in the asymmetric unit, and crystals contain approximately 43% solvent. These crystals are inherently non-isomorphous and so selenomethionine-derivatized protein has been prepared and crystals grown for MAD phasing experiments.
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    Murine class I major histocompatibility complex H–2Dd: expression, refolding and crystallization (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 260-262 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A truncated soluble form of the murine class I major histocompatibility antigen complex H–2Dd was cloned using an Escherichia coli based system. It was expressed, refolded in vitro and crystallized in a complex with murine β2 microglobulin and the peptide RGPGRAFVTI from the V3-loop of the gp160 HIV-1 protein. Crystals belonging to the space group P212121 with cell dimensions a = 51.3, b = 92.5, c = 108.8 Å were obtained using two different crystallization conditions. The crystals contain one complex per asymmetric unit and diffract to at least 2.4 Å resolution.
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    Crystallization of Escherichia coli RuvA complexed with a synthetic Holliday junction (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 263-265 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: During homologous recombination in Escherichia coli the RuvA, B and C proteins interact specifically with the Holliday junction formed by the action of RecA to promote the strand-exchange reaction. RuvA, a homotetrameric protein of molecular weight 88 kDa, has been overexpressed in E. coli, purified and co-crystallized with a synthetic Holliday junction substrate made from four 18-base deoxyoligonucleotides. Crystals were grown using the hanging-drop vapour-diffusion method with sodium acetate as the precipitant. The crystals diffract to a resolution of 6 Å and belong to the monoclinic system, space group C2, with cell parameters a = 148, b = 148, c = 106 Å and β = 123°. The X-ray analysis of these crystals should reveal the structure of the Holliday junction and its mode of binding to RuvA, providing new insights into the molecular mechanism of genetic recombination.
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    Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 865-868 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.
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    Refined structure of the FKBP12–rapamycin–FRB ternary complex at 2.2 Å resolution (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 736-744 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the FKBP12–rapamycin–FRB ternary complex has now been refined at 2.2 Å resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12–rapamycin binding (FRB) domain of FKBP12–rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity. The conformation of rapamycin in the ternary complex is very similar to that observed in the FKBP12–rapamycin binary complex, with an r.m.s. difference of only 0.30 Å. However, a slight (9°) rotation repositions the FRB-binding face of rapamycin in the ternary complex. There are extensive rapamycin–protein interactions and relatively few interactions between the two protein partners FKBP12 and FRB, these interactions mainly involving residues in the 40s and 80s loops of FKBP12 and α1 and α4 of FRB. The high-resolution refinement has revealed the crucial role of several buried waters in the formation of the ternary complex.
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    Crystallization and preliminary X-ray analysis of α-D-glucuronidase from Bacillus stearothermophilus T-6 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 869-872 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: α-D-Glucuronidases cleave the α-1,2-glycosidic bond of the 4-O-methyl-α-D-glucuronic acid side chain in xylan. Of the xylan-debranching hydrolases, these enzymes are the least studied and characterized. The α-glucuronidase gene (aguA) from Bacillus stearothermophilus T-6 has been cloned, sequenced and overproduced in Escherichia coli. The gene encodes for a protein of 679 amino acids with a calculated molecular weight of 78480 and a pI of 5.42. α-Glucuronidase T-6 shows high homology to the α-glucuronidases of Thermotoga maritima (60% identity) and of Trichoderma reesei (44% identity). Based on the amino-acid sequence similarity, it is likely that these enzymes represent a new class of glycosyl hydrolases. Crystallographic studies of α-glucuronidase T-6 were initiated to study the mechanism of catalysis, as well as to provide a structural basis for rational introduction of enhanced thermostability by site-specific mutagenesis. In this report, the crystallization and preliminary crystallographic characterization of the native α-glucuronidase T-6 enzyme is described. Two crystal forms were found suitable for detailed crystal structure analysis. The T1 form was obtained by the vapour-diffusion method using PEG 4000 as a precipitant and 2-propanol as an organic additive. The crystals belong to a primitive tetragonal crystal system (space group P41212 or P43212) with unit-cell dimensions a = b = 76.1 and c = 331.2 Å. These crystals are mechanically strong, are stable in the X-ray beam and diffract X-rays to better than 2.4 Å resolution. A full 3.0 Å resolution diffraction data set (97.3% completeness, Rmerge 9.8%) has recently been collected on one crystal at room temperature using a rotating-anode X-ray source and an R-AXIS IIc imaging-plate detector. The M1 form was obtained and characterized by similar techniques. The best crystallization occurred at a slightly lower pH and a lower concentration of 2-propanol. The crystals belong to a primitive monoclinic crystal system (space group P21) with unit-cell dimensions a = 65.8, b = 127.4, c = 96.6 Å and β = 97.9°. These crystals are also quite strong and stable, and diffract to better than 2.8 Å resolution. A full 2.8 Å resolution diffraction data set (96.2% completeness, Rmerge 7.6%) has recently been collected on one crystal at room temperature using the same R-AXIS IIc setup. Both forms are currently being used to obtain crystallographic phasing via isomorphous heavy-atom derivatives and selenomethionine MAD experiments.
