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  • International Union of Crystallography (IUCr)
  • 1995-1999  (9,528)
  • 1980-1984  (5,963)
  • 1975-1979  (6,726)
  • 1930-1934
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  • 1
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 140-144 
    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.
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  • 2
    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.
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  • 3
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 278-281 
    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.
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 249-270 
    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.
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  • 5
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 190-198 
    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.
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  • 6
    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.
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  • 7
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 305-310 
    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.
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  • 8
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 390-392 
    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.
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  • 9
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 725-730 
    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.
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  • 10
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 740-748 
    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.
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  • 11
    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.
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  • 12
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 760-766 
    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.
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  • 13
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 772-779 
    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.
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  • 14
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 767-771 
    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.
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  • 15
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 925-937 
    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.
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  • 16
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 805-813 
    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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  • 17
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 814-818 
    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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  • 18
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 819-823 
    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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  • 19
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 792-804 
    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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  • 20
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 824-826 
    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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  • 21
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 827-829 
    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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  • 22
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 833-834 
    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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  • 23
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 835-836 
    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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  • 24
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 228-234 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 25
    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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  • 26
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1082-1083 
    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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  • 27
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    Acta crystallographica 51 (1995), S. 1089-1091 
    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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  • 28
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    Acta crystallographica 51 (1995), S. 1103-1103 
    ISSN: 1399-0047
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 29
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    Acta crystallographica 51 (1995), S. 1103-1103 
    ISSN: 1399-0047
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 30
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    Acta crystallographica 52 (1996), S. 30-42 
    ISSN: 1399-0047
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: With a size of 372 kDa, the F1 ATPase particle is the largest asymmetric structure solved to date. lsomorphous differences arising from reacting the crystals with methyl-mercury nitrate at two concentrations allowed the structure determination. Careful data collection and data processing were essential in this process as well as a new form of electron-density modification, `solvent flipping'. The most important feature of this new procedure is that the electron density in the solvent region is inverted rather than set to a constant value, as in conventional solvent flattening. All non-standard techniques and variations on new techniques which were employed in the structure determination are described.
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  • 31
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    Acta crystallographica 51 (1995), S. 550-559 
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    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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  • 32
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    Acta crystallographica 51 (1995), S. 560-566 
    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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  • 33
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    Acta crystallographica 51 (1995), S. 541-549 
    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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  • 34
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    Notes: A loop-deleted mutant form of 3-isopropylmalate dehydrogenase from Thermus thermophilus was constructed to investigate the relationship between the flexibility of the structure and the thermostability of the enzyme. The structure of the mutant enzyme was determined by X-ray crystallography and was found to be almost the same as that of the native enzyme with a reduced temperature factor. Although the mutant protein had lost the flexible loop, its function and thermostability had remained unchanged. This phenomenon can be explained by an internal reprieve tolerance mechanism.
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  • 35
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    Acta crystallographica 52 (1996), S. 129-142 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The canine parvovirus structure (CPV) [Tsao, Chapman, Agbandje, Keller, Smith, Wu, Luo, Smith, Rossmann, Compans & Parrish (1991). Science, 251, 1456–1464] has been refined by a real-space refinement procedure [Chapman (1994). Acta Cryst. A51, 69–801. The fit of an atomic model to electron density was optimized while taking into account the resolution limit of the data and the stereochemistry of the structure. The refined model had a reasonable free R factor [Brtinger (1992). Nature (London), 355, 472–4751 of 0.29. The method is particularly fast and convenient when only a small fraction of the crystallographic asymmetric unit needs to be refined, as is the case when there is high non-crystallographic redundancy. Cycles of refinement for virus capsids were completed in about 1/50th of the time required for equivalent reciprocal-space procedures.
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  • 36
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    Acta crystallographica 52 (1996), S. 160-164 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of a tetragonal crystal of bovine pancreatic RNase B complexed with d(pA)4 was determined by molecular replacement and difference Fourier methods. This crystal belongs to space group P41212 and has unit-cell dimensions a = b = 44.5, c = 156.5 Å. The model consists of the enzyme and a tetranucleotide with fractional occupancies, suggesting multiple modes of oligonucleotide binding. It does not include any polysaccharide residues or solvent molecules. After refinement at 2.7 Å, the R value was 0.163 with acceptable stereochemistry. The model illustrates a set of well defined interactions for substrate binding, particularly between the central dinucleotide and the enzyme.
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  • 37
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    Acta crystallographica 52 (1996), S. 192-193 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant transaldolase from Escherichia coli, an enzyme of the pentose phosphate pathway has been crystallized by the vapor-diffusion method using polyethylene glycol 6000 as precipitant. The crystals are orthorhombic, space group P212121 with cell dimensions a = 68.9, b = 91.3 and c = 130.5 Å and diffract to 2 Å resolution on a conventional X-ray source. The asymmetric unit very likely contains two subunits, corresponding to a packing density of 2.9 Å3 Da−1.
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  • 38
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    Notes: Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 Å resolution. The crystals belong to space group P212121, with cell constants a = 73.33, b = 68.86, c = 59.73 Å, and contain one dimeric molecule of Mr 32 000 per asymmetric unit. The structure was solved by molecular-replacement techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy term. During the final steps, positional and anisotropic thermal parameters of the atoms were refined. The R factor for the 49 209 unique reflections in the 10.0–1.49 Å resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu2+, two Zn2+, and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 Å2, while the calculated r.m.s. coordinate error for the refined model is 0.036 Å. As suggested by the primary structure homology to any other known intracellular eukaryotic superoxide dismutase (〉 50%), the typical structural scaffolding of flattened antiparallel eight-stranded (β-barrel is well conserved in X. laevis Cu,Zn superoxide dismutase b, together with the coordination geometry of the metal centers in the active site. The higher thermal stability of the bb X. laevis superoxide dismutase homodimer, with respect to dimers involving the a-type isoenzyme subunit(s), can be related, on the basis of the high-resolution structure, to side-chain and solvent interactions centered on residue Tyr149, in both b-type subunits. The analysis of the overall solvent structure reveals a number of equivalent water molecule sites in the two subunits, and in homologous superoxide dismutase models. Their locations are discussed in detail and classified on the basis of their structural role.
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  • 39
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    Acta crystallographica 52 (1996), S. 201-202 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Haemorrhagin I from the snake venom of Agkistrodon acutus (AaHI) has been crystallized using the hanging-drop vapour diffusion method. The crystals belong to space group P41212 or P43212 with unit-cell dimensions a = b = 63.61 and c = 95.69 Å. There is one molecule in the asymmetric unit. Data to 2.35 Å resolution have been collected using a single-crystal.
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  • 40
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    Acta crystallographica 52 (1996), S. 215-217 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of 7α-hydroxysteroid dehydrogenase from E. coli, which is a tetramer in its active form, have been obtained by a hanging-drop vapor-diffusion method in the presence of the coenzyme NAD+. Crystals as large as 0.25 × 0.25 × 0.75 mm could be grown within a month at pH 8.5 with polyethylene glycol as precipitating agent. Preliminary X-ray crystallographic analysis revealed that they belong to one of the enantiomorphic space groups P41212 or P43212 with dimensions a = b = 81.66 and c = 214.6 Å, having two subunits in an asymmetric unit. The crystals diffract to at least 2.3 Å resolution.
