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  • International Union of Crystallography (IUCr)
  • 1995-1999  (9,528)
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Year
  • 1
    Electronic Resource
    Electronic Resource
    A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 140-144 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is often found in the crystallization of enzyme–inhibitor complexes that an inhibitor causes crystal packing which is different to that of native protein. This is the case for crystals of human non-pancreatic secreted phospholipase A2 (124 residues) containing six molecules in the asymmetric unit when the protein is complexed with a potential acylamino analogue of a phospholid. The hexameric structure was determined by molecular replacement using the structure of monomeric native protein as a probe. As an extension to the experiment, it was tested whether a backbone polypeptide composed of 17% of a known monomeric structure could find its correct position on a target molecule in molecular replacement. A probe model composed of the backbone atoms of the N-terminal 77 residues of lysine-, arginine-, ornithine-binding protein (LAO, a total of 238 residues) liganded with lysine correctly finds its position on LAO liganded with histidine which crystallizes as a monomer in the asymmetric unit. The results indicate that as little as 17% of total diffracting matter can be used in molecular replacement to solve crystal structures or to obtain phase information which can be combined with phases obtained by the isomorphous-replacement method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010024
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  • 2
    Electronic Resource
    Electronic Resource
    Crystallization of the NAD(P)-dependent glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 240-242 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NAD(P)-dependent glutamate dehydrogenase from Pyrococcus furiosus has been crystallized by the hanging-drop method of vapour diffusion using lithium sulfate as the precipitant. The crystals belong to the tetragonal system and are in space group P42212 with unit-cell dimensions of a = b = 167.2, c = 172.9 Å. Consideration of the values of Vm and possible packing of the molecules within the cell suggest that the asymmetric unit contains a trimer. P. furiosus belongs to the family of Archaea and is one of the most thermostable organisms known, having an optimal growth temperature of 376 K. The glutamate dehydrogenase isolated from this organism has a half-life of 12 h at 373 K and, therefore, the determination of the structure of this enzyme will be important in advancing our understanding of how proteins are adapted to enable them to survive at such extreme temperatures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994012862
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  • 3
    Electronic Resource
    Electronic Resource
    Shaped protein single crystals (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 278-281 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The formation of protein single crystals grown with the shape controlled by the geometry of the capillary used as a growth cell is presented. The shaped crystals show strong birefringence under crossed nicols and diffract as single crystals up to 1.74 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994013065
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  • 4
    Electronic Resource
    Electronic Resource
    NMR – this other method for protein and nucleic acid structure determination (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 249-270 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: For a quarter of a century X-ray diffraction in single crystals was unique in its ability to solve three-dimensional structures of proteins and nucleic acids at atomic resolution. The situation changed in 1984 with the completion of a protein structure determination by nuclear magnetic resonance (NMR) spectroscopy in solution, and today NMR is a second widely used method for biomacromolecular structure determination. This review describes the method of NMR structure determination of biological macromolecules, and attempts to place NMR structure determination in perspective with X-ray crystallography. NMR is most powerful for studies of relatively small systems with molecular weights up to about 30000, but these structures can be obtained in near-physiological milieus. The two techniques have widely different time scales which afford different insights into internal molecular mobility as well as different views of protein or nucleic acid molecular surfaces and hydration. Generally, in addition to information on the average three-dimensional structure, NMR provides information on a wide array of short-lived transient conformational states. Combining information from the two methods can yield a more detailed insight into the structural basis of protein and nucleic acid functions, and thus provide a more reliable platform for rational drug design and the engineering of novel protein functions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010188
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  • 5
    Electronic Resource
    Electronic Resource
    X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 190-198 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of the B-DNA dodecamer d(CGCGTTAACGCG) duplex (T2A2), with the inverted tetranucleotide core from the duplex d(CGCGAATTCGCG) [A2T2, Dickerson & Drew (1981). J. Mol. Biol. 149, 761–768], and its netropsin complex (T2A2–N) have been determined at 2.3 Å resolution. The crystals are orthorhombic, space group P212121, unit-cell dimensions of a = 25.7, b = 40.5 and c = 67.0 Å, for T2A2 and a = 25.49, b = 40.87, c = 67.02 Å for T2A2–N and are isomorphous with A2T2. The native T2A2 structure, with 70 water molecules had a final R value of 0.15 for 1522 reflections (F 〉 2σ), while for the netropsin complex, with 87 water molecules, the R value was 0.16 for 2420 reflections. In T2A2, a discontinuous string of zigzagging water molecules hydrate the narrow A·T minor groove. In T2A2–N, netropsin binds in one orientation in the minor groove, covering the TTAA central region, by displacing the string of waters, forming the majority of hydrogen bonds with DNA atoms in one strand, and causing very little perturbation of the native structure. The helical twist angle in T2A2 is largest at the duplex center, corresponding to the cleavage site by the restriction enzymes HpaI and HincII. The sequence inversion AATT→TTAA of the tetranucleotide at the center of the molecule results in a different path for the local helix axis in T2A2 and A2T2 but the overall bending is similar in both cases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994010759