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    Crystallization and preliminary X-ray analysis of a nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 877-879 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Periplasmic nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 contains two molybdopterin guanine dinucleotide cofactors and one [4Fe–4S] cluster as prosthetic groups and catalyzes the conversion of nitrate to nitrite. Crystals of the oxidized form of this enzyme were obtained using PEG as precipitant and belong to space group P3121 or P3221, with unit-cell dimensions a = b = 106.3, c = 135.1 Å. There is one monomer of 80 kDa in the asymmetric unit, which corresponds to a Matthews ratio of 2.75 Å3 Da−1. Using cryo-cooling procedures and X-rays from a rotating-anode generator, diffraction was observed to beyond 3.0 Å resolution.
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    Crystallization of the haptoglobin–hemoglobin complex (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 883-884 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two orthorhombic forms of crystals of the haptoglobin–hemoglobin complex were obtained using polyethylene glycol as precipitant. These crystals did not diffract well enough for data collection and work on the complex is no longer continued. However, the description of the crystallization conditions may be useful in future endeavors to obtain suitable crystals.
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    Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 542-543 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molybdenum-responsive ModE regulatory protein from Escherichia coli has been purified and used in crystallization trials. Two crystal forms have been observed. Form I is tetragonal, P41212 (or enantiomorph), with a = b = 72.3, c = 246.2 Å and diffracts to medium resolution. Form II is orthorhombic, P21212, with a = 82.8, b = 127.9, c = 64.0 Å and diffraction has been observed beyond 2.8 Å resolution. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure–activity relationship in regulating the uptake of molybdate in bacteria.
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    Crystallization and preliminary X-ray analysis of arabinanase A from Pseudomonas fluorescens subspecies cellulosa (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 544-546 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of 1,5-α-arabinanase A from Pseudomonas fluorescens subspecies cellulosa have been obtained by vapour diffusion. The crystals belong to the space group P6122 with unit-cell parameters a = b = 91.6, c = 179.4 Å with one molecule in the asymmetric unit. The native crystals and, to a much greater extent, heavy-atom soaked crystals are sensitive to radiation which necessitates cryocooling. Suitable cryocooling conditions have been established, though a shrinkage of the unit cell is observed, with a = b = 88.8 and c = 176.9 Å.
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    Crystallization and preliminary X-ray diffraction studies of blasticidin S deaminase from Aspergillus terreus (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 547-548 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Blasticidin S deaminase from Aspergillus terreus was crystallized with polyethylene glycol 8000. Two types of crystals were grown under the same crystallization conditions. One type grew as thin plates, while the other had a rhombic shape. The rhombic shaped crystal was suitable for high-resolution crystal structure analysis. Precession photographs and diffraction data showed that the crystal belonged to orthorhombic space group P212121, with unit-cell dimensions a = 70.33, b = 146.56 and c = 56.48 Å. The calculated Vm value was acceptable when a tetramer of the enzyme was contained in an asymmetric unit. Preliminary diffraction data were collected to a resolution of 2.0 Å with good statistics.