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  • 41
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    Notes: Overexpressed dimeric E. coli aspartyl-tRNA synthetase (AspRS) has been crystallized in its free state and complexed with yeast tRNAAsp. Triclinic crystals of the enzyme alone (a = 104.4, b = 107.4, c = 135.0 Å, α = 102.9, β = 101.0, γ = 106.3°), have been grown using ammonium sulfate as the precipitant and monoclinic crystals (a = 127.1, b = 163.6, c = 140.1 Å, β = 111.7°), space group C2, have been grown using polyethylene glycol 6000. They diffract to 2.8 and 3.0 Å, respectively. Crystals of the heterologous complex between E. coli AspRS and yeast tRNA have been obtained using ammonium sulfate as the precipitant and 2-propanol as the nucleation agent. They belong to the monoclinic space group P21 (a = 76.2, b = 227.3, c = 82.3 Å, β = 111.7°) and diffract to 2.7 Å.
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  • 42
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    Acta crystallographica 52 (1996), S. 226-228 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: T4 deoxynucleotide kinase catalyzes the phosphorylation of 5-hydroxymethyldeoxycytidylate, dTMP and dGMP while excluding dCMP and dAMP. In order to understand the mechanism of this remarkable specificity, the enzyme was over-expressed in Escherichia coli, purified and crystallized for X-ray diffraction analysis. The crystals belong to the monoclinic space group C2 with cell dimensions a = 155.2, b = 58.5, c = 75.7 Å, β = 108.1°. There are two protein monomers in the asymmetric unit related by a twofold axis. Diffraction data to 2.0 Å resolution have been collected.
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  • 43
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    Acta crystallographica 52 (1996), S. 380-392 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Collagenase from the fly larvae Hypoderma lineatum cleaves triple-helical collagen in a single region. It was crystallized at neutral pH in the absence of inhibitor and 1.8 Å data were collected using synchrotron radiation and a Mark II prototype detector. The structure was solved by combining multiple isomorphous replacement methods and rotation translation function in real space. Refinement between 7 and 1.8 Å using the program X-PLOR led to a final R factor of 16.9%. The overall fold is similar to that of other trypsin-like enzymes but the structure differs mainly by the presence of a β-sheet at position 31–44. The two embedded molecules of the asymmetric unit are related by a pseudo twofold axis. The β-sheet 31–44 of one molecule is involved in hydrogen bonds with binding-pocket residues of the other molecule. It thus completely prevents access to the active site. The specificity of this enzyme probably results from the position of Phe192 and Tyr99 at the entrance of the active site.
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  • 44
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    Acta crystallographica 52 (1996), S. 411-413 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two new crystal forms of calmodulin from Gallus gallus are reported. Crystals in space group P1 (cell dimensions a = 59.7, b = 53.1, c = 24.6 Å, α = 93.2, β = 96.7, γ = 89.2 and Z = 2), grow as long thin needles. Water content on density considerations is \sim50%. They diffract to \sim2.0 Å but give wide multiply peaked spot profiles. Crystals in space group P212121 (cell dimensions a = 32.2, b = 56.0, c = 67.3 Å and Z = 4), grow as clusters of thin tablets and contain \sim30% water by volume. These small crystals (\sim0.4 × 0.15 × 0.1 mm) diffracted well to \sim 1.4 Å and some appreciable intensities were observed at resolutions better than 1.2 Å.
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  • 45
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    Acta crystallographica 52 (1996), S. 235-251 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Genetic algorithms have been investigated as computational tools for the de novo phasing of low-resolution X-ray diffraction data from crystals of icosahedral viruses. Without advance knowledge of the shape of the virus and only approximate knowledge of its size, the virus can be modeled as the symmetry expansion of a short list of nearly tetrahedrally arranged lattice points which coarsely, but uniformly, sample the icosahedrally unique volume. The number of lattice points depends on an estimate of the non-redundant information content at the working resolution limit. This parameterization permits a simple matrix formulation of the model evaluation calculation, resulting in a highly efficient survey of the space of possible models. Initially, one bit per parameter is sufficient, since the assignment of ones and zeros to the lattice points yields a physically reasonable low-resolution image of the virus. The best candidate solutions identified by the survey are refined to relax the constraints imposed by the coarseness of the modeling, and then trials whose intensity-based statistics are comparatively good in all resolution ranges are chosen. This yields an acceptable starting point for symmetry-based direct phase extension about half the time. Improving efficiency by incorporating the selection criterion directly into the genetic algorithm's fitness function is discussed.
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  • 46
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    Acta crystallographica 52 (1996), S. 289-298 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Chitinase from barley seeds is a monomeric enzyme with 243 amino-acid residues and it plays a role as a defense protein. Its structure, previously determined at 2.8 Å resolution by multiple isomorphous replacement method, is mainly α-helical [Hart, Monzingo, Ready, Ernst & Robertus, (1993). J. Mol. Biol. 229, 189–193]. The crystallization and preliminary X-ray data of the same enzyme in a different crystal form has been reported independently [Song, Hwang, Kim & Suh, (1993). Proteins, 17, 107–109}, the asymmetric unit of which contains two chitinase molecules. As a step toward understanding the general principles of catalysis, reported here is the structure of chitinase from barley seeds in this crystal form, as determined by molecular replacement and subsequently refined at 2.0 Å resolution, with incorporation of partial data to 1.9 Å (R factor of 18.9% for 31 038 unique reflections with Fo〉 2σF in the range 8.0–1.9 Å). The r.m.s. deviations from ideal stereochemistry are 0.013 Å for bond lengths and 1.32° for bond angles. A superposition of the two independent molecules in the asymmetric unit gives an r.m.s. difference of 0.55 Å for all protein atoms (0.43 and 0.74 Å for main-chain and side-chain atoms, respectively). When the refined model of each chitinase molecule in the asymmetric unit is superposed with the starting model, the r.m.s. difference for all shared protein atoms is 0.99 Å for molecule 1 and 0.85 Å for molecule 2, respectively. Through a sequence comparison with homologous plant chitinases as well as a structural comparison with the active sites of other glycosidases, key catalytic residues have been identified and the active site has been located in the three-dimensional structure of the barley chitinase. The present structure, refined at an effective resolution of 2.0 Å with incorporation of partial data to 1.9 Å, represents a significant improvement in resolution compared to the previously reported model. The improved resolution has enabled the location of solvent atoms, including water molecules near the catalytic residues, in addition to the positioning of protein atoms with greater accuracy.
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  • 47
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    Acta crystallographica 52 (1996), S. 518-520 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In 1961 Rossmann & Blow published a simple procedure for analytically combining the phase probabilities derived from various isomorphous derivatives or other phase-determining procedures [Rossmann & Blow (1961). Acta Cryst. 14, 641–647]. However, they found it necessary to make an approximation in obtaining the expression for the lack of closure (ε) of the phase triangle. In 1970 Hendrickson & Lattman [Hendrickson & Lattman (1970). Acta Cryst. B26, 136–143] suggested an alternative method of defining the lack of closure of the phase triangle which did not require any approximation in deriving the same analytical expression for the phase-probability function. It is now shown that it is possible to avoid the Rossmann-Blow approximation and thereby maintain the original meaning of the lack of closure as defined by Blow & Crick [(1959). Acta Cryst. 12, 794–802] and Dickerson, Kendrew & Strandberg [(1961). Acta Cryst. 14, 1188–1195].
