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  • 1
    Electronic Resource
    Electronic Resource
    A flexible and efficient procedure for the solution and phase refinement of protein structures (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1137-1147 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 Å) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage (∼5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized α-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490000932X
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  • 2
    Electronic Resource
    Electronic Resource
    Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 Å resolution (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 257-271 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of a complex of ribonuclease from Streptomyces aureofaciens (RNase Sa) with guanosine-2′-monophosphate (2′-GMP) has been refined against synchrotron data recorded from a single crystal using radiation from beamline X31 at EMBL, Hamburg, and an imaging plate scanner. The crystals are in space group P212121 with cell dimensions a = 64.7, b = 78.8 and c = 39.1 Å. The structure has two enzyme molecules in the asymmetric unit, complexed with 2′-GMP inhibitor with occupancies of 1 and {2 \over 3} (different to the 3′-GMP complex crystal structure where only one of the two independent RNase Sa molecules binds nucleotide), 492 associated water molecules and one sulfate ion, and was refined using all data between 10.0 and 1.7 Å to a final crystallographic R factor of 13.25%. Binding of the base to the enzyme confirms the basis for the guanine specificity but the structural results still do not provide direct evidence of the identity and role of the particular residues involved in the catalytic process. New native RNase Sa data to 1.8 Å were recorded to provide a reference set measured under comparable experimental conditions. The crystals are in the same space group and have the same lattice as those of the 2′-GMP complex. The native structure with 423 water molecules was refined in a similar manner to the complex to a final R factor of 13.87%. 1.77 Å resolution data were independently measured on a 2′-GMP complex crystal at UCLA using an R-AXIS II image plate scanner mounted on a conventional source. The cell dimensions were essentially the same as above. 2′-GMP was bound more fully to molecule A than to molecule B of the RNase Sa. The structure was refined to an R factor of 14.64% with 388 water molecules. This work follows on from the structure determination of native RNase Sa and its complex with 3′-GMP [Sevcik, Dodson & Dodson (1991). Acta Cryst. B47, 240–253].
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444992007261
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  • 3
    Electronic Resource
    Electronic Resource
    Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 805-813 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Liver alcohol dehydrogenase (LADH) is a ZnII-dependent dimeric enzyme. LADH with the active-site ZnII substituted by CuII resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure of the active site CuII-substituted LADH complex with NADH and dimethyl sulfoxide (DMSO). The structure was solved by molecular replacement. The space group is P21 with cell dimensions a = 44.4, b = 180.6, c = 50.8 Å and β = 108°. There is one dimer of the enzyme in the asymmetric unit. The refinement was carried out to a crystallographic R-factor of 16.1% for 41 119 unique reflections in the resolution range 12.0 to 2.1 Å. The coordination geometry of CuII in LADH is compared with the active-site metal coordination in the Zn–LADH–NADH–DMSO complex and blue-copper proteins. The distances from the metal to the protein ligands (Cys46, His67 and Cys174) are similar for the ZnII and CuII ions. The distances of the O atom of the inhibitor DMSO to the CuII ion in the two subunits of the dimer are 3.19 and 3.45 Å. These are considerably longer than the corresponding distances for the ZnII enzyme, 2.19 and 2.15 Å. The CuII ion is positioned nearly in the plane of the three protein ligands (NS2) with a geometry similar to the trigonal arrangement of the three strongly bound ligands (N2S) in blue-copper proteins. This coordination probably accounts for the similarity of the spectral characteristics of CuII–LADH and type I copper proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499500045X
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  • 4
    Electronic Resource
    Electronic Resource
    Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 176-188 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995007608
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  • 5
    Electronic Resource
    Electronic Resource
    wARP: Improvement and Extension of Crystallographic Phases by Weighted Averaging of Multiple-Refined Dummy Atomic Models (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 448-455 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: wARP is a procedure that substantially improves crystallographic phases (and subsequently electron-density maps) as an additional step after density-modification methods such as solvent flattening and averaging. The initial phase set is used to create a number of dummy atom models which are subjected to least-squares or maximum-likelihood refinement and iterative model updating in an automated refinement procedure (ARP). Averaging of the phase sets calculated from the refined output models and weighting of structure factors by their similarity to an average vector results in a phase set that improves and extends the initial phases substantially. An important requirement is that the native data have a maximum resolution beyond \sim2.4 Å. The wARP procedure shortens the time-consuming step of model building in crystallographic structure determination and helps to prevent the introduction of errors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997005696
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  • 6
    Electronic Resource
    Electronic Resource
    Protein Crystal Growth in the Advanced Protein Crystallization Facility on the LMS Mission: a Comparison of Sulfolobus solfataricus Alcohol Dehydrogenase Crystals Grown on the Ground and in Microgravity (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 386-390 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of alcohol dehydrogenase from Sulfolobus solfataricus were grown in the Advanced Protein Crystallization Facility during the Life and Microgravity Sciences Spacelab mission on the US Space Shuttle. Large diffracting crystals were obtained by dialysis, whereas only poor-quality crystals were obtained by vapour diffusion. The quality of both the microgravity and ground-based crystals was analysed by X-ray diffraction. There was some improvement in terms of size and diffraction resolution limit for the microgravity crystals. However, the twinning observed in the Earth-grown crystals was also present for those grown in microgravity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997011992