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    Crystallization and preliminary X-ray crystallographic analysis of the unusual ferritin from Listeria innocua (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 552-553 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Single crystals of ferritin extracted from Listeria innocua have been obtained by the vapour-diffusion method using PEG 1000 as precipitant. The crystals are orthorhombic, space group P212121, with unit-cell dimensions a = 87.7, b = 137.5, c = 173.1 Å. The crystals diffract to 2.9 Å resolution on a rotating-anode X-ray source and to 2.35 Å resolution on a synchrotron X-ray source. The asymmetric unit contains one molecule formed by 12 subunits, corresponding to a packing density of 2.41 Å3 Da−1
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    Crystallization of L-aspartate oxidase, the first enzyme in the bacterial de novo biosynthesis of NAD (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 549-551 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The flavoenzyme L-aspartate oxidase from Escherichia coli was crystallized using the hanging-drop vapour-diffusion technique with PEG 4000 as precipitant. The crystals belong to space group P3121 (or P3221) with unit-cell parameters a = b = 84.9, c = 159.9 Å. A solvent content of 42% corresponds to a monomer (60 kDa) in the asymmetric unit. A complete 2.8 Å resolution data set was collected using a rotating-anode X-ray generator.
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    Crystallization of ClfA and ClfB fragments: the fibrinogen-binding surface proteins of Staphylococcus aureus (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 554-556 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant constructs encoding the fibrinogen-binding domains of ClfA and ClfB from Staphylococcus aureus have been crystallized. ClfA was crystallized in the orthorhombic space group P212121 with unit-cell parameters a = 39.58, b = 81.39 and c = 112.65 Å. A complete data set was recorded to 2.1 Å resolution and had a Vm of 2.3 Å3 Da−1 with 46.5% solvent, suggesting one molecule per asymmetric unit. Co-crystals of ClfA with the 17 amino-acid C-terminal peptide of fibrinogen γ-chain diffracted to 2.1 Å resolution and had unit-cell parameters a = 39.11, b = 81.39 and c = 109.51 Å in the space group P212121. ClfB was crystallized in the tetragonal space group P41212 or P43212 with unit-cell parameters a = 96.31, b = 96.31 and c = 84.13 Å and diffracted to 2.45 Å resolution. The estimated Vm of 2.6 Å3 Da−1 with 53% solvent indicated one molecule in the asymmetric unit.
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    Determining the molecular-packing arrangements on protein crystal faces by atomic force microscopy (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1023-1035 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Previous atomic force microscopy (AFM) studies and periodic bond-chain (PBC) analyses of tetragonal lysozyme crystals have suggested that the (110) face consists of chains of molecules related to one another by 43 axes parallel to the crystal face. In this study, high-resolution AFM images of the (110) face were obtained and analyzed in order to verify this prediction. A computer program was employed which constructs the theoretical AFM image corresponding to a specific crystallographic molecular-packing arrangement and AFM tip shape. The packing arrangement and tip shape were varied in order to obtain the maximum possible correlation between experimental and theoretical images. The prediction from PBC analysis of an arrangement involving 43 helices was confirmed in this manner, while the alternate arrangement, consisting of molecules related to one another by 21 axes, was not observed. However, the surface structure was found to differ significantly even from this crystallographic arrangement. The molecules were found to pack slightly closer about what will become the 43 axes within the interior of the crystal, suggesting the occurrence of surface reconstruction or rearrangement on the tetragonal lysozyme (110) face. This study represents a new approach for more precise determination of the molecular-packing arrangements on protein crystal faces employing AFM.
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    Crystallization and preliminary diffraction analysis of Escherichia coli cysteinyl-tRNA synthetase (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1046-1047 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the 52 kDa monomeric Escherichia coli cysteinyl-tRNA synthetase complexed with ATP and cysteine have been grown by hanging-drop vapor diffusion from solutions containing ammonium sulfate as the precipitating agent. The crystals form long hexagonal rods in the space group P321 with unit-cell dimensions a = b = 82.3, c = 168.9 Å. There is one enzyme molecule in the asymmetric unit. A complete native data set has been collected from a rotating-anode source to a resolution of 2.7 Å at 103 K, with an Rmerge of 6.7%.