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  • 48
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    Acta crystallographica 52 (1996), S. 521-528 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Thc crystal structure of an α-chymotrypsin inhibitor (P6122; a = 61.4, c = 210.9 Å) isolated from winged bean (Psophocarpus. tetragonolobus) seeds has been determined at 2.95 Å resolution by the molecular-replacement method using the 2.6 Å coordinates of Erythrina trypsin inhibitor (ETI) as the starting model (57% sequence homology). This protease inhibitor, WCI, belongs to the Kunitz (STI) family and is a single polypeptide chain with 183 amino-acid residues having a molecular weight of 20 244 Da. Structure refinement with RESTRAIN and X-PLOR has led to a crystallographic R factor of 19.1% for 3469 observed reflections (I 〉 2σ) in the resolution range 8–2.95 Å. A total of 56 water molecules have been incorporated in the refined model containing 181 amino-acid residues. In the refined structure the deviations of bond lengths and bond angles from ideal values are 0.015 Å and 2.2°, respectively. The inhibitor molecule is spherical and consists of 12 antiparallel β-strands with connecting loops arranged in a characteristic folding (a six-stranded β-barrel and a six-stranded lid on one hollow end of the barrel) common to other homologous serine protease inhibitors in the Kunitz (STI) family as well as to some non-homologous proteins like interleukin-lα and interleukin-lβ. In the structure the conformation of the protruding reactive-site loop is stabilized through hydrogen bonds mainly formed by the side chain of Asnl4, which intrudes inside the cavity of the reactive-site loop, with the side-chain and main-chain atoms of some residues in the loop region. A pseudo threefold axis exists parallel to the barrel axis of the structure. Each of the three subdomains comprises of four β-strands with connecting loops.
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  • 49
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    Acta crystallographica 52 (1996), S. 566-568 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The amyloidogenic Leu55Pro variant of transthyretin has been expressed, purified and crystallized in space group C2. The cell constants are a = 149.99, b = 78.74, c = 98.95 Å, β = 100.5° and the crystals diffract to 2.7 Å resolution. There are eight monomers in the asymmetric unit giving a VM = 2.6 Å3 Da−1 and 53% solvent content. In the wild-type protein, the crystals are orthorhombic with two monomers in the asymmetric unit. The wild-type protein is a tetramer composed of four identical subunits [Blake, Geisow, Oatley, Rerat & Rerat (1978). J. Mol. Biol. 121, 339–356.] and a molecular-replacement solution for the Leu55Pro variant was obtained using one monomer of the wild-type protein as a model. Rigid-body refinement of the eight monomers in the asymmetric unit and subsequent refinement using molecular dynamics were performed with X-PLOR, leading to a current R factor of 20.3% for all the data. The crystallographic packing of the molecules is different from the one presented by the wild-type protein, opening new perspectives for understanding how this protein aggregates to form amyloid fibrils.
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  • 50
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    Acta crystallographica 52 (1996), S. 569-570 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new crystal form of the histone octamer, crystallized in 1.6 M KCl, 1.6 M phosphate, diffracts to appreciably better than 2.6 Å resolution. The crystals have space group P61 or P65 and lattice parameters a = b = 158.29, c = 103.27 Å, α = β = 90, γ = 120°, with one molecule per asymmetric unit. The new crystals promise to yield more detail of the histone basic domains and a higher resolution structure for the histone octamer.
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  • 51
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    Acta crystallographica 52 (1996), S. 579-580 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The ParE subunit of Escherichia coli topoisomerase IV has been crystallized in the presence of the non-hydrolyzable ATP analogue, 5′-adenylyl-β,γ-imidodiphosphate (ADPNP). The crystals are of the orthorhombic space group, P212121, with unit-cell dimensions a = 92.6, b = 119.1, c = 135.3 Å. Data have been collected to 3.5 Å resolution from frozen native crystals. Self-rotation function analysis of these data indicate the position of a molecular twofold axis. Higher resolution native data are being collected and a derivative search is underway.
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  • 52
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    Acta crystallographica 52 (1996), S. 589-590 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Spo0F, a member of a superfamily of bacterial response regulatory proteins, is crucial to the regulation of sporulation in Bacillus subtilis. As there were difficulties in reproducing crystals of wild-type Spo0F, we report here the crystallization and preliminary studies of a mutant, Y13S protein, which gave well diffracting reproducible crystals. The crystals of the mutant obtained by the hanging-drop method belong to the tetragonal space group P41212 (P43212) a = b = 105.1, c = 85.9 Å. Diffraction data were collected at 2.8 Å at the laboratory source and subsequently 2.05. Å data were collected upon flash freezing the crystal at the Stanford Synchrotron Radiation Laboratory. This mutant participates in the phosphorelay in a similar manner to the wild-type protein. The presence of divalent cations are essential for wild-type phosphorylation and the present mutant crystal form is obtained in the presence of calcium.
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  • 53
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    Acta crystallographica 52 (1996), S. 591-593 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the hydroxynitrile lyase from Hevea brasiliensis overexpressed in Pichia pastoris have been obtained by the hanging-drop technique at 294 K with ammonium sulfate and PEG 400 as precipitants. The crystals belong to the orthorhombic space group C2221 with cell dimensions of a = 47.6, b = 106.8 and c = 128.2 Å. The crystals diffract to about 2.5 Å resolution on a rotating-anode X-ray source.
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  • 54
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Uridine 5′-diphospho-N-acetylenolpyruvylglucosamine reductase (MurB), the second enzyme in the peptidoglycan synthetic pathway of Escherichia coli, has been crystallized in two previously unreported forms, one orthorhombic and the other monoclinic. MurB (molecular mass 38 kDa) crystallizes in a range of conditions that utilize polyethylene glycol fractions as precipitants, and crystals can be grown with or without the enzyme's substrate, uridine 5′-diphospho-N-acetylenolpyruvylglucosamine. X-ray diffraction from crystals of the orthorhombic form extends to 2 Å resolution and shows the symmetry and systematic absences of space group P212121. These crystals show significant variations in cell dimensions at room temperature and at 100 K. A crystal used to collect a 2.0 Å resolution data set at a synchrotron source showed cell dimensions at ca 100 K of a = 51.0, b = 79.3 and c = 87.1 Å, indicating one molecule peroasymmetric unit. The monoclinic crystals scatter X-rays to 3.0 Å resolution consistent with space group P21, unit-cell dimensions (ca 100 K) a = 50.7, b = 92.4, c = 85.5 Å, and β = 104°, and two molecules per asymmetric unit. Mercury derivatives have been prepared with both orthorhombic and monoclinic forms, and efforts are underway to exploit these derivatives to determine the structure of this protein.
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  • 55
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    Acta crystallographica 52 (1996), S. 609-609 
    ISSN: 1399-0047
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 56
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    Acta crystallographica 52 (1996), S. 864-865 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Peroxidase from the brown alga Ascophyllum nodosum, a non-heme vanadium-dependent haloperoxidase, has been purified to homogeneity and crystallized from ammonium sulfate solutions in a form suitable for X-ray diffraction analysis. The crystals have been grown by the vapour-diffusion technique using the sitting-drop method. X-ray diffraction studies show that the crystals belong to the tetragonal space group P41212 or P43212 with a = b = 114.3 and c = 276.0 Å. The crystals diffract to at least 2.4 Å resolution.
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  • 57
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 869-870 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human salivary cystatin, a thiol proteinase inhibitor, has been implicated in potential antimicrobial and antiviral functions of saliva. A variant of human salivary cystatin SN expressed and purified in an Escherichia coli expression system lacking residues 12–16 near the N-terminus (Δ12–16) has been crystallized by the vapor-diffusion technique. The crystals are of the hexagonal space group P622 and have cell constants of a = 85.41, b = 85.41, c = 131.6 Å, α = β = 90, γ = 120°, and contain two molecules of molecular weight 13 500 per asymmetric unit. The crystals diffract up to a resolution of 2.2 Å and are suitable for X-ray diffraction analysis.
