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  • International Union of Crystallography (IUCr)
  • American Meteorological Society
  • Annual Reviews
  • 2000-2004  (17,322)
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Publisher
Years
Year
  • 101
    Electronic Resource
    Electronic Resource
    Crystallographic phasing of myristoyl-CoA–protein N-myristoyltransferase using an iodinated analog of myristoyl-CoA (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 393-400 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Myristoyl-CoA–protein N-myristoyltransferase (Nmt; E.C. 2.1.3.97) catalyzes the covalent attachment of myristate to the N-terminal glycine amine of many eukaryotic and viral proteins. The molecular structure of the ternary complex of Saccharomyces cerevisiae Nmt1p with a bound non-hydrolyzable myristoyl-CoA analog, S-(2-oxopentadecyl)-CoA, and a competitive peptidomimetic inhibitor, SC-58272, was solved to 2.9 Å resolution by X-ray crystallography. The structure determination utilized diffraction data from an iodinated ternary complex in which a newly designed and synthesized compound, S-(13-iodo-2-oxotridecyl)-CoA, was substituted for S-(2-oxopentadecyl)-CoA. Replacing the two terminal fatty acid C atoms of myristate by iodine produced, under the same crystallization conditions, heavy-atom-derivatized crystals of defined site occupancy that were isomorphous to the native complex. This approach for obtaining experimental phase information can be extended to other crystal structures of protein–fatty acyl complexes. The synthesis of S-(13-iodo-2-oxotridecyl)-CoA and the phasing procedure are described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490100052X
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  • 102
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 320-322 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The plant phospholipase D (PLD) is considered to be a key enzyme involved in various physiological processes such as signal transduction and membrane metabolism. Crystals of the PLD protein from Vigna unguiculata have been produced from the recombinant 768 amino-acid protein. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 157.7, b = 65.6, c = 90.2 Å, β = 111.5°. There is one molecule in the asymmetric unit. Frozen crystals diffract to at least 1.94 Å resolution using synchrotron radiation. A search for heavy-atom derivatives using ytterbium and tungstate is currently under way in order to solve the three-dimensional structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900020825
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  • 103
    Electronic Resource
    Electronic Resource
    Structure of fibroblast growth factor 9 shows a symmetric dimer with unique receptor- and heparin-binding interfaces (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 378-384 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Fibroblast growth factors (FGFs) constitute a family of at least 20 structurally related heparin-binding polypeptides active in regulating cell growth, survival, differentiation and migration. FGF9, originally discovered as a glia-activating factor, shares 30% sequence identity with other FGFs and has a unique spectrum of target-cell specificity. FGF9 crystallized in the tetragonal space group I41, with unit-cell parameters a = b = 151.9, c = 117.2 Å. The structure of the glycosylated protein has been refined to an R value of 21.0% with Rfree = 24.8%) at 2.6 Å resolution. The four molecules in the asymmetric unit are arranged in two non-crystallographic dimers, with the dimer interface composed partly of residues from N- and C-terminal extensions from the FGF core structure. Most of the receptor-binding residues identified in FGF1– and FGF2–receptor complexes are buried in the dimer interface, with the β8–β9 loop stabilized in a particular conformation by an intramolecular hydrogen-bonding network. The potential heparin-binding sites are in a pattern distinct from FGF1 and FGF2. The carbohydrate moiety attached at Asn79 has no structural influence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900020813
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  • 104
    Electronic Resource
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    Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 385-392 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The isotropic crystallographic model of the structure of xylanase I from Thermoascus aurantiacus (TAXI) has now been refined anisotropically at 1.14 Å resolution to a standard residual of R = 11.1% for all data. TAXI is amongst the five largest proteins deposited in the Protein Data Bank to have been refined with anisotropic displacement parameters (ADPs) at this level of resolution. The anisotropy analysis revealed a more isotropic distribution of anisotropy than usually observed previously. Adding ADPs resulted in high-quality electron-density maps which revealed discrepancies from the previously suggested primary sequences for this enzyme. Side-chain conformational disorder was modelled for 16 residues, including Trp275, a bulky residue at the active site. An unrestrained refinement was consistent with the protonation of the catalytic acid/base glutamate and the deprotonation of the nucleophile glutamate, as required for catalysis. The thermal stability of TAXI is reinterpreted in the light of the new refined model.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900019089
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  • 105
    Electronic Resource
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    Purification, crystallization and preliminary X-ray diffraction of anthocyanidin synthase from Arabidopsis thaliana (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 425-427 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Anthocyanidin synthase (ANS) from Arabidopsis thaliana is a non-haem iron(II)-dependent dioxygenase reported to catalyse the conversion of leucoanthocyanidins to anthocyanidins. Anthocyanidins are precursors of anthocyanins, which are a major family of pigments in higher plants. ANS was crystallized by the vapour-diffusion method using polyethylene glycol as a precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 61.0, b = 73.2, c = 87.0 Å, and diffract to 2.4 Å using Cu Kα radiation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900019818
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  • 106
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    Crystallization and preliminary X-ray crystallographic analysis of RNase HIII from Bacillus subtilis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 438-440 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The genome of Bacillus subtilis contains three different genes encoding RNase H homologs: RNases HI, HII and HIII. RNase HIII from B. subtilis degrades RNA in RNA–DNA hybrids in an Mg2+-dependent manner like Escherichia coli RNase HI. However, they belong to different classes; the former belongs to the `class II' or `large' RNase H family, while the latter belongs to the `class I' or `small' RNase H family. RNase HIII of B. subtilis has been overexpressed in E. coli and crystallized at 296 K using sodium formate as a precipitant. The native X-ray diffraction data have been collected to 2.8 Å resolution using synchrotron radiation. The crystals are hexagonal, belonging to the space group P61, with unit-cell parameters a = b = 86.89, c = 214.49 Å, α = β = 90.0, γ = 120.0°. A self-rotation function calculation indicated the presence of two monomers of the recombinant RNase HIII in the crystallographic asymmetric unit, giving a VM of 3.43 Å3 Da−1 and a solvent content of 64.2%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901000440
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  • 107
    Electronic Resource
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    Purification, crystallization and preliminary X-ray diffraction analysis of the fructose-1,6-/sedoheptulose-1,7-bisphosphatase of Synechococcus PCC 7942 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 454-456 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Fructose-1,6-/sedoheptulose-1,7-bisphosphatase of Synechococcus PCC 7942, overexpressed from Escherichia coli, has been purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals were monoclinic, with unit-cell parameters a = 80.1, b = 84.2, c = 104.3 Å, β = 101.7°. They belonged to space group P21 and diffracted to at least 2.2 Å resolution. The calculated VM value, based on a tetramer in the asymmetric unit, was 2.2 Å3 Da−1.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901002177
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  • 108
    Electronic Resource
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    Preliminary X-ray diffraction studies of the transcriptional inhibitory antibody Fab41.4 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 462-464 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The binding of transcription factor ATF-1 to DNA contributes to gene expression and regulation of cell growth. Antibody Mab41.4, raised against ATF-1, and its derivatives Fab41.4 and scFv41.4 inhibit specific DNA binding in vitro and induce apoptotic death of tumor cells in vivo. Structural studies of Fab41.4 were performed to gain insight into the mechanism of action of this potentially therapeutic antibody. The optimal conditions for crystallization of Fab41.4 were determined. Crystals were needle-like in appearance, displayed C2 space-group symmetry and diffracted to a resolution of 1.6 Å. The unit-cell parameters were determined to be a = 186.64, b = 40.22, c = 55.58 Å, α = γ = 90, β = 96.93°. The data set was 97.7% complete. Molecular replacement was performed, resulting in an R value of 44.6%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901001135