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    Crystallization and preliminary crystallographic analysis of winged bean acidic lectin (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 564-565 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The acidic lectin (WBAII) from the winged bean (Psophocarpus tetragonolobus) binds to the H-antigenic determinant on human erythrocytes and to the T-antigenic disaccharide Gal-β1,3-GalNAc. Two crystal forms of WBAII were obtained in the presence of methyl-α-D-galactose. Form I belongs to space group R3 with unit-cell dimensions a = b = 182.11, c = 44.99 Å and has one dimer in the asymmetric unit. Form II belongs to space group C2 with unit-cell dimensions a = 135.36, b = 127.25, c = 139.98 Å, β = 95.9° and has four dimers in the asymmetric unit. Intensity data were collected to 3.0 Å and to 3.5 Å from crystals of form I and II, respectively. The structures were solved by the molecular-replacement method using the coordinates of the basic form of winged bean lectin.
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    Crystallization and preliminary X-ray study of chloroplast glyceraldehyde-3-phosphate dehydrogenase (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 566-567 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts has been crystallized by vapour diffusion in the pH range 7–8.5 in (NH4)2SO4 and Tris–HCl buffer or potassium phosphate buffer at room temperature. Crystals of the A4 isoform, grown at pH 8.5 in Tris–HCl buffer, diffract to 3.0 Å (at 100 K) using synchrotron radiation. The crystals belong to the orthorhombic C222 space group, with unit-cell dimensions a = 145.9, b = 185.9 and c = 106.3 Å, and probably contain one tetramer per asymmetric unit. Structure determination by molecular replacement is in progress.
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    Preliminary X-ray analysis of a new crystal form of recombinant pig kidney DOPA decarboxylase (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 568-570 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: DOPA decarboxylase is responsible for the synthesis of the key neurotransmitters dopamine and serotonin via decarboxylation of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan, respectively. The crystals of recombinant DOPA decarboxylase differ from those previously reported for the enzyme purified from pig kidney. They belong to space group P622 with unit-cell dimensions a = b = 302.6, c = 178.1 Å. Both the self-rotation function and the good diffraction quality of these crystals (2.5 Å on a synchrotron source) suggest that there should be at least three protein dimers in the asymmetric unit. Diffraction data sets have been collected for the native enzyme and a heavy-atom derivative.
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    Purification, crystallization and preliminary X-ray crystallographic analysis of recombinant murine Golgi mannosidase IA, a class I α-mannosidase involved in Asn-linked oligosaccharide maturation (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 571-573 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Golgi mannosidase IA is a class I α-mannosidase which catalyzes the conversion of Man9GlcNAc2 or Man8GlcNAc2 oligosaccharide substrates to Man5GlcNAc2 during the maturation of Asn-linked oligosaccharides. The enzyme is a type II membrane protein, and a recombinant form of mannosidase IA from mouse, lacking the transmembrane domain, has been expressed in Pichia pastoris, purified to homogeneity and crystallized by the hanging-drop vapor-diffusion method. The crystals grow as thin rods, with unit-cell dimensions a = 54.9, b = 135.01, c = 69.9 Å. The crystals exhibit the symmetry of space group P2221 and diffract to 2.8 Å resolution. The asymmetric unit contains one monomer (∼53 kDa) and has a solvent content of 59%.
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    Crystallization and preliminary X-ray crystallographic analysis of deoxycytidylate hydroxymethylase from bacteriophage T4 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1061-1063 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Deoxycytidylate hydroxymethylase from bacteriophage T4 is a homodimeric enzyme in which each polypeptide chain consists of 246 amino-acid residues. It has been crystallized in the presence of its substrate, deoxycytidine monophosphate, at room temperature using sodium citrate as precipitant. The crystals are monoclinic, belonging to space group C2, with unit-cell parameters a = 174.22, b = 53.12, c = 75.17 Å, β = 115.29°. The asymmetric unit contains one homodimer, with a corresponding Vm of 2.65 Å3 Da−1 and solvent content of 54%. Native diffraction data to 1.6 Å resolution have been collected from two crystals using synchrotron radiation.