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  • 58
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    Acta crystallographica 52 (1996), S. 879-881 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Concanavalin A was co-crystallized in two crystal forms with 3,6-di-O-methyl- (α-D-mannopyranosyl) α- D-mannopyranoside, which is primarily responsible for the high-affinity binding of N-linked carbohydrates to concanavalin A. Both crystal forms have space group P21 and contain a complete concanavalin A tetramer in the asymmetric unit. Form A was crystallized using polyethylene glycol methyl ether as the precipitant and has unit-cell dimensions a = 59.83, b = 64.84 and c = 125.92 Å, β = 93.87°. Form B was obtained using phosphate as the precipitant and has unit-cell dimensions a = 81.94, b = 66.75 and c = 108.92 Å, β = 97.58°. Form B was stable in the X-ray beam for several days and diffracted to 3.15 Å resolution. Form A crystals could not withstand X-ray radiation at room temperature, but produced high-quality data under cryogenic conditions. The latter are suitable for a 2.3 Å resolution structure determination by molecular replacement.
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  • 59
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    Acta crystallographica 52 (1996), S. 890-892 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Carboxypeptidase G2 is a zinc-dependent exopeptidase which has applications in cancer therapy. Crystallization of carboxypeptidase G2, first achieved more than a decade ago, yields large crystals; however, problems with non-isomorphism between native crystals as well as failure to obtain any useful heavy-atom derivatives have precluded structure solution. A modification of the crystallization protocol leading to a promising new crystal form which diffracts beyond 3.0 Å resolution on a rotating-anode source is now reported. These crystals are readily indexed on an apparent C-centred orthorhombic lattice with a = 81.35, b = 230.9 and c = 105.5 Å, but the correct crystal system is monoclinic. The crystals have space group P21, with a = 81.35, b = 105.5, c = 122.4 Å and β = 109.3°. There are two possible non-equivalent monoclinic indexings with these lattice constants. A partial native data set collected at the SRS, Daresbury, indicates that 1.9 Å diffraction is attainable. Structure determination using MIR methods is in progress.
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  • 60
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    Acta crystallographica 52 (1996), S. 937-941 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The one-wavelength anomalous scattering (OAS) X-ray diffraction data of azurin II, a copper-containing protein from Alcaligenes xylosoxidans were collected at the Photon Factory, Japan at a `routine' wavelength of 0.97 Å. The structure had been originally solved by the molecular-replacement method [Dodd, Hasnain, Abraham, Eady & Smith (1995). Acta Cryst. D51, 1052–1064]. As a technique of ab initio structure determination, the direct method [Fan, Hao, Gu, Qian, Zheng & Ke (1990). Acta Cryst. A46, 935–939] was attempted to break the phase ambiguity intrinsic to OAS data. The phases were then improved using the solvent-flattening method. The final electron-density map clearly shows most Cα positions and many side chains and it is traceable without prior knowledge of the structure. It is concluded that the direct method is capable of phasing anomalous scattering data collected at one wavelength from moderate-sized native proteins (Mw ∼ 20 kDa) which contain copper or atoms with a similar scattering power.
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  • 61
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mutations in the human `protective protein' result in the human lysosomal storage disease galactosialidosis. The structure of the human `protective protein' has been determined using X-ray crystallography to a resolution of 2.2 Å. Initial phases were obtained from molecular replacement calculations. A very partial search model comprising 30% of the scattering mass, was constructed from the atomic model of the wheat serine carboxypeptidase. This truncated probe was used to find the position of two monomers in the asymmetric unit. Subsequently, `bootstrapping' cycles, consisting of twofold averaging and model expansion, retrieved the electron density for residues initially missing. In particular, it proved possible to add a domain (more than 110 residues) to the initial partial search model. In total, 314 residues per asymmetric unit were added to the 588 residues of the initial model. Factors contributing to our success are discussed.
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  • 62
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    Acta crystallographica 52 (1996), S. 950-958 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of the azurin mutant Met121Ala and its azide derivative Met121Ala-azide from Pseudomonas aeruginosa have been determined. The final crystallographic R values are 21.3 and 19.4% for the two structures, respectively. In the Met121Ala mutant, the distance between the copper ion and His117 increases by 0.34 Å compared with the wild-type structure. The removal of the methionine in the apical position induces a shortening of the distance from the copper ion to the carbonyl O atom of Gly45 from 2.97 to 2.74 Å. In the Met121Ala-azide structure, the azide anion occupies the cavity created by replacing the Met121 side chain with the smaller methyl group of Ala. The azide anion binds with a terminal N atom to the copper ion at a distance of about 2.04 Å. In addition, the copper ion has moved out of the trigonal plane by about 0.26 Å towards the azide anion. Thus, the copper site in this structure has a distorted tetrahedral arrangement. The spectroscopic characteristics show, in addition, that the copper sites in the two structures are distinctively different. The Met121Ala mutant still maintains the properties of an ordinary type 1 copper site while the Met121Ala-azide derivative has an absorption maximum at about 409 nm and the copper hyperfine coupling has increased to a value intermediate between those of type 2 copper and the wild-type azurin.
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  • 63
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    Acta crystallographica 52 (1996), S. 983-996 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The tetragonal form of hen egg-white lysozyme is the most investigated protein crystal for growth studies, but the relationship between its surface morphology and internal structure is still not well understood. One method of determining this relationship for inorganic crystals is by employing the periodic bond chain (PBC) theory of Hartman & Perdok [Hartman & Perdok (1955). Acta Cryst. 8, 49–52, 521–524, 525–529]. However, complexities resulting from the packing arrangements and the number of intermolecular bonds in protein crystals have resulted in the use of only simplified versions of this theory so far. In this study a more complete PBC analysis of tetragonal lysozyme crystals was carried out, coupled with an approach incorporating the molecular orientations of the crystal structure. The analysis revealed the existence of a helical tetramer building block of the entire crystal structure, centered around the 43 crystallographic axes, resulting in double-layered slices and PBC's throughout. The analysis also indicated that the crystallizing units for the faces are at least as large as this tetramer, with the experimental evidence suggesting that it is a tetramer unit for the {101} faces and an octamer unit for the {110} faces. The {110} faces were shown to be molecularly smooth F faces, while the {101} to be essentially rough S faces. The predicted morphology and growth mechanisms were found to explain numerous experimental observations from electron and atomic force microscopy, etching studies, lysozyme aggregation studies and measurements of growth kinetics.
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  • 64
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    Acta crystallographica 52 (1996), S. 1016-1017 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the human salivary α-amylase inhibitor from wheat have been obtained. A native data set was collected to 2.1 Å resolution with 90% completeness at laboratory sources. The crystals belong to the trigonal system, space group P31 (or enantiomer) with a = b = 79.31, c = 60.56 Å. Crystal density analysis and self-rotation function studies suggest the presence of four subunits in the asymmetric unit.
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  • 65
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals have been grown of a mannose-specific lectin from bluebell (Scilla campanulata) bulbs in a form suitable for X-ray diffraction studies. The crystals, which diffract to high resolution, grew in hanging drops by vapour diffusion, equilibrating with a solution of 70% saturated ammonium sulfate at pH 4.7–4.8 at 293 K, in the absence of any mannose saccharides. Crystals are orthorhombic, P21212, with unit-cell dimensions a = 70.78, b = 93.69, c = 46.92 Å. The functional lectin molecule is organized as a tetramer of four identical 14 kDa subunits, with only two subunits in the asymmetric unit. Data to 1.86 Å resolution have been recorded and the structure determined by the molecular replacement method.