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  • 109
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    Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 480-487 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The three-dimensional structure of a tryptophan-containing variant of the IgG-binding B1 domain of protein L has been solved in two crystal forms to 1.7 and 1.8 Å resolution. In one of the crystal forms, the entire N-terminal histidine-tag region was immobilized through the coordination of zinc ions and its structural conformation along with the zinc coordination scheme were determined. However, the ordering of the histidine tag by zinc does not affect the overall structure of the rest of the protein. Structural comparisons of the tryptophan-containing variant with an NMR-derived wild-type structure, which contains a tyrosine at position 47, reveals a common fold, although the overall backbone root-mean-square difference is 1.5 Å. The Y47W substitution only caused local rearrangement of several side chains, the most prominent of which is the rotation of the Tyr34 side chain, resulting in a 6 Å displacement of its hydroxyl group. A small methyl-sized cavity bounded by β-strands 1, 2 and 4 and the α-helix was found in the structures of the Y47W-substituted protein L B1 domain. This cavity may be created as the result of subsequent side-chain rearrangements caused by the Y47W substitution. These high-resolution structures of the tryptophan-containing variant provide a reference frame for the analysis of thermodynamic and kinetic data derived from a series of mutational studies of the protein L B1 domain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901000373
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  • 110
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    The structure of human mitochondrial branched-chain aminotransferase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 506-515 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: X-ray crystal structures of three forms of human mitochondrial branched-chain aminotransferase (BCAT) were solved by molecular-replacement methods, using Escherichia coli BCAT as the search model. The enzyme is a homodimer and the polypeptide chain of each monomer has two domains. The small domain is composed of residues 1–175 and the large domain is composed of residues 176–365. The active site is close to the dimer interface. The 4′-aldehyde of the PLP cofactor is covalently linked to the ε-amino group of the active-site lysine, Lys202, via a Schiff-base linkage in two of the structures. In the third structure, the enzyme is irreversibly inactivated by Tris. The overall fold of the dimer in human mitochondrial BCAT is similar to the structure of two bacterial enzymes, E. coli BCAT and D-amino acid aminotransferase (D-AAT). The residues lining the putative substrate-binding pocket of human BCAT and D-AAT are completely rearranged to allow catalysis with substrates of opposite stereochemistry. In the case of human mitochondrial branched-chain aminotransferase, a hydrogen-bond interaction between the guanidinium group of Arg143 in the first monomer with the side-chain hydroxyl of Tyr70 in the second monomer is important in the formation of the substrate-binding pocket.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901001925
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  • 111
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    Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 536-544 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Integration of the reverse-transcribed HIV cDNA into the host DNA is a required step in viral replication. The virus-encoded integrase protein catalyzes the initial DNA breaking and joining reactions that mediate cDNA integration. Here, the identification by X-ray crystallography of a small-molecule binding site on the integrase catalytic domain is reported. The small-molecule family studied consists of a core of arsenic or phosphorus surrounded by four aromatic groups. Two arsenic derivatives were visualized bound to integrase. In each case, two molecules bound at symmetry-related sites on the catalytic domain dimer interface. The first compound studied, tetraphenyl arsonium, did not inhibit integrase. However, a synthetic compound substituting a catechol for one of the phenyl rings, dihydroxyphenyltriphenylarsonium, bound to the same site and did inhibit the enzyme. Changes in the vicinity of the catalytic site were seen with the inhibitory compound only, potentially explaining its mechanism of action. Further substituting phosphonium for arsonium yielded a compound with an IC50 in the low micromolar range. These findings may be useful in designing new inhibitors of integrase, which is at present the only one of the three HIV enzymes for which clinically useful inhibitors are not available.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901001652
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  • 112
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    Conformational stabilization and crystallization of the SecA translocation ATPase from Bacillus subtilis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 559-565 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: SecA is the peripheral membrane-associated subunit of the enzyme complex `preprotein translocase' which assists the selective transport of presecretory proteins into and across bacterial membranes. The SecA protein acts as the molecular motor that drives the translocation of presecretory proteins through the membrane in a stepwise fashion concomitant with large conformational changes accompanying its own membrane insertion/retraction reaction cycle coupled to ATPase activity. The high flexibility of SecA causes a dynamic conformational heterogeneity which presents a barrier to growth of crystals of high diffraction quality. As shown by fluorescence spectroscopy, the Tm of the endothermic transition of cytosolic SecA from Bacillus subtilis is shifted to higher temperatures in the presence of 30% glycerol, indicating stabilization of the protein in its compact membrane-retracted conformational state. High glycerol concentrations are also necessary to obtain three-dimensional crystals suitable for X-ray diffraction analysis, suggesting that stabilization of the conformational dynamics of SecA may be required for effective crystallization. The SecA crystals grow as hexagonal bipyramids in the trigonal space group P3112; they possess unit-cell parameters a = 130.8, b = 130.8, c = 150.4 Å at 100 K and diffract X-rays to approximately 2.70 Å using a high-flux synchrotron-radiation source.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901001202
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  • 113
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    Crystallization of Clonorchis sinensis 26 kDa glutathione S-transferase and its fusion proteins with peptides of different lengths (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 579-581 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A Clonorchis sinensis 26 kDa glutathione S-transferase (CsGST) and its fusion proteins containing 14 and 48 amino-acid peptides at the N-terminus have been crystallized using polyethylene glycol monomethylether 550 as a precipitant. Crystals of the three proteins show very similar crystal properties: they diffract to at least 2.3 Å resolution and belong to the orthorhombic space group P212121. The unit-cell parameters of CsGST crystals were a = 66.64 (1), b = 68.91 (1), c = 123.41 (2) Å, which are very close to those of the crystals of the two fusion proteins. In addition, CsGST fusion proteins containing varying extents of N-terminal-extended peptides are incorporated into a crystal, indicating that the extended peptides have little effect on crystal packing. These results suggest that the crystallization system of CsGST/peptide fusion protein may be generally applicable to obtain crystals of small peptides.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900019314
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  • 114
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    Crystallization and preliminary X-ray studies of meso-2,3-butanediol dehydrogenase from Klebsiella pneumoniae IAM1063 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 857-859 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Meso-2,3-butanediol dehydrogenase (meso-BDH) has been crystallized and preliminary X-ray crystallographic characterization of meso-BDH crystals has been performed. Single crystals of meso-BDH were prepared in two forms by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. Form I crystals belong to space group C2, with unit-cell parameters a = 215.5, b = 79.4, c = 134.8 Å, β = 98.22°, and form II crystals belong to space group P21, with unit-cell parameters a = 69.16, b = 109.78, c = 127.28 Å, β = 102.29°. The crystals diffracted to 2.0 and 1.7 Å resolutions, respectively, using synchrotron radiation.