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    Crystallization and preliminary X-ray crystallographic analysis of a Trichoderma reesei β-mannanase from glycoside hydrolase family 5 (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1058-1060 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the catalytic core domain of a Trichoderma reesei β-mannanase belonging to glycoside hydrolase family 5 have been grown by the sitting-drop method at room temperature using ammonium sulfate as precipitant. The crystals grow as thin colourless plates and belong to space group P21, with unit-cell parameters a = 50.0, b = 54.3, c = 60.2 Å, β = 111.3°, and have a single monomer of mannanase in the asymmetric unit. Native data to 2.0 Å resolution have been collected at room temperature using synchrotron radiation. Data for a platinum derivative have been collected to 1.65 Å at 110 K in a very short time at the CCLRC Daresbury synchrotron source, using a charge-coupled device (CCD) as detector.
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    Crystallization and preliminary X-ray diffraction studies of the neurotoxic, heterodimeric phospholipase A2 from the Taiwan viper (Vipera russelli formosensis) (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1064-1065 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 28 kDa heterodimeric complex from Taiwan viper (F4/F7 complex) is composed of a neurotoxic phospholipase A2 (F4) and a non-toxic PLA2-like component (F7). Despite a high sequence identity (65%), the biological and pharmacological activities of F4 and F7 are contrasting. The complex is a structural analogue of Vipoxin found in the venom of the Bulgarian viper Vipera ammodites meridionalis. It is unclear how and why such varied bioactivities are expressed in these similar components. The F4/F7 complex has been crystallized using hanging-drop vapour diffusion and macroseeding techniques. The space group is monoclinic P2_1 with unit-cell dimensions a=74.92, b=85.13, c=78.16 Å and \beta=95.12°. X-ray intensity data to 2.0 Å resolution have been collected at 120 K and the structure has been solved using the molecular-replacement method. There are four F4/F7 complex molecules in the asymmetric unit, which do not exhibit any local point-group symmetry.
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    Expression, purification and crystallization of recombinant human TRAIL (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1101-1104 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: TRAIL (also known as Apo-2L) belongs to the tumour necrosis factor (TNF) cytokine family and induces rapid apoptosis in a wide variety of tumour cell lines upon binding to the death-signalling receptors on the cell membrane. Normal cells are resistant to TRAIL, owing to the expression of decoy receptors which lack functional death domains and antagonize TRAIL-induced apoptosis. Soluble and functional human TRAIL, expressed in Escherichia coli and refolded into a functional form, has been crystallized. The crystals belong to space group P63 with unit-cell dimensions a = b = 65.61, c = 131.70 Å. The asymmetric unit contains two molecules of TRAIL, with a crystal volume per protein mass (Vm) of 2.41 Å3 Da−1 and a solvent content of about 42% by volume. A native and a platinum-derivative data set to 2.8 and 3.5 Å resolution, respectively, were obtained from frozen crystals. Structure determination by a combined molecular replacement and isomorphous replacement method is in progress.
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    Structure of a new crystal form of human Hsp70 ATPase domain (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1105-1107 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Hsp70 proteins are highly conserved proteins induced by heat shock and other stress conditions. An ATP-binding domain of human Hsp70 protein has been crystallized in two major morphological forms at pH 7.0 in the presence of PEG 8000 and CaCl2. Both crystal forms belong to the orthorhombic space group P212121, but show no resemblance in unit-cell parameters. Analysis of the crystal structures for both forms shows a 1–2 Å shift of one of the subdomains of the protein. This conformational change could reflect a `natural' flexibility of the protein which might be relevant to ATP binding and may facilitate the interaction of other proteins with Hsp70 protein.
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    Structure of human apolactoferrin at 2.0 Å resolution. Refinement and analysis of ligand-induced conformational change. Addendum (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1108-1108 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The coordinates and structure factors have now been deposited with the Protein Data Bank for the high-resolution structure described in the paper by Jameson, Anderson, Norris, Thomas & Baker [Acta Cryst. (1998). D54, 1319–1335]. The PDB reference code for this structure is 1cb6.
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    Crystallization and preliminary X-ray diffraction analysis of cytochrome P450sca-2 from Streptomyces carbophilus involved in production of pravastatin sodium, a tissue-selective inhibitor of HMG-CoA reductase (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1209-1211 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome P450sca-2 from Streptomyces carbophilus catalyzes the hydroxylation of ML-236B sodium salt to pravastatin sodium, a tissue-selective inhibitor of 3-hydroxy-3-methylglutaryl-coenzymeA (HMG-CoA) reductase. HMG-CoA reductase is a key enzyme in cholesterol biosynthesis. Crystals of the protein were obtained by the vapour-diffusion method, using ammonium sulfate as a precipitant. The crystals belong to the trigonal space group P3121 (or its enantiomorph, P3221) with unit-cell dimensions a = 103.5, c = 79.8 Å. Assuming the presence of one molecule in the asymmetric unit, the calculated value of Vm is 2.68 Å3 Da−1. A native data set was collected to a resolution of 2.2 Å.