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  • 6
    Electronic Resource
    Electronic Resource
    Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochrome c' from two bacterial species (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 282-289 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of cytochrome c′ from two bacterial species, Alcaligenes sp and Alcaligenes denitrificans, have been determined from X-ray diffraction data to 3.0 Å resolution using the anomalous scattering of the single Fe atom in each to identify and refine a weak molecular-replacement solution. Molecular-replacement studies, with the program AMORE, used two isomorphous data sets (from the two species), two independent search models (the cytochromes c′ from Rhodospirillum molischianum and Rhodospirillum rubrum), both with and without side chains, and two different resolution ranges (10.0–4.0 and 15.0–3.5Å) to generate a large number of potential solutions. No single solution stood out and none appeared consistently. The Fe-atom position in each structure was then determined from its anomalous-scattering contribution and all molecular- replacement solutions were discarded which did not (i) place the Fe atom correctly and (ii) orient the molecule such that a crystallographic twofold axis generated a dimer like those of the two search models. Finally, electron-density maps phased solely by the Fe-atom anomalous scattering were calculated. As these were combined and subjected to solvent flattening and histogram matching (with the program SQUASH), correlation with the remaining molecular-replacement solutions identified one as correct and enabled it to be improved and subjected to preliminary refinement. The correctness of the solution is confirmed by parallel isomorphous-replacement studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994012874
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  • 7
    Electronic Resource
    Electronic Resource
    Using sampling techniques in protein crystallization (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 305-310 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystallization of homogeneous or highly purified macromolecules depends on many variables such as precipitant, pH, choice of buffer, protein concentration, temperature, the participation of different mono- and divalent ions, as well as the presence of minute amounts of detergent and organic molecules. Finding the best combination among these many parameters is a multi-variable optimization problem. This kind of problem can be treated mathematically by sampling techniques. We have used this technique for protein crystallization. The iterative procedure starts with random sampling, followed by quantitative evaluation and cycles with weighted sampling. A simple procedure, derived from this concept and called MON48, has been successfully applied to many protein crystallization problems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994011728
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  • 8
    Electronic Resource
    Electronic Resource
    Characterization of lysozyme crystals with unusually low solvent content (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 390-392 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Studies on the low-humidity (88%) forms of tetragonal and monoclinic lysozyme, resulting from water-mediated transformations, have provided a wealth of information on the variability in protein hydration, its structural consequences and the water structure associated with proteins, in addition to facilitating the delineation of the rigid and the flexible regions in the protein molecule and the invariant features in its hydration shell. Surprisingly, monoclinic lysozyme continues to diffract even when the environmental humidity is drastically reduced, thus permitting the structural study of the enzyme at different levels of hydration. As part of a study in this direction, three very low humidity forms, two of them occurring at a nominal relative humidity of 38% and the other at 5% relative humidity, have been characterized. These have unprecedented low solvent contents of 16.9, 17.6 and 9.4%, respectively, as determined by the Matthews method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994009790
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  • 9
    Electronic Resource
    Electronic Resource
    Structure of anionic salmon trypsin in a second crystal form (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 725-730 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 Å, resolution. The crystals are orthorhombic and belong to space group P21212 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 Å. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b = 84.33 and c = 39.11 Å [Smalås & Hordvik (1993). Acta Cryst. D49, 318–330]. The presence of a sulfate group involved in several hydrogen bonds to active-site residues, and the location of an additional benzamidine site in the crystal lattice, are the most striking differences between the present and the previous structure. Superposition of main-chain atoms in the two structures give an overall r.m.s. difference of 0.26 Å, with the main differences located to areas with different molecular packing. The overall coordinate error is estimated to be between 0.20 and 0.25 Å, by the method of Luzzati.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995000333
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  • 10
    Electronic Resource
    Electronic Resource
    The direct rotation function: Patterson correlation search applied to molecular replacement (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 740-748 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Most rotation functions try to achieve maximal correlation between two Patterson functions by systematically rotating one and computing the overlap with the other. In contrast, the direct rotation function rotates a search model relative to the crystal unit cell and evaluates the linear correlation coefficient (Patterson correlation, PC) between squared normalized structure-factor amplitudes of the observed and calculated diffraction data. Structure factors are calculated from the rotated search model in a P1 unit cell identical to that of the target crystal. PC makes use of all self-Patterson vectors of the search model. A comparison of the direct rotation function, a real-space rotation function, and a fast rotation function suggests that the direct rotation function provides a considerable enhancement of the signal-to-noise ratio compared to other two. Combined with PC refinement, the direct rotation function was successful in solving multidomain macromolecular crystal structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995001284
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