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    URL: http://dx.doi.org/10.1107/S0907444901004012
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  • 115
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    Crystallization and preliminary X-ray study of haem-binding protein from the bloodsucking insect Rhodnius prolixus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 860-861 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Rhodnius haem-binding protein (RHBP) from the bloodsucking insect Rhodnius prolixus, a 15 kDa protein, has been crystallized using polyethylene glycol as a precipitant. X-ray diffraction data have been collected at a synchrotron source. The crystals belong to the space group P41(3)212, with unit-cell parameters a = b = 64.98, c = 210.68 Å, and diffract beyond 2.6 Å resolution.
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    URL: http://dx.doi.org/10.1107/S0907444901004437
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  • 116
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    Crystallization and preliminary X-ray analysis of the complex of the ε-subunit and the central domain of the γ-subunit from the Escherichia coli ATP synthase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 722-724 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A complex of the ε-subunit and the central domain of the γ-subunit from the ATP synthase of Escherichia coli has been purified and crystallized and preliminary X-ray analysis has been carried out. The crystals belong to space group C2221, with unit-cell parameters a = 76.7, b = 176.1, c = 67.1 Å (at 100 K). Determination of the structure of this protein complex promises to greatly improve the understanding of energy coupling between the F0 and F1 sectors within the enzyme complex.
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    URL: http://dx.doi.org/10.1107/S0907444901003018
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  • 117
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    Human phosphoglucose isomerase: expression, purification, crystallization and preliminary crystallographic analysis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 592-595 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Phosphoglucose isomerase (PGI) is the second enzyme in the glycolytic pathway and catalyzes an aldose–ketose isomerization. Outside the cell, PGI has been found to function as both a cytokine and as a growth factor. The human pgi gene was cloned and the expressed enzyme was purified to homogeneity. Isomorphous crystals were obtained under two conditions and belong to the P212121 space group, with unit-cell parameters a = 80.37, b = 107.54, c = 270.33 Å. A 94.7% complete data set was obtained and processed to a limiting resolution of 2.6 Å. The asymmetric unit contains two hPGI dimers according to density calculations, a self-rotation function map and molecular-replacement solution.
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    URL: http://dx.doi.org/10.1107/S0907444901001238
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  • 118
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    Structural studies on the cobra venom factor: isolation, purification, crystallization and preliminary crystallographic analysis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 596-598 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cobra venom factor (CVF) is the complement-activating protein in cobra venom. It is a three-chain glycoprotein with a molecular weight of 149 000 Da. In serum, CVF forms a bimolecular enzyme with the Bb subunit of factor B. The enzyme cleaves C3 and C5, causing complement consumption in human and mammalian serum. CVF is frequently used to decomplement serum to investigate the biological functions of complement and serves as a tool to investigate the multifunctionality of C3. Furthermore, CVF bears the potential for clinical application to deplete complement in situations where complement activation is involved in the pathogenesis of disease. CVF was isolated from Indian cobra (Naja naja naja) venom. The protein was crystallized at room temperature using the sitting-drop vapour-diffusion technique. The crystals diffract to 2.7 Å resolution and belong to the tetragonal space group P41, with unit-cell parameters a = b = 62.7, c = 368.1 Å.
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    URL: http://dx.doi.org/10.1107/S0907444901001342
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  • 119
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    Crystallization and preliminary crystallographic studies of a phospholipase A2 from the venom of the Brazilian snake Bothrops moojeni (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 599-601 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A phospholipase A2 purified from the venom of the snake Bothrops moojeni has been crystallized by vapour-diffusion techniques in hanging drops at 291 K. The crystals, which were grown in the absence of Ca2+, belong to the cubic system, space group P432, with unit-cell parameters a = b = c = 91.86 Å, and contain one molecule in the asymmetric unit (VM = 2.71 Å3 Da−1). X-ray diffraction experiments provide data to 2.35 Å resolution collected on a rotating-anode home source at cryogenic temperatures. The structure has been solved via molecular-replacement techniques using a single monomer of the crystallographic structure of the phospholipase from the Western diamondback rattlesnake (Crotalus atrox) as a search model.
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    URL: http://dx.doi.org/10.1107/S0907444901001639
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  • 120
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    Preliminary crystallographic studies of EcTI, a serine proteinase inhibitor from Enterolobium contortisiliquum seeds (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 602-604 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Enterolobium contortisiliquum trypsin inhibitor (EcTI) belongs to the Kunitz family of plant inhibitors, which are widely distributed in nature, especially in plant seeds. EcTI is composed of two polypeptide chains with a total of 174 residues, homologous to other inhibitors from the same family. EcTI crystals, which were obtained with the acupuncture-gel technique, diffract to 2.0 Å resolution and belong to space group P21, with unit-cell parameters a = 37.12, b = 38.42, c = 54.08 Å, β = 98.08°. Molecular-replacement techniques using Erythrina caffra trypsin inhibitor (PDB code 1tie) as the search model indicate one monomer in the asymmetric unit. The secondary-structure content of EcTI was determined by circular dichroism spectroscopy, yielding values compatible with the expected topology.
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    Crystallization and functional analysis of a soluble deglycosylated form of the human costimulatory molecule B7-1 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 605-608 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The interactions of B7-1 with CD28 and CTLA-4 modulate the course of human immune responses, making B7-1 an important target for developing structure-based therapeutics. B7-1 is, however, one of the most heavily glycosylated proteins found at the leukocyte cell surface, complicating the structural analysis of this molecule. Methods for the production, crystallization and selenomethionine labelling of a soluble deglycosylated form of this molecule are described. The protein readily forms both tetragonal plate and bipyramidal crystals belonging to space groups I4122, with unit-cell parameters a = b = 56.9, c = 298.7 Å, and P4122 (or P4322), with unit-cell parameters a = b = 89.0, c = 261.9 Å, respectively. The I4122 and primitive crystal forms diffract to 2.7 and 3.5 Å, respectively. Surface plasmon resonance-based assays indicate that the ligand-binding properties of sB7-1 are unaffected by deglycosylation. Since none of the methods relied on any special structural properties of sB7-1, it is proposed that this novel combination of procedures could in principle be adapted to the systematic analysis of many other glycoproteins of structural or functional interest.