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    Crystallization and preliminary X-ray analysis of the 6-phospho-α-glucosidase from Bacillus subtilis (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1212-1214 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 6-Phospho-α-glucosidase (GlvA) is the protein involved in the dissimilation of α-glycosides accumulated via a phosphoenolpyruvate-dependent maltose phosphotransferase system (PEP-PTS) in Bacillus subtilis. The purified enzyme has been crystallized in a form suitable for X-ray diffraction analysis. Thin rod-like crystals have been grown by the hanging-drop method in the presence of manganese and NAD. They diffract beyond 2.2 Å using synchrotron radiation and belong to the space group I222 (or its enantiomorph) with unit-cell dimensions a = 83.26, b = 102.56, c = 145.31 Å and contain a single molecule of GlvA in the asymmetric unit.
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    Dynamic light-scattering and preliminary crystallographic studies of the sensor domain of the haem-based oxygen sensor FixL from Rhizobium meliloti (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1215-1218 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: FixL is a transmitter protein in a two-component system which acts as an oxygen sensor when the symbiotic Rhizobia resides in root nodules of host plants. The oxygen-sensor domain of Rhizobium meliloti FixL (RmFixLH) was purified by His-tag affinity and isoelectronic focusing chromatographies, without the use of gel-filtration chromatography. Dynamic light-scattering measurements of RmFixLH thus obtained revealed it to be monodispersive and present as a homodimer in solution. A single crystal of RmFixLH in the met (Fe3+) form was grown in 100 mM acetic acid/NaOH buffer at pH 4.6 in the presence of 200 mM ammonium acetate, using 40%(w/v) PEG 4000 as a precipitant. A crystal of the ferrous CO form of RmFixLH was also prepared by reduction of the met crystal with Na2S2O4 in an atmosphere of CO. The crystals (0.2 × 0.05 × 0.01 mm) belong to the monoclinic system (C2) with unit-cell parameters a = 60.94, b = 37.44, c = 54.14 Å, β = 115.29° and diffract X-rays to 1.7 Å resolution at station BL44B2 of SPring-8, Japan. Bijvoet difference Patterson maps show a clear peak corresponding to the haem iron in RmFixLH.
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    Crystal structure of epidoxorubicin–formaldehyde virtual crosslink of DNA and evidence for its formation in human breast-cancer cells (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1516-1523 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Epidoxorubicin and daunorubicin are proposed to be cytotoxic to tumor cells by catalyzing production of formaldehyde through redox cycling and using the formaldehyde for covalent attachment to DNA at G bases. The crystal structure of epidoxorubicin covalently bound to a d(CGCGCG) oligomer was determined to 1.6 Å resolution. The structure reveals slightly distorted B-form DNA bearing two molecules of epidoxorubicin symmetrically intercalated at the termini, with each covalently attached from its N3′ to N2 of a G base via a CH2 group from the formaldehyde. The structure is analogous to daunorubicin covalently bound to d(CGCGCG) determined previously, except for additional hydrogen bonding from the epimeric O4′ to O2 of a C base. The role of drug–DNA covalent bonding in cells was investigated with synthetic epidoxorubicin–formaldehyde conjugate (Epidoxoform) and synthetic daunorubicin–formaldehyde conjugate (Daunoform). Uptake and location of drug fluorophore in doxorubicin-resistant human breast-cancer cells (MCF-7/ADR cells) was observed by fluorescence microscopy and flow cytometry. The fluorophore of Daunoform appeared more rapidly in cells and was released more rapidly from cells than the fluorophore of Epidoxoform over a 3 h exposure period. The fluorophore appeared predominantly in the nucleus of cells treated with both conjugates. The difference in uptake is explained in terms of the slower rate of hydrolysis of Epidoxoform to the species reactive with DNA and a proposed slower release from DNA based upon the crystal structures.