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  • 66
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    Acta crystallographica 52 (1996), S. 1033-1035 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The RalGDS is a guanine nucleotide dissociation stimulator which activates the Ral protein, a Ras-like small GTPase. The C-terminal domain of the RalGDS (C-RalGDS) binds tightly to the effector loop of Ras suggesting that the RalGDS may be a crossing point of two signal tranduction pathways associated with the Ras and Ral proteins. C-RalGDS has been purified and crystallized in space group C2, with unit-cell dimensions a = 108.8, b = 30.7, c = 51.3 Å, β = 91.7° at 277 K and a = 103.8, b = 30.55, c = 51.4 Å, β = 94.9° for data collected at 100 K. The crystals diffract to 1.8 Å at a synchrotron radiation source. To use the multiple-wavelength anomalous diffraction method for phasing, a selenomethionine derivative of the protein has also been crystallized.
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  • 67
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    Acta crystallographica 52 (1996), S. 1012-1015 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 2Co2+-insulin crystals were subjected to hydrostatic pressures of up to 30 bar in a nitrogen gas cell. Changes in the diffraction pattern occurred at pressures as low as 5 bar. Analysis with standard image-processing software showed unit-cell dimension changes resulting in reductions in volume of up to 2.6%.
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  • 68
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two crystal forms of lysinal derivatives of Achromobacter protease I have been obtained. The first, modified by benzyloxycarbonyl-Val-lysinal crystallizes in the monoclinic space group P21 with unit-cell dimensions of a = 39.6, b = 71.2, c = 45.6 Å and β = 98.4°. The second, modified by benzyloxycarbonyl-Leu-Leu-lysinal crystallizes in the orthorhombic space group I222 (or I212121) with unit-cell dimensions of a = 98.7, b = 102.2 and c = 55.8 Å. The space groups and the unit-cell dimensions of the present two lysinal derivatives are different to those of the protease and TLCK- modified one. The space group of the protease is P1 with cell dimensions a = 39.53, b = 40.34, c = 43.92 Å, α = 114.81, β = 113.75 and γ = 74.00° and that of the TLCK-modified one is also P1 with cell dimensions of a = 37.30, b = 42.74, c = 48.02 Å, α = 120.10, β = 112.81 and γ = 68.54°. Diffraction to 1.9 Å resolution for the Val-lysinal modified crystal and to 2.2 Å resolution for the Leu-Leu-lysinal modified crystal has been observed using a rotating-anode X-ray generator. Full structure determinations of these lysinal-modified protease crystals may lead to an understanding of the molecular basis of enzyme–substrate interactions in the catalytic process of this protease.
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  • 69
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    Acta crystallographica 52 (1996), S. 655-667 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3′-terminal deoxycytidine residue, has been determined at 2.2 Å resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c = 59.36 Å;α = β = 90,γ = 120°)with one duplex in an asymmetric unit. The structure was solved by molecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections (86%). The duplexes are approximately linear, their global helix axes are inclined by 10° with respect to the 32-screw axes, and they are stacked on top of each other in a head-to-tail fashion. The twist between the junction base pairs of the stacked duplexes is negligible resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the organization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord with Calladine's rules. Almost all the 2′-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4′ on the 3′ side, or, through water bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the 2′-hydroxyl groups restrains the conformation of the sugar-phosphate backbone and the glycosidic torsion angles of this RNA fragment. The lack of intermolecular packing contacts in the grooves provides a clear picture of the groove solvation.
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  • 70
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    Acta crystallographica 52 (1996), S. 712-721 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of bovine lens γIIIb-crystallin at 2.5 Å resolution previously reported was interpreted using a consensus sequence derived from related vertebrate sequences on the assumption that γIIIb-crystallin derived from the γC-crystallin gene. It has recently been shown that γIIIb is a product of the bovine γD gene. The structure of γIIIb has now been refined with the bovine γD sequence using new 1.95 Å resolution synchrotron data. The crystallographic R factor was 20.4% for all 33 104 reflection data between 8.0 and 1.95 Å measured at 277(1) K. The electron density fully supported the assignment of the γD sequence to γIIIb. The crystal belongs to space group P212121 with two molecules of molecular mass 20 749 Da in the asymmetric unit in which 219 water molecules were located. The two-domain four-Greek-key motif highly symmetrical protein is very similar in structure to γB-crystallin (81% sequence identity). There is a single amino-acid deletion in γD in the linker region connecting the two domains. The intermolecular oganization in the crystal lattice is quite different from γB as a result of key mutations involving surface residues Leu51, Ile103 and His155. These point mutations will contribute to the intermolecular behaviour of the γ-crystallins in the eye lens, where they are major components of the densely packed, high refractive index regions of the lens.
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  • 71
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    Acta crystallographica 52 (1996), S. 766-775 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystallization of a DNA double helix with overhanging bases at the 5′-ends of both strands, results in the formation of two crystallographically independent (C·G)*G triplets. In a previous report [Van Meervelt, Vlieghe, Dautant, Gallois, Précigoux & Kennard (1995). Nature (London), 374, 742–744] the unique molecular packing of the duplex and the Hoogsteen hydrogen-bond pattern and parallel backbone orientation of the guanine-containing strands in the triplets was described. The fine structural details and hydration of the d(GCGAATTCG) crystal structure refined to 2.05 Å (R = 0.168, 86 water molecules, two Mg2+ cations) are now presented. Helical parameters, stacking effects, the geometry at the duplex-triplex junction, and the hydration of the minor groove are discussed and compared with related theoretical and crystal structures.
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  • 72
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    Acta crystallographica 52 (1996), S. 829-832 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A computer program, called OOPS, is described which facilitates and speeds up the process of rebuilding a protein structure inside its electron density and reduces the chances of local errors persevering throughout the crystallographic protein structure determination process. The program uses a set of criteria to judge how reasonable each protein residue is and it generates macros for the macromolecular crystallographic model-building program O [Jones, Zou, Cowan & Kjeldgaard (1991). Acta Cryst. A47, 110–119] which, when executed, will take the crystallographer on a journey along all suspect residues.
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  • 73
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    Acta crystallographica 52 (1996), S. 826-828 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two user-friendly computer programs are described for use in macromolecular X-ray crystallography, xdlMAP-MAN provides an interface for electron-density map exchange between some of the most commonly used phase refinement, structure refinement and model- building programs. In addition, it contains several options to analyse and abstract such maps. xdlDATA-MAN provides similar functionality for the analysis and manipulation of macromolecular reflection data sets. Both programs have a simple graphical user interface, and their source code has been put into the public domain.
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  • 74
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    Acta crystallographica 52 (1996), S. 842-857 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and `random noise'. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from this laboratory in which the presence (and employment) of non-crystallographic symmetry was crucial to the solution and refinement of the structure.