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    The crystals of a mannose-specific jacalin-related lectin from Morus nigra are merohedrally twinned (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 609-611 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: MornigaM, a lectin from Morus nigra, belongs to the mannose-binding subgroup of the family of jacalin-related plant lectins. It was crystallized in the P65 space group, with unit-cell parameters a = b = 110.74, c = 159.28 Å. The partially merohedrally twinned crystals could be detwinned and a subsequent molecular-replacement solution could be found using the coordinates of jacalin. Preliminary analysis clearly shows the tetrameric assembly of this protein. Furthermore, data from MornigaM crystals soaked in a mannose solution were collected.
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    Purification, crystallization and preliminary X-ray studies of thermostable alkaline phosphatase from Thermus sp. 3041 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 614-615 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Thermostable alkaline phosphatase from Thermus sp. 3041 has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group P21221, with unit-cell parameters a = 57.7, b = 69.9, c = 111.5 Å. Diffraction data were collected to 2.54 Å with a completeness of 91.1% (87.8% for the last shell), an Rmerge value of 0.105 (0.312) and an I/σ(I) value of 9.5 (3.6).
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    Crystallization and preliminary X-ray crystallographic analysis of the surE protein from Thermotoga maritima (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 612-613 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The surE protein from Thermotoga maritima is a 247-residue protein of unknown function. Its homologues are well conserved among both the eubacteria and the archaea. It has been overexpressed in soluble form in Escherichia coli. The protein has been crystallized at 296 K using 2-propanol as a precipitant. X-ray diffraction data have been collected to 1.9 Å resolution using synchrotron radiation. The crystals belong to the trigonal space group P3121 (or P3221), with unit-cell parameters a = b = 115.96, c = 78.60 Å, α = β = 90, γ = 120°. The asymmetric unit contains two monomers of the surE protein, with a corresponding VM of 2.72 Å3 Da−1 and a solvent content of 54.7%.
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    Crystallization and preliminary X-ray diffraction studies of the guanylate kinase-like domain of PSD-95 protein from rat (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 616-617 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The PSD-95 (postsynaptic density-95) protein, one of the members of the MAGUK (membrane-associated guanylate kinase) family, is composed of three PDZ domains, one SH3 domain and one guanylate kinase-like (GK) domain. The GK domain mediates the scaffolding function of PSD-95 by protein–protein interaction. Here, the GK domain was subcloned, expressed as an intein fusion protein, purified without the intein and then crystallized at room temperature by the hanging-drop vapour-diffusion method using PEG 8000 as a precipitant. The complete native data set was collected to a resolution of 2.35 Å using flash-cooling. The crystals belong to the primitive tetragonal space group P43 (or P41), with unit-cell parameters a = b = 70.03 (4), c = 37.64 (1) Å.
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    Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 619-627 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae regulates the expression of the gene on corynebacteriophages that encodes diphtheria toxin (DT). Other genes regulated by DtxR include those that encode proteins involved in siderophore-mediated iron uptake. DtxR requires activation by divalent metals and holo-DtxR is a dimeric regulator with two distinct metal-binding sites per three-domain monomer. At site 1, three side chains and a sulfate or phosphate anion are involved in metal coordination. In the DtxR–DNA complex this anion is replaced by the side chain of Glu170 provided by the third domain of the repressor. At site 2 the metal ion is coordinated exclusively by constituents of the polypeptide chain. In this paper, five crystal structures of three DtxR variants focusing on residues Glu20, Arg80 and Cys102 are reported. The resolution of these structures ranges from 2.3 to 2.8 Å. The side chain of Glu20 provided by the DNA-binding domain forms a salt bridge to Arg80, which in turn interacts with the anion. Replacing either of the salt-bridge partners with an alanine reduces repressor activity substantially and it has been inferred that the salt bridge could possibly control the wedge angle between the DNA-binding domain and the dimerization domain, thereby modulating repressor activity. Cys102 is a key residue of metal site 2 and its substitution into a serine abolishes repressor activity. The crystal structures of Zn-Glu20Ala-DtxR, Zn-Arg80Ala-DtxR, Cd-Cys102Ser-DtxR and apo-Cys102Ser-DtxR in two related space groups reveal that none of these substitutions leads to dramatic rearrangements of the DtxR fold. However, the five crystal structures presented here show significant local changes and a considerable degree of flexibility of the DNA-binding domain with respect to the dimerization domain. Furthermore, all five structures deviate significantly from the structure in the DtxR–DNA complex with respect to overall domain orientation. These results confirm the importance of the hinge motion for repressor activity. Since the third domain has often been invisible in previous crystal structures of DtxR, it is also noteworthy that the SH3-like domain could be traced in four of the five crystal structures.
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    Structure of a new polymorphic monoclinic form of human transthyretin at 3 Å resolution reveals a mixed complex between unliganded and T4-bound tetramers of TTR (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 957-967 
    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 new polymorphic form of human transthyretin (hTTR) with a lattice containing a unique assembly of apo hTTR and TTR–T4 complex has been determined to 3 Å resolution. The monoclinic form of human TTR reported here crystallizes in space group P21, with unit-cell parameters a = 76.7 (6), b = 96.7 (8), c = 81.7 (4) Å, β = 106.8 (4)°. The asymmetric unit contains two tetramers of transthyretin related by the non-crystallographic symmetry (NCS) operation of a 90.28° rotation between two hTTR molecules around an axis close to crystallographic z. The r.m.s. difference between the two tetramers calculated from their Cα positions is 0.48 Å. The structure was refined using 15.0–3.0 Å resolution data to R = 22.9% and Rfree = 28.9% for reflections F 〉 0.0σ(F), and R = 19.7% and Rfree = 25.8% for reflections F 〉 3.0σ(F). The intermolecular interactions involve the tips of α-helices and loops around Arg21, Glu61 and Ser100 of all monomers. The electron-density maps revealed residual thyroxine (T4) bound in only one of the two unique tetrameric TTR molecules, with an occupancy of 53%, while the second tetramer is unliganded. One thyroxine ligand is bound in a way similar to the orientations described for the orthorhombic form of the hTTR–T4 complex. The T4 bound in the second site is positioned similar to 3′,5′-dinitro-N-acetyl-L-thyronine in its hTTR complex. Differences in the size of the central channel defined by the D, A, G and H β-strands of two monomeric subunits are observed between the apo TTR and T4-bound tetramer. The averaged distances between Ala108 Cα and its equivalent measured across each binding site are 12.34 Å for the T4-bound and 10.96 Å for the unliganded TTR tetramer, respectively. The observed differences might reflect the mechanics of the ligand binding in the channel and possibly explain the observed negative cooperativity effect for ligand binding.