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    Structure of an insulin dimer in an orthorhombic crystal: the structure analysis of a human insulin mutant (B9 Ser→Glu) (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1524-1532 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of human insulin mutant B9 (Ser→Glu) was determined by an X-ray crystallographic method at 2.5 Å resolution with an R factor of 0.165 under non-crystallographic restraints. The crystals were grown at low pH (〈3.8) and belong to the orthorhombic P212121 space group with unit-cell dimensions a = 44.54, b = 46.40, c = 51.85 Å and one dimer per asymmetric unit without further aggregation. The structure in this crystal form can be regarded as a model for a discrete insulin dimer and displays the following features compared with the structure of 2Zn insulin. (i) The overall dimer is expanded and more symmetric. The two A chains are about 2 Å more distant from each other, while the two B chains are about 0.8 Å further apart. Both monomers are more similar to molecule 1 than molecule 2 of the 2Zn insulin dimer. (ii) The dimer structure is stabilized by protonation and neutralization of the carboxyl groups at lower pH and, in addition, by formation of a hydrogen-bond network among the side chains of residues GluB9, HisB13 and HisB10 on the dimer-forming surface of both monomers, resulting from a structural rearrangement. (iii) The B-chain amino-terminal segment is in an open state (O state), i.e. a state different from the well known R and T states found in the insulin hexamer. In the O state, the B-chain N-terminal segment is in an extended conformation and is detached from the rest of the molecule. This conformational state has also been observed in the monomeric crystal structure of despentapeptide (B26–B30) and desheptapeptide (B24–B30) insulin, as well as in the solution structure of an engineered insulin monomer. It suggests that the O state may be the characteristic conformation of insulin in lower aggregation forms and may be relevant to the formation of insulin fibrils. In addition, based on the crystallization process, the smallest possible building blocks of insulin crystal are also discussed.
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    The CXXC motif: crystal structure of an active-site variant of Escherichia coli thioredoxin (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1533-1538 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 2.2 Å crystalline structure of an oxidized active-site variant of Escherichia coli thioredoxin (Trx) has been solved. Trx is a 12 kDa enzyme which catalyzes the oxidation of dithiols and the reduction and isomerization of disulfides in other proteins. Its active site contains the common structural motif CXXC. Protein-disulfide isomerase (PDI), a 57 kDa homolog of Trx, contains four Trx-like domains. The three-dimensional structure of PDI is unknown. PDI-deficient Saccharomyces cerevisiae are inviable. An active-site variant of Trx which complements PDI-deficient yeast has the active-site sequence Cys32-Val33-Trp34-Cys35 (CVWC). The reduction potential of oxidized CVWC Trx (E°′ = −0.230 V) is altered significantly from that of the wild-type enzyme (E°′ = −0.270 V). However, the structure of the oxidized CVWC enzyme is almost identical to that of wild-type Trx. The addition of valine and tryptophan in the active site is likely to increase the reduction potential, largely by decreasing the pKa of the Cys32 thiol in the reduced enzyme. Unlike in wild-type Trx, significant protein–protein contacts occur in the crystal. Protein molecules related by a crystallographic twofold axis form a dimer in the crystal. The dimer forms as an extension of the twisted mixed β-sheet which composes the backbone of each Trx structure.
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    The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1539-1545 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.
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    Combination of methods used in the structure solution of pyruvate:ferredoxin oxidoreductase from two crystal forms (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1546-1554 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the homodimeric 267 kDa pyruvate:ferredoxin oxidoreductase (PFOR) of Desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. Phases were obtained from multiwavelength anomalous dispersion (MAD), solvent flattening (SF), molecular replacement (MR) using a 5 Å resolution electron-density search model, multiple isomorphous replacement (MIR) and, finally, electron-density averaging (DA) procedures. It is shown how the combination of all these techniques was used to overcome problems arising from incompleteness of MAD data and weak phasing power of MIR data. A real-space refinement (RSR) procedure is described to improve MR solutions and obtain very accurate protein envelopes and non-crystallographic symmetry (NCS) transformations from 5 Å resolution phase information. These were crucial for the phase extension to high resolution by DA methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999008410
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