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  • 75
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Dodecaheme cytochrome c has been purified from Desulfovibrio (D.) desulfuricans ATCC 27774 cells grown under both nitrate and sulfate-respiring conditions. Therefore, it is likely to play a role in the electron-transfer system of both respiratory chains. Its molecular mass (37768 kDa) was determined by electrospray mass spectrometry. Its first 39 amino acids were sequenced and a motif was found between amino acids 32 and 37 that seems to exist in all the cytochromes of the c3 type from sulfate-reducing bacteria sequenced at present. The midpoint redox potentials of this cytochrome were estimated to be −68, −120, −248 and −310 mV. Electron paramagnetic resonance spectroscopy of the oxidized cytochrome shows several low-spin components with a gmax spreading from 3.254 to 2.983. Two crystalline forms were obtained by vapour diffusion from a solution containing 2% PEG 6000 and 0.25–0.75 M acetate buffer pH = 5.5. Both crystals belong to monoclinic space groups: one is P21, with a = 61.00, b = 106.19, c = 82.05 Å, β = 103.61°, and the other is C2 with a = 152.17, b = 98.45, c = 89.24 Å, β = 119.18°. Density measurements of the P21 crystals suggest that there are two independent molecules in the asymmetric unit. Self-rotation function calculations indicate, in both crystal forms, the presence of a non-crystallographic axis perpendicular to the crystallographic twofold axis. This result and the calculated values for the volume per unit molecular weight of the C2 crystals suggest the presence of two or four molecules in the asymmetric unit.
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  • 76
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 901-908 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glutaraldehyde cross-linking followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis has been used to detect aggregates of iysozyme in solutions which lead to crystals. In solutions of varying NaCl content, the number of aggregates was found to be related to the ionic strength of the solution. Solutions of 1% NaCl, pH 4.0 were monomeric while those containing 7–15% NaCl, pH 4.0 were shown to be as much as 36% aggregated and 64% monomeric. The aggregates detected at the highest salt and protein concentration studied were composed of dimers, trimers and tetramers. The aggregates increased by addition of single units suggesting the aggregation pathway to be that of monomer addition. The kinetics of the cross-linking reaction were slow preventing a study of either the time dependence of aggregation or the effect of temperature on aggregate distributions. Comparison of the total aggregate concentrations for NaCl and Na2SO4 showed that the concentration of aggregates was related to the ionic strength of the solution suggesting that in both crystallization and precipitation, electrostatic shielding of like-charged protein molecules is necessary in order for aggregation to occur.
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  • 77
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    Acta crystallographica 52 (1996), S. 959-965 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A dynamic conformational flexibility of a protein might be a source of non-covalent structural heterogeneity, causing diminished diffracting ability of crystals and disorder in a crystal structure of soybean lipoxygenase L3. Room-temperature data, space group C2, correspond to a structure with large channels lined mostly or in part by disordered fragments of the molecule or flexible loops with an increased thermal vibration. A rapid change in temperature of \sim200 K creates a wave of a stress-induced modulation that propagates in the crystal changing its reciprocal space into a three-dimensional quilt-like mixture of C and P intertwined lattices. Low-temperature data indicate a transformation from the dynamic to static disorder, leading to a primitive unit cell with 10% reduced volume. The molecules, formerly related by a twofold axis are rotated by \sim7° and are shifted along the diagonal to be \sim4 Å, closer together. During a routine data collection for the flash-frozen crystals of similar properties such phenomena could easily go unnoticed leading to biased results because of such effects and possibly improper indexing of the data.
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  • 78
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    Acta crystallographica 52 (1996), S. 1004-1011 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Interest in a pair of highly isomorphous structures often focuses on the differences between them. In cases where substantial correlated model errors exist or where there are differences in the quality of the two experimental data sets (cases quite common in macromolecular crystallography), independent refinement of the two structures does not lead to the most accurate estimate of the differences between them. An alternative procedure that has proven effective in some such cases is difference refinement, in which the residual between observed and calculated differences in structure-factor amplitudes between the two structures is minimized. A Bayesian approach has been used to extend the range of applicability of difference refinement to cases where there is only partial correlation in model errors and where the overlap between the data sets is limited. The resulting method, Bayesian difference refinement, uses residuals to be minimized that vary smoothly between difference refinement and independent refinement. When the errors in the two structural models are very similar, difference refinement is used; when they are very different, independent refinement is used; and when they are partially correlated, a combination of the two is used. The procedure is very simple to apply and does not significantly increase the computational demands of refinement.
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  • 79
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    Acta crystallographica 52 (1996), S. 1018-1020 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of a 26-nucleotide pseudoknot RNA, PK26, have been grown. The RNA was produced using phosphoramidite chemistry and was purified by denaturing polyacrylamide electrophoresis. The crystallization was robust with respect to changes in the number of nucleotides and to the salt used as precipitant. The crystals belong to space group P4122 or P4322 with unit-cell dimensions a = b = 61.6, c = 98.9 Å. The best crystals diffract X-rays to 2.9 Å. Three different sequences incorporating a single 5-bromo-deoxyuridine or 5-bromo-uridine nucleotide were also crystallized. Two of these derivatives are being used to determine the structure by multiple isomorphous replacement.
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  • 80
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    Acta crystallographica 52 (1996), S. 1041-1045 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Influenza C virus contains a single surface glycoprotein in its lipid envelope which is the hemagglutinin-esterase-fusion glycoprotein (HEF). HEF binds cell-surface receptors, is a receptor-destroying enzyme (a 9-O-acetylesterase), and mediates the fusion of virus and host cell membranes. A bromelain-released soluble form of HEF has been crystallized. Two different tetragonal forms have been identified from crystals with the same morphology [P1(3)22, a = b = 154.5, c = 414.4 Å, and P41(3)212, a = b = 217.4, c = 421.4 Å]. Both crystal forms share a common packing scheme. Synchrotron data collection and flash cooling of crystals have been used for high-resolution data collection.
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  • 81
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    Acta crystallographica 52 (1996), S. 1075-1081 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The feasibility of phasing protein structures through the use of the isomorphous and anomalous signal of selenomethionyl (Se-Met) derivative and diffraction data collected with a standard laboratory Cu Kα X-ray source has been investigated. Interpretable electron-density maps were obtained for the core domain of avian sarcoma virus integrase, a typical medium-sized protein having four Met residues in a sequence of 156 amino acids. The r.m.s. difference between 3.1 Å experimental phases obtained from Se-Met Cu Kα data and the final phases calculated from the refined model is 55°. A procedure combining single isomorphous replacement/single anomalous scattering phasing and solvent flattening for data based on a single Se-Met derivative and Cu Kα radiation has been tested on this and another protein. The results are encouraging enough to indicate that such procedures might be recommended when a synchrotron source is not readily available.
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  • 82
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    Acta crystallographica 53 (1997), S. 220-221 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A mannose-specific lectin from Calystegia sepium has been crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. The needle-shaped crystals are orthorhombic, space group C2221 with cell dimensions a = 55.2(1), b = 55.9 (1), c = 196.1 (1) Å. Fresh crystals diffract to 1.9 Å resolution on a synchrotron radiation source. The asymmetric unit contains a dimer of two identical 16 kDa subunits with a packing density of 2.36 Å3 Da−1. Intensity data have been observed beyond 2.0 Å, but reasonable statistics restricted the usable range to 2.0 Å.
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  • 83
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    Acta crystallographica 53 (1997), S. 227-228 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two crystal forms of component 1 (the MoFe protein) of nitrogenase from Klebsiella pneumoniae have been isolated and characterized. The triclinic form has cell dimensions a = 76.0, b = 109.6, c = 144.6 Å, α = 80.3, β = 74.9 and γ = 69.6°, diffracts to around 3.0 Å and has two molecules in the asymmetric unit. The monoclinic form belongs to space group P21 with a = 76.6, b = 127.8, c = 109.1 Å and β = 104.6° (frozen at 100 K), diffracts to 1.5 Å and has one molecule in the asymmetric unit. At this resolution the outstanding questions concerning the structure and the operation of the enzyme, in particular the linkage between the Fe4S4 units in the P clusters, the true geometry of the apparently trigonal Fe atoms in the FeMoco and the reduction site itself, should be answerable.