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    Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 968-976 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 Å resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven β-strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd2+ ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.
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    Crystallization and preliminary X-ray analysis of clade I catalases from Pseudomonas syringae and Listeria seeligeri (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1184-1186 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Haem-containing catalases are homotetrameric molecules that degrade hydrogen peroxide. Phylogenetically, the haem-containing catalases can be grouped into three main lines or clades. The crystal structures of seven catalases have been determined, all from clades II and III. In order to obtain a structure of an enzyme from clade I, which includes all plant, algae and some bacterial enzymes, two bacterial catalases, CatF from Pseudomonas syringae and Kat from Listeria seeligeri, have been crystallized by the hanging-drop vapour-diffusion technique, using PEG and ammonium sulfate as precipitants, respectively. Crystals of P. syringae CatF, with a plate-like morphology, belong to the monoclinic space group P21, with unit-cell parameters a = 60.6, b = 153.9, c = 109.2 Å, β = 102.8°. From these crystals a diffraction data set to 1.8 Å resolution with 98% completeness was collected using synchrotron radiation. Crystals of L. seeligeri Kat, with a well developed bipyramidal morphology, belong to space group I222 (or I212121), with unit-cell parameters a = 74.4, b = 121.3, c = 368.5 Å. These crystals diffracted beyond 2.2 Å resolution when using synchrotron radiation, but presented anisotropic diffraction, with the weakest direction perpendicular to the long c axis.
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    Crystallization and preliminary X-ray diffraction studies of recombinant Escherichia coli 4-diphosphocytidyl-2-C-methyl-D-erythritol synthetase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1189-1191 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Diphosphocytidyl-methylerythritol (DPCME) synthetase is involved in the mevalonate-independent pathway of isoprenoid biosynthesis, where it catalyses the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate and CTP. The Escherichia coli enzyme has been cloned, expressed in high yield, purified and crystallized. Elongated tetragonal prismatic crystals grown by the hanging-drop vapour-diffusion method using polyethylene glycol (PEG) 4000 as the precipitant belong to space group P41212 (or P43212), with unit-cell parameters a = b = 73.60, c = 175.56 Å. Diffraction data have been recorded to 2.4 Å resolution using synchrotron radiation.
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    The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1192-1195 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Fab fragments of a family of mouse esterolytic monoclonal antibodies MS6-12, MS6-126 and MS6-164 have been obtained by digestion of whole antibodies with papain, purified and crystallized in a range of different forms either alone or in complex with a transition-state analogue. The crystals diffract X-rays to resolutions between 2.1 and 1.2 Å and are suitable for structural studies. The determination of these structures could be important in understanding the different catalytic power of each of these related catalytic antibodies.
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    Structure of human muscle creatine kinase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1196-1200 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of human muscle creatine kinase has been determined by the molecular-replacement method and refined at 3.5 Å resolution. The structures of both the monomer and the dimer closely resemble those of the other known structures in the creatine kinase family. Two types of dimers, one with a non-crystallographic twofold symmetry axis and the other with a crystallographic twofold symmetry axis, were found to occur simultaneously in the crystal. These dimers form an infinite `double-helix'-like structure along an unusual long crystallographic 31 axis.
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    Molray – a web interface between O and the POV-Ray ray tracer (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1201-1203 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110–119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.
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    A test of macromolecular crystallization in microgravity: large well ordered insulin crystals (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1204-1207 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of insulin grown in microgravity on Space Shuttle Mission STS-95 were extremely well ordered and unusually large (many 〉2 mm). The physical characteristics of six microgravity and six earth-grown crystals were examined by X-ray analysis employing superfine φ slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined from each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had sevenfold lower mosaicity, had 54-fold higher reflection peak heights and diffracted to significantly higher resolution than their earth-grown counterparts. A single mosaic domain model could account for the observed reflection profiles in microgravity crystals, whereas data from earth crystals required a model with multiple mosaic domains. This statistically significant and unbiased characterization indicates that the microgravity environment was useful for the improvement of crystal growth and the resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.
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    The structure and domain organization of Escherichia coli isocitrate lyase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1209-1218 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Enzymes of the glyoxylate-bypass pathway are potential targets for the control of many human diseases caused by such pathogens as Mycobacteria and Leishmania. Isocitrate lyase catalyses the first committed step in this pathway and the structure of this tetrameric enzyme from Escherichia coli has been determined at 2.1 Å resolution. E. coli isocitrate lyase, like the enzyme from other prokaryotes, is located in the cytoplasm, whereas in plants, protozoa, algae and fungi this enzyme is found localized in glyoxysomes. Comparison of the structure of the prokaryotic isocitrate lyase with that from the eukaryote Aspergillus nidulans reveals a different domain structure following the deletion of approximately 100 residues from the larger eukaryotic enzyme. Despite this, the active sites of the prokaryotic and eukaryotic enzymes are very closely related, including the apparent disorder of two equivalent segments of the protein that are known to be involved in a conformational change as part of the enzyme's catalytic cycle.
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    The C1 subunit of α-crustacyanin: the de novo phasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1230-1237 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The previously unknown crystal structure of the C1 subunit of the carotenoid-binding protein α-crustacyanin has been determined using the anomalous scattering available at 1.77 Å wavelength to determine the partial structure of the S atoms intrinsic to the native protein. The resulting `heavy-atom' phases, in conjunction with near-atomic resolution (dmin = 1.15 Å) data, were then used to initiate successful structure determination using a direct-methods approach. This is, to the authors' knowledge, the first time such a small anomalous signal (∼1%) has been used to aid the determination of a macromolecular structure. As well as the structure itself, the methods used during data collection and those used in the elucidation of the sulfur `heavy-atom' partial structure are described here. As predicted, the C1 subunit adopts a tertiary structure typical of the lipocalin superfamily: an eight-stranded antiparallel β-barrel with a repeated +1 topology. The β-barrel has a calyx shape with the two molecules in the asymmetric unit interacting in such a way that the open ends of each calyx face each other, although they do not form a single elongated pocket. A comparison of this structure with those of other members of the lipocalin superfamily has allowed speculation as to the nature of carotenoid binding by the protein.
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    Crystallization and preliminary X-ray analysis of a depressant insect toxin from the scorpion Buthus martensii Karsch (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1313-1315 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Depressant insect toxins are a distinct group of scorpion neurotoxins for which no three-dimensional structures are yet available. A depressant insect toxin named BmK dITAP3 from the scorpion Buthus martensii Karsch (BmK) has been purified and crystallized. Single crystals of dITAP3 grew in the presence of the detergent CYMAL-6 using the hanging-drop vapour-diffusion method with ammonium sulfate as precipitant. A set of diffraction data to 2.6 Å resolution has been collected. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group R3, with unit-cell parameters a = b = 73.29, c = 68.90 Å, α = β = 90, γ = 120°. Assuming two molecules in the asymmetric unit, the estimated solvent content is 53.4%.