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  • 7
    Electronic Resource
    Electronic Resource
    High-resolution structure of the complex between carboxypeptidase A and L-phenyl lactate (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 534-540 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structures of native carboxypeptidase A and of the enzyme–inhibitor complex with L-phenyl lactate have been refined at 1.54 and 1.45 Å resolution to R factors of 0.151 and 0.161, respectively. Crystals of the complex were isomorphous with the native crystals (space group P21, a = 51.60, b = 60.27, c = 47.25 Å, β = 97.27°). The high-resolution electron density allowed correction of many side-chain positions in the classical carboxypeptidase A model. This reflects the advantages of the high-quality complete synchrotron data collected with an imaging plate detector. The conformational changes in the active centre of the enzyme upon binding of the inhibitor are restricted to only two residues, Tyr248 and Arg145. L-Phenyl lactate is bound in the S1′ pocket and forms hydrogen bonds to Arg145, Glu270 and to the zinc-bound water molecule. The present structure provides an explanation for the higher stability of the complexes with the products of esterolysis in comparison with those of amidolysis. This is consistent with the finding that product release is rate limiting for esters but not for peptides.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993007267
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  • 8
    Electronic Resource
    Electronic Resource
    Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 Å (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 202-209 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 for all data between 10.0 and 1.65 Å resolution, using data collected on the Hendrix–Lentfer imaging plate at the EMBL outstation in Hamburg. The r.m.s. deviations from stereochemical ideality are 0.010 and 0.011 Å for bonds and planes, respectively. Although crystallized in the presence of the nucleotide product MgATP, the high-resolution structure reveals the bound nucleotide to be MgADP reflecting the low intrinsic ATPase activity of PGK. Although the two domains of this enzyme are found to be some 4.5° closer together than is found in the yeast and horse-muscle apo-enzyme structures, this structure represents the `open' rather than the `closed', catalytically competent form, of the enzyme.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993011138
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  • 9
    Electronic Resource
    Electronic Resource
    High-resolution structures of single-metal-substituted concanavalin A: the Co,Ca-protein at 1.6 Å and the Ni,Ca-protein at 2.0 Å (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 749-756 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular structures of cobalt- and nickel-substituted concanavalin A have been refined at 1.6 and 2.0 Å resolution, respectively. Both metal derivatives crystallize in space group I222 with approximate cell dimensions a = 89, b = 87 and c = 63 Å and one monomer in the asymmetric unit. The final R factor for Co-substituted concanavalin A is 17.8% for 29 211 reflections with F 〉 1.0σ(F) between 8.0 and 1.6 Å. For Ni-substituted concanavalin A the final R factor is 15.9% for 16 128 reflections with F 〉 1.0σ(F) between 8.0 and 2.0 Å resolution. Both structures contain a transition-metal binding site and a calcium-binding site but, unlike Cd-substituted concanavalin A, do not have a third metal-binding site. The Co-substituted concanavalin A structure diffracts to the highest resolution of any concanavalin A structure reported to date. A comparison of the structures of Ni-, Co-, Cd-substituted and native concanavalin A gives an indication of coordinate errors, which is a useful baseline for comparisons with saccharide complexes of concanavalin A described in other work. We also give a detailed account of multiple conformations which were found for five side-chain residues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994002143
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  • 10
    Electronic Resource
    Electronic Resource
    Comparison of different X-ray data-collection systems using the crystal structure of octreotide (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 60-68 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The octapeptide octreotide crystallizes with three peptide molecules and about 20% water in the asymmetric unit, and in many ways possesses diffraction properties similar to those of a `mini-protein' consisting of 24 amino-acid residues. It diffracts to about 1.0 Å but data in the range 1.4–1.0 Å are weak. It provides a suitable test of different macromolecular X-ray data-collection techniques, especially of their ability to measure weak reflections accurately. In contrast to typical proteins it is possible to perform a full anisotropic refinement, that we believe provides a more objective test of the quality of the data than the internal consistency of equivalent reflections. We have collected a total of six data sets. The X-ray sources included synchrotron radiation, Cu Kα rotating anodes and Mo Kα sealed tubes; position-sensitive two-dimensional detectors from four manufacturers and a four-circle diffractometer with scintillation counter were employed. Two of the six data sets were collected at low temperature. Reasonable anisotropic refinement was possible with all area-detector data sets, although significant differences in the precision of the final model were observed. In addition we tested the ability of automated Patterson interpretation to solve the structure using the six independent data sets. The structure solution was only successful using the synchrotron or rotating-anode data sets, i.e. for the more intense sources. It appears that for structure solution the maximum resolution of the data is critical, whereas for refinement the accuracy of the data is more important.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994006116
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