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  • 84
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    Acta crystallographica 53 (1997), S. 302-310 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Soybean leghemoglobin a is a small (16 kDa) protein facilitating the transport of O2 to respiring N2-fixing bacteria at low free-O2 tension. The crystal structure of soybean ferric leghemoglobin a nicotinate has been refined at 2.3 Å resolution. The final R factor is 15.8% for 6877 reflections between 6.0 and 2.3 Å. The structure of soybean leghemoglobin a (143 residues) is closely similar to that of lupin leghemoglobin II (153 residues), the proteins having 82 identical residues when the sequences are aligned. The new structure provides support for the conclusion that the unique properties of leghemoglobin arise principally from a heme pocket considerably larger and more flexible than that of myoglobin, a strongly ruffled heme group, and a proximal histidine orientation more favourable to ligand binding.
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  • 85
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    Notes: C-phycocyanin and allophycocyanin from the green alga Spirulina platensis were isolated and crystallized by gel-acupuncture techniques. A novel two-step chromatographic procedure was used for purification. Blue hexagonal crystals were obtained by diffusing magnesium chloride into the protein solution for a week, followed by diffusion of PEG 6000 in order to complete the reduction of the solubility of the protein in the capillary tube used as a growth cell. In the case of allophycocyanin, crystals with a size of 0.4 × 0.3 × 0.3 mm were characterized by X-ray diffraction. They belong to space group P6322 with unit-cell parameters a = b = 102.04, c = 131.22 Å. The crystals of C-phycocyanin belong to either space group P6 or P63 with unit-cell constants a = b = 182.38, c = 60.87 Å, α = β = 90, γ = 120°. The crystals diffract beyond 2.4 and 2.5 Å resolution, respectively, using a rotating anode as an X-ray source.
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  • 86
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    Notes: A chromoprotein from Pleurotus salmoneostramineus L. Vass. has been purified and crystallized. The needle-shaped crystal has monoclinic space group C2 with the cell dimensions of a = 118.5, b= 59.7,0 c = 31.8 Å and β = 114°. The crystal diffracts to 1.8 Å resolution with a synchrotron radiation X-ray source.
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  • 87
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    Acta crystallographica 53 (1997), S. 345-347 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ab inito quantum chemical calculations are performed to quantify the stabilizing role of long C—H···O=C contacts in nucleic acid base pairing, which was suggested by Leonard, McAuley-Hecht, Brown & Hunter [(1995). Acta Cryst. D51, 136–139]. For the Watson-Crick adenine-uracil pair, a contribution of about 6% to the total bond energy is obtained. This weakly bonding effect is primarily a result of electrostatic attraction between the total positive charge of adenine C(2)—H and the negative end of the dipole uracil O(2)=C.
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  • 88
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    Acta crystallographica 53 (1997), S. 355-363 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A lysozyme isolated from the milk of a monotreme, the echidna, Tachyglossus aculeatus multiaculeatus, has been crystallized (space group P21, with unit-cell dimensions a = 37.1, b = 42.0, c = 38.1 Å, β = 91° and Z = 2) and the structure refined to an R value of 0.167 for all measured data in the resolution range 7.0–1.9 Å. It had previously been inferred from sequence homology with α-lactalbumins that echidna milk lysozyme (EML) would bind one calcium ion per molecule. This has been confirmed in the present study in which the largest peak in a difference Fourier synthesis is associated with a calcium ion. The calcium binding site of EML is very similar to that observed in baboon and human α-lactalbumins, and in a human lysozyme engineered to contain a calcium-binding site. The overall fold of the protein is similar to that of chick-type lysozymes. EML, like pigeon lysozyme, has only 125 residues terminating at a cysteine but in EML this forms a disulfide with a cysteine at residue 9 whereas the equivalent cysteine residue in all other lysozymes of known sequence occurs at position 6. These changes cause some minor structural rearrangements. The binding of calcium appears to have had little effect on the polypeptide backbone conformation and caused only small changes in the conformation of side chains coordinating the calcium ion. A homology modelling study [Acharya, Stuart, Phillips, McKenzie & Teahan (1994). J. Protein Chem. 13(6), 569–584] correctly predicted the overall structure of EML and the nature of its calcium binding site but generally failed to model some more subtle differences observed in the EML structure as evidenced by the fact that the homology model more closely resembles the starting structure from which the model was derived than it does the crystal structure.
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  • 89
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    Acta crystallographica 53 (1997), S. 406-418 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Copper-containing nitrite reductases (NiR's) have been conveniently subdivided into blue and green NiR's which are thought to be redox partners of azurins and pseudo-azurins, respectively. Crystal structures of two green NiR's have recently been determined. Alcaligenes xylosoxidans has been shown to have a blue-copper nitrite reductase (AxNiR) and two azurins with 67% homology both of which donate electrons to it effectively. The first crystal structure of a blue NiR (AxNiR) in its oxidized and nitrite-bound forms, with particular emphasis to the Cu sites, is presented. The Cu-Smet distance is the same as those in the green NiR's. Thus, the length of this interaction is unlikely to be responsible for differences in colour. Crystallographic data presented here taken together with structural data of other single Cu type-1 proteins and their mutants suggest that the displacement of Cu from the strong ligand plane is perhaps the cause for the differences in colour observed for otherwise `classical' blue Cu centre. Nitrite is observed binding to the catalytic Cu in a bidentate fashion displacing the water molecule, offering a neat rationalization for the XAFS observation that the type-2 Cu-ligand distances increase on nitrite binding as a result of increased coordination. These results are discussed in terms of enzyme mechanism.
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  • 90
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    Acta crystallographica 53 (1997), S. 419-425 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of crystal form IX of bovine pancre- atic ribonuclease A (space group P212121) is reported at 1.6 Å resolution. The structure was refined to an R factor of 15.0% and includes coordinates for two sulfate ions, four methanol molecules and 82 waters. The structure could be superimposed on the highest resolution crystal structure of bovine pancreatic fibonuclease available (in space group P21) with an r.m.s, difference in main-chain atomic positions of 0.51 Å. Most of the larger differences between the two structures could be related to crystal lattice contacts. Superposition of the new structure with eight other structures of ribonuclease in six crystal forms resulted in an r.m.s, deviation from the average structure of 0.43 Å for all main-chain atoms. This similarity among structures exists in spite of the fact that all nine molecules are in different crystal environments.
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  • 91
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    Acta crystallographica 53 (1997), S. 438-447 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Osmotic pressure, small-angle X-ray scattering and quasi-elastic light scattering were used to study the medium-range interaction potentials between macromolecules in solution. These potentials determine macromolecular crystallization. Calf eye lens γ-crystallins were used as a model system with the charge, and therefore the interactions, varied with pH. The second virial coefficient was determined under the same conditions with each of the three techniques. Osmotic pressure and quasi-elastic light scattering can be used conveniently in the laboratory to rapidly test the type of interactions (either attractive or repulsive) present in the solution. The measurement is direct with osmotic pressure, whereas with quasi-elastic light scattering, the directly measured coefficient is a combination of thermodynamic and hydrodynamic terms. X-rays, which require more sophisticated equipment such as synchrotron radiation facilities, can provide more detailed information on the interparticle potentials when models are used. At low ionic strength, two potentials were found necessary to account for the temperature and pH phase diagram as a function of protein concentration. The first potential is the van der Waals attractive potential that was previously shown to account for the fluid-fluid phase separation at low temperature. The second potential is an electrostatic coulombic repulsive potential which is a function of the protein charge and thus of the pH. The interaction trail could be followed at protein concentrations as low as 10 mg ml−1. The results as a whole are expected to be valid for all compact low molecular weight proteins at low ionic strength.