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    Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 775-783 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Haemoglobin from the bar-headed goose (Anser indicus) has higher oxygen affinity than that from its lowland relatives such as greylag goose (A. anser). The crystal structure of bar-headed goose aquomet haemoglobin was determined at 2.3 Å resolution and compared with the structures of the goose oxy, human, horse and other avian haemoglobins and the sequences of other avian haemoglobins. Four amino-acid residues differ between greylag goose and bar-headed goose haemoglobins, among which Alaα119 and Aspβ125 in bar-headed goose haemoglobin reduces the contacts between the α1 and β1 subunits compared with Pro and Glu, respectively, and therefore may increase the oxygen affinity by loosening the α1β1 interface. Compared with human oxy haemoglobin, the relative orientation of two αβ dimers in the bar-headed goose aquomet and oxy Hbs are rotated by about 4°, indicating a unique quaternary structural difference from the typical R state. This new `RH' state is probably correlated with the higher oxygen affinity of bar-headed goose haemoglobin.
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    Structure of C-phycocyanin from Spirulina platensis at 2.2 Å resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 784-792 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of C-phycocyanin from the cyanobacterium S. platensis has been determined at 2.2 Å resolution. The crystals belong to the monoclinic crystal form, which has not been previously reported for phycobiliprotein structures. The structure was solved using the molecular-replacement method with a final R value of 18.9% (Rfree = 23.7%) after model building and refinement. In the crystals used for the study, the C-phycocyanin hexamers formed by face-to-face association of two trimers are arranged in layers rather than in columns. Three different kinds of packing between adjacent hexamers in the layer were compared. The tight packing of two adjacent hexamers formed by four trimers in the asymmetric unit brings β155 PCB chromophores close together, so it is possible that lateral energy transfer takes place through the β155–β155 route.
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    Structure of the N-terminal domain of Yersinia pestis YopH at 2.0 Å resolution (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 793-799 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Yersinia pestis, the causative agent of bubonic plague, injects effector proteins into the cytosol of mammalian cells that enable the bacterium to evade the immune response of the infected organism by interfering with eukaryotic signal transduction pathways. YopH is a modular effector composed of a C-terminal protein tyrosine phosphatase (PTPase) domain and a multifunctional N-terminal domain that not only orchestrates the secretion and translocation of YopH into eukaryotic cells but also binds tyrosine-phosphorylated target proteins to mediate substrate recognition. The crystal structure of the N-terminal domain of YopH (YopHN; residues 1–130) has been determined at 2.0 Å resolution. The amino-acid sequences that target YopH for secretion from the bacterium and translocation into eukaryotic cells form integral parts of this compactly folded domain. The structure of YopHN bears no resemblance to eukaryotic phosphotyrosine-binding domains, nor is it reminiscent of any known fold. Residues that have been implicated in phosphotyrosine-dependent protein binding are clustered together on one face of YopHN, but the structure does not suggest a mechanism for protein–phosphotyrosine recognition.
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    Solving a 300 kDa multimeric protein by low-resolution MAD phasing and averaging/phase extension (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 800-805 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the conjugative coupling protein TrwBΔN70 from Escherichia coli plasmid R388 was solved using two crystal forms. This large multimeric membrane protein of 437 residues per monomer is involved in cell-to-cell single-strand DNA transfer. Diffraction data to 2.4 Å were available from trigonal crystals obtained from ammonium sulfate and to 2.5 Å from monoclinic crystals grown from tartrate. A single tantalum bromide (Ta6Br_{12}^{2+}) derivative of the trigonal form, which presented a protein hexamer with C6 local symmetry in the asymmetric unit, was used in a three-wavelength MAD experiment to achieve 4.5 Å resolution for initial phases. Sixfold averaging and phase extension increased the effective phasing resolution and eventually produced a straightforwardly traceable electron-density map. The monoclinic structure was solved by molecular replacement, i.e. a hexamer of the trigonal form was used as a search model. Two such hexamers are present in the asymmetric unit.
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    Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 806-812 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NH3-dependent NAD+ synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD+. The structural behavior of the active site, including stabilization of flexible loops 82–87 and 204–225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82–87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg2+ in the ATP-binding site may contribute to the stabilization of the major loop 204–225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg2+ position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg2+.
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    X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 829-839 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of canavalin, the vicilin-class storage protein from jack bean, was refined to 1.7 Å resolution in a highly twinned rhombohedral crystal of space group R3 and unit-cell parameters a = b = c = 83.0 Å, α = β = γ = 111.1°. The resulting R and Rfree were 0.176 and 0.245, respectively. The orthorhombic crystal structure (space group C2221, unit-cell parameters a = 136.5, b = 150.3, c = 133.4 Å) was also refined with threefold non-crystallographic symmetry restraints. R and Rfree were 0.181 and 0.226, respectively, for 2.6 Å resolution data. No significant difference in the protein structure was seen between these two crystal forms, nor between these two and the hexagonal and cubic crystal forms reported elsewhere [Ko et al. (1993), Acta Cryst. D49, 478–489; Ko et al. (1993), Plant Physiol. 101, 729–744]. A phosphate ion was identified in the lumen of the C-terminal β-barrel. Lattice interactions showed that the trimeric molecule could be well accommodated in both `top-up' and `bottom-up' orientations in a rhombohedral unit cell of the R3 crystal and explained the presence of a high twin fraction. The large inter-trimer stacking interface of the C2221 crystal may account for its relative stability. Atomic force microscopy (AFM) investigations of the growth of three crystal forms of canavalin indicate the rhombohedral form to be unique. Unlike the other two crystal forms, it contains at least an order of magnitude more screw dislocations and stacking faults than any other macromolecular crystal yet studied, and it alone grows principally by generation of steps from the screw dislocations. The unusually high occurrence of the screw dislocations and stacking faults is attributed to mechanical stress produced by the alternate molecular orientations in the rhombohedral crystals and their organization into discrete domains or blocks. At boundaries of alternate domains, lattice strain is relieved by the formation of the screw dislocations.
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    Checking nucleic acid crystal structures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 813-828 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191–205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751–759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.
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    Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 840-846 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.
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    Crystallization and preliminary crystallographic data of fructose-1,6-bisphosphatase from human muscle (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 847-849 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The enzyme human muscle fructose-1,6-bisphosphatase, which plays a critical role in gluconeogenesis, has been crystallized in the presence of 2-propanol, polyethylene glycol and magnesium chloride at pH 7.5. The space group was determined to be P42212, with unit-cell parameters a = b = 73.57, c = 146.50 Å, α = β = λ = 90° and one subunit in the asymmetric unit. A 99.6% complete data set to 2.04 Å has been collected at the National Synchrotron Light Source.
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    Purification, crystallization and preliminary X-ray analysis of the Fab fragment from MNAC13, a novel antagonistic anti-tyrosine kinase A receptor monoclonal antibody (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1307-1309 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The monoclonal antibody MNAC13 is a potent antagonist that prevents the binding of nerve-growth factor (NGF) to its tyrosine kinase A receptor (TrkA) in a variety of systems. Structural studies of the FabMNAC13 fragment were performed to gain insights into the mechanism of action of this potentially therapeutic monoclonal antibody. The optimal conditions for crystallization of FabMNAC13 were determined. Crystals appeared as prismatic bundles, displayed P212121 space-group symmetry and diffracted to a resolution of 1.8 Å. The unit-cell parameters were determined to be a = 52.73, b = 67.55, c = 111.43 Å. The data set was 99.5% complete. Molecular replacement was performed, resulting in a correlation coefficient of 0.55 and an R value of 0.40. The structure refinement is now in progress.
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    Crystallization and preliminary X-ray diffraction analysis of the 1,3-1,4-β-D-glucanase from Fibrobacter succinogenes (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1303-1306 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The truncated 1,3-1,4-β-glucanase (1,3-1,4-β-D-glucan 4-glucanohydrolase; E.C. 3.2.1.73) from Fibrobacter succinogenes was crystallized in four different forms by the vapour-diffusion method. Form A crystals have the largest trigonal P321 unit cell, diffracting to 3.0 Å resolution with four to six molecules per asymmetric unit. Form B and C crystals belong to the same monoclinic space group P21, but the form B unit cell is twice as large as the unit cell of form C. Form B crystals diffract to 2.5 Å resolution and contain four molecules per asymmetric unit. Form C crystals diffract to 2.1 Å resolution and contain two molecules per asymmetric unit. Form D crystals have the smallest orthorhombic P212121 unit cell, containing only one molecule per asymmetric unit, and diffract beyond 2.1 Å resolution. The crystallization conditions for form B and C crystals are almost identical, except that form C crystals were grown in the presence of 2 mM Ca2+ ions. It is likely that Ca2+ directly binds to the glucanase, leading to unit-cell shrinkage as observed in other Bacillus glucanase crystals. A self-rotation search identified non-crystallographic twofold axes that combine with the crystallographic twofold dyads to give 222 symmetry for both form A and form B crystals, indicating that the glucanase has a tendency to pack in 222 symmetry.
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    Rotations and rotation matrices (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1355-1359 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In molecular replacement, a model, described as a list of orthogonal coordinates, is to be moved into a new position and orientation. The orthogonal coordinate system also has to be related to the crystallographic system, which may not be orthogonal, and crystallographic symmetry must be considered, which applies to coordinates expressed as fractions of the unit cell. Elementary properties of rotation matrices and their representation as polar or Eulerian angles are discussed.
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    COMO: a program for combined molecular replacement (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1127-1134 
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    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The combined molecular-replacement protocol uses a limited six-dimensional search to solve a structure by the molecular-replacement method, with the sampling of the rotational degrees of freedom guided by the rotation function. This protocol therefore automatically combines the information on the rotational and translational parameters of the search model. The combined molecular-replacement protocol has been implemented in a new computer program, COMO. The calculation of the Patterson correlation translation function has been optimized to improve its speed performance. A packing check is implemented that automatically removes impossible solutions and thereby increases the signal in the calculation. A family of atomic models can be used as the search model; the program will automatically select the model that gives the best result. The command interface is well organized and requires the definition of only a few critical parameters by the user. In addition, a graphical user interface has been constructed for the program. The program has been used to solve several difficult molecular-replacement problems. A case is presented where the program automatically determined the orientation and position of five copies of a search model in a high-symmetry space group.
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    Pushing the boundaries of molecular replacement with maximum likelihood (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1373-1382 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular-replacement method works well with good models and simple unit cells, but often fails with more difficult problems. Experience with likelihood in other areas of crystallography suggests that it would improve performance significantly. For molecular replacement, the form of the required likelihood function depends on whether there is ambiguity in the relative phases of the contributions from symmetry-related molecules (e.g. rotation versus translation searches). Likelihood functions used in structure refinement are appropriate only for translation (or six-dimensional) searches, where the correct translation will place all of the atoms in the model approximately correctly. A new likelihood function that allows for unknown relative phases is suitable for rotation searches. It is shown that correlations between sequence identity and coordinate error can be used to calibrate parameters for model quality in the likelihood functions. Multiple models of a molecule can be combined in a statistically valid way by setting up the joint probability distribution of the true and model structure factors as a multivariate complex normal distribution, from which the conditional distribution of the true structure factor given the models can be derived. Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success.
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    Patterson correlation methods: a review of molecular replacement with CNS (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1390-1396 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: This paper presents a review of the principles of molecular replacement with the audience of the CCP4 Study Weekend in mind. A complementary presentation with animated Patterson maps is available online (http://cci.lbl.gov/r̃wgk/ccp4sw2001/). The implementation of molecular-replacement methods in the Crystallography and NMR System (CNS) is presented and discussed in some detail. The three principal components are the direct rotation function, Patterson correlation refinement and the fast translation function. CNS is available online and is free of charge for academic users.
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    Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kα wavelength (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1480-1490 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The anomalous signal of S atoms is easily detected at the Cu Kα wavelength of a non-synchrotron source with current data-collection methods. The position of sulfur and other anomalous scatterers can be located through an anomalous difference Fourier map (F+ − F−, φcalc − 90°). It has been discovered experimentally that even low-quality preliminary phases are often sufficient to find anomalous scatterers. Their anomalous signal in the native crystal can contribute to significant improvement in phase refinement. This technique has been applied to solve the crystal structures of orthorhombic lysozyme and thaumatin. Furthermore, the structure of trypsin was solved using only the diffraction data set from a native crystal collected at a single wavelength (Cu Kα) from a rotating-anode X-ray generator. The anomalous scattering of sulfur was essential to solve the structure of trypsin which was initially phased from a single intrinsic Ca2+ atom. The positions of the S atoms of lysozyme and thaumatin were found using the initial SIRAS phases and used in phase refinement. The overall figures of merit and those in each resolution shell were consistently improved. This resulted in much improved electron-density maps even when the diffraction data were limited to 2.5 Å resolution or worse. Furthermore, peaks from S atoms and other anomalous scatterers in anomalous difference Fourier maps can confirm the tracing of the peptide chain and also provide independent unbiased confirmation of molecular-replacement results. Thus, the anomalous signal of S atoms can contribute to many aspects of solving protein structures and should be used routinely.