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  • 92
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    Acta crystallographica 53 (1997), S. 464-468 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of apo duck ovotransfemn (APODOT) has been determined at a resolution of 4.0 Å by the molecular replacement method using the structure of duck ovotransfemn (DOT) as the search model. The DOT structure contains two iron binding sites; one in the N-terminal lobe lying between domains N1 and N2 and one in the C-terminal lobe between domains C1 and C2. Both lobes have a closed structure. Models of various forms of both the N and C lobes were used in the search. The final model was refined to give an R factor of 0.22. The comparison of the structure of APODOT with that of DOT shows that both the N and the C lobes are in an open form, where the N2 and C2 domains undergo large rigid-body rotations of 51.6 and 49.9° relative to the N1 and C1 domains, respectively. The interface between the N and C lobes, which is formed by the N1—C1 contact in the core of the molecule does not change significantly. The DOT molecule may be described in terms of three rigid bodies; the N1 and C1 domains as one rigid body forming the static core of the molecule and the N2 and C2 domains as two other rigid bodies which, on the release of iron, move away from the static core of the molecule to form the open structure of APODOT.
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  • 93
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    Acta crystallographica 53 (1997), S. 472-473 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: PR1A3 antibody binds specifically to the tumour-associated cell-surface antigen, carcinoembryonic antigen. Crystals of the Fab fragment of the PR1A3 antibody were obtained by vapour diffusion against mother liquor containing Tris–HC1 buffer, pH 8.6, magnesium chloride and polyethylene glycol 4000 as precipitating agent. Crystals belong to the monoclinic space group P21 with cell dimensions a = 42.2, b = 216.7, c = 45.9 Å and β = 95.6°. Two Fab fragments are proesent in the asymmetric unit. Diffracted intensities up to 2.9 Å resolution have been measured from frozen crystals.
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  • 94
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    Acta crystallographica 52 (1996), S. 1214-1215 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of a novel histidine protein kinase domain of the anaerobic sensor protein ArcB from Escherichia coli have been obtained by a hanging-drop vapor-diffusion method with micro- and macroseeding techniques. Preliminary X-ray crystallographic analysis revealed that they belong to space group P212121 with dimensions a = 30.56, b = 34.93 and c = 110.78 Å, having one molecule in the crystallographic asymmetric unit. The crystals diffract to at least 2.0 Å resolution.
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  • 95
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    Acta crystallographica 52 (1996), S. 1222-1223 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The highly glycosylated protein, human heparin binding protein, has been crystallized in the primitive orthorhombic space group P212121 with cell dimensions a = 39.0, b = 66.2 and c = 101.4 Å. Ethanol was used as precipitant and glycerol as additive. A full data set has been collected to 3.1 Å and diffraction was observed to at least 2.3 Å. A molecular replacement solution using human neutrophile elastase as a search model was obtained, showing one molecule per asymmetric unit. The crystal packing showed no bad contacts and the R factor was 44.8% after ten cycles of rigid-body refinement.
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  • 96
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    Notes: A strategy is presented for refining anomalous scattering models and calculating protein phases directly from the Bijvoet and dispersive differences of a macromolecular multiwavelength anomalous diffraction (MAD) experiment. This procedure, incorporated in the program MADPHSREF, is especially amenable for exploiting the weak perturbations to normal scattering produced by inner-shell electronic transitions of asymmetric metal and protein ligand assemblies. The protocol accounts for more than one type of anomalous scatterer, incorporates stereochemical restraints, treats the data in local scaling groups, and partly compensates for correlated errors. Approximating maximum likelihood by averaging observation variances and covariances over all values of phase considerably improved error estimation. Probabilistic rejection of aberrant observations, re-evaluated before each refinement cycle, improved refinement convergence and accuracy compared with other less flexible rejection criteria. MADPHSREF allows the facile combination of MAD phase information with phase information from other sources. For the suifite reductase hemoprotein (SiRHP), relative weights for MAD and multiple isomorphous replacement (MIR) phases were determined by matching histograms of electron density. Accurate metal-cluster geometries and the associated errors in atomic positions can be determined from refinement against anomalous differences using normal scattering phases from a refined structure. When applied to MAD data collected on SiRHP, these methods confirmed the Fe4S4 cluster asymmetry initially observed in the refined 1.6 Å resolution structure and resulted in a MAD-phased, experimental, electron-density map that is of better quality than the combined MAD/MIR map originally used to determine the structure.
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  • 97
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    Acta crystallographica 53 (1997), S. 458-460 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 kDa) of the M1 protein. X-ray diffraction studies indicated that the crystals are in space group P3121 or P3221, with a = 66.17, c = 135.30 Å. Vm calculations showed that there are two monomers in the asymmetric unit.
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  • 98
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    Acta crystallographica 53 (1997), S. 480-481 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Staphylokinase, a 17 kDa protein, produced by certain strains of Staphylococcus aureus functions as a fibrin-specific plasminogen activator. During its interaction with plasminogen, staphylokinase is converted into a low molecular weight form by loss of ten amino-terminal residues. This low molecular weight form of recombinant staphylokinase has been crystallized using the hanging-drop vapor-diffusion technique with polyethylene glycol 4000 as precipitant. Crystals belong to the orthorhombic space group C2221 with unit-cell dimensions a = 43.78, b = 59.86 and c = 103.25 Å and one molecule in the asymmetric unit. These crystals diffract to about 2.4 Å resolution.
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  • 99
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    Acta crystallographica 53 (1997), S. 482-484 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: RNA guanylyltransferase, or capping enzyme (E.C. 2.7.7.50) catalyzes the transfer of GMP from GTP to diphosphate-terminated RNA to form the cap structure GpppN. Chlorella virus capping enzyme expressed in E. coli has been purified, treated with GTP and crystallized. X-ray diffraction data have been collected from these crystals as well as for a mercury derivative obtained by soaking the crystals in thimerosal. Selenomethionine RNA guanylyltransferase was purified and crystallized in a similar fashion. The space group is C2221 and the cell parameters are a = 93.3, b = 214.9, c = 105.8 Å. Two Hg atoms and two subsets of Se atoms have been localized using difference Patterson and Fourier methods, suggesting that there are two molecules per asymmetric unit.
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    Acta crystallographica 53 (1997), S. 513-523 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The ferritins are a multigene family of proteins that concentrate and store iron in all prokaryotic and eukaryotic cells. 24 monomeric subunits which fold as four-helix bundles assemble to form a protein shell with 432 cubic symmetry and an external diameter of ∼130 Å. The iron is stored inside the protein shell as a mineralized core ∼80 Å in diameter. Recombinant amphibian red cell M ferritin crystallizes in ∼2 M (NH4)2SO4 at pH 4.6 in a space group that has not been reported previously. Electron microscopy, precession photography, Patterson and Fourier maps of the native protein and a UO{_2^{2+}} derivative, and simulations were used to determine that the unit-cell dimensions are a = b = 169.6, c = 481.2 Å, α = β = γ = 90° and the space group is P41212 or P43212. A preliminary model of the structure was obtained by molecular replacement, with amphibian red cell L ferritin as the model. In contrast to previously determined ferritin crystal structures which have intermolecular contacts at the twofold and threefold molecular axes, M ferritin crystals have a novel intermolecular interaction mediated by interdigitation of the DE loops of two molecules at the fourfold molecular axes.
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