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    Crystallization and preliminary X-ray diffraction analysis of a cold-adapted uracil-DNA glycosylase from Atlantic cod (Gadus morhua) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1706-1708 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Uracil-DNA glycosylase (UDG) is a DNA-repair enzyme involved in the removal of uracil from DNA. The Atlantic cod UDG (cUDG) possesses typical cold-adaptation features, with higher catalytic efficiency and lower thermal stability than the mammalian counterparts. cUDG has been crystallized by the vapour-diffusion method using sodium citrate as the precipitant at pH 7.5. The crystals are monoclinic and belong to space group P21, with unit-cell parameters a = 68.58, b = 67.19, c = 68.64 Å, β = 119.85°. There are two molecules in the asymmetric unit, with a corresponding VM value of 2.71 Å3 Da−1 and a solvent content of 54.7%. Synchrotron diffraction data have been collected to 1.9 Å resolution using cryogenic conditions (120 K).
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    Tobacco uroporphyrinogen-III decarboxylase: characterization, crystallization and preliminary X-ray analysis (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1709-1711 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Uroporphyrinogen-III decarboxylase from Nicotiana tabacum is a plastidial enzyme involved in the biosynthesis of chlorophyll and haem. Sedimentation equilibrium with protein producing diffracting crystals clearly indicates that the enzyme is a homodimer under similar ionic strength conditions to those found in the chloroplast stroma. Additionally, dynamic light scattering reveals an ionic strength dependence for this oligomerization state. Crystals were obtained in the hexagonal space group P622 with one molecule per asymmetric unit and diffracted to 2.3 Å resolution using synchrotron radiation.
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    Preparation and crystallization of the stimulatory and inhibitory complexes of GTP cyclohydrolase I and its feedback regulatory protein GFRP (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1153-1156 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mammalian GTP cyclohydrolase I is a decameric enzyme in the first and rate-limiting step in the biosynthesis of tetrahydrobiopterin, which is an essential cofactor for enzymes producing neurotransmitters such as catecholamines and for nitric oxide synthases. The enzyme is dually regulated by its feedback regulatory protein GFRP in the presence of its stimulatory effector phenylalanine and its inhibitory effector biopterin. Here, both the stimulatory and inhibitory complexes of rat GTP cyclohydrolase I bound to GFRP were crystallized by vapour diffusion. Diffraction data sets at resolutions of 3.0 and 2.64 Å were collected for the stimulatory and inhibitory complexes, respectively. Each complex consists of two GTPCHI pentamer rings and two GFRP pentamer rings, with pseudo-52 point-group symmetry.
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    Crystallization and preliminary X-ray analysis of catalase–peroxidase from the halophilic archaeon Haloarcula marismortui (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1157-1158 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Catalase–peroxidases are bifunctional enzymes found in many microorganisms. Crystals of catalase–peroxidase from the halophilic archaeon Haloarcula marismortui were obtained using the hanging-drop vapour-diffusion method. The rhombic plate-shaped crystals were grown from purified protein solution using (NH4)2SO4 as precipitant at 293 K. The crystal belongs to the monoclinic system, space group C2, and diffracted beyond 2.0 Å resolution.
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    Preparation and crystallization of a Bacillus subtilis arsenate reductase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1718-1721 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Arsenate reductase (AR) in B. subtilis is encoded by the chromosomal arsC gene. Together with arsB and arsR, arsC participates in detoxification processes for the arsenate and arsenite ions. Full-length arsenate reductase without any modification has been expressed in Escherichia coli and purified in a soluble form. The recombinant protein has been crystallized at 277 K using polyethyleneglycol (PEG) or poly(ethyleneglycol) methyl ether (PME) as the main precipitant. At least two forms of crystals large enough for data collection have been obtained from wild-type protein under different conditions. An orthorhombic crystal diffracted to beyond 2.2 Å with space group P212121 and unit-cell parameters a = 51.22, b = 91.62, c = 101.93 Å. A near-complete data set has been collected to 2.5 Å. The application of the flash-annealing technique was crucial for high resolution during the data collection. The SeMet-substituted AR has also been produced and crystallized under very similar conditions as the wild type, but the unit-cell parameters are very different. The crystals of the SeMet protein diffracted to higher resolution than those of the wild type.
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    Expression, purification and crystallization of Aspergillus nidulans NmrA, a negative regulatory protein involved in nitrogen-metabolite repression (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1722-1725 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NmrA repressor protein of Aspergillus nidulans was overproduced in Escherichia coli and purified to homogeneity. Gel-exclusion chromatography showed that NmrA was monomeric in solution under the buffer conditions used. The protein was crystallized in three forms, belonging to trigonal, monoclinic and hexagonal space groups. Two of these crystal forms (A and B) diffract to high resolution and thus appear suitable for structure determination. Crystal form A belongs to space group P3(1)21, with unit-cell parameters a = b = 76.8, c = 104.9 Å. Crystal form B belongs to space group C2, with unit-cell parameters a = 148.8, b = 64.3, c = 110.2 Å, β = 121.8°.
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    Crystallization and preliminary X-ray diffraction analysis of glutathione-dependent dehydroascorbate reductase from spinach chloroplasts (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1726-1728 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glutathione-dependent dehydroascorbate reductase (GSH-DHAR) catalyzes the reduction of dehydroascorbate to ascorbate using reduced glutathione as the electron donor. GSH-DHAR from spinach chloroplasts produced in Escherichia coli was crystallized by the hanging-drop vapour-diffusion method. The crystals were monoclinic, space group C2, with unit-cell parameters a = 98.25, b = 39.96, c = 106.86 Å, β = 110.46°. The asymmetric unit contained two molecules, giving a crystal volume per enzyme mass (VM) of 2.06 Å3 Da−1 and a solvent content of 40.3%. A full set of X-ray diffraction data were collected to 2.2 Å Bragg spacing from three native crystals with an overall Rmerge of 6.5% and a completeness of 93.4%.
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    Crystallization of quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni: crystals with unique optical properties (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1732-1734 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni is a functional electron-transfer protein containing both a haem c and a pyrroloquinoline quinone cofactor. The enzyme has been crystallized at 277 K using polyethylene glycol 6000 as precipitant. The crystals belong to space group C2, with unit-cell parameters a = 98.1, b = 74.3, c = 92.2 Å, β = 105.9°. A native data set with a resolution of 2.44 Å resolution has been collected. The approximate orientation of the haem group with respect to the unit-cell axes has been determined from the optical properties of the crystals.
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    Spherical plant viruses: interactions in solution, phase diagrams and crystallization of brome mosaic virus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1799-1812 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Brome mosaic virus (BMV) is a small icosahedral plant virus of mean diameter 268 Å. Interactions between BMV particles in solution were studied by means of small-angle X-ray scattering in order to find crystallization conditions. The interactions between biomacromolecules as large as these viruses have not yet been systematically studied by this method. As it is known that usually proteins crystallize in, or close to, attractive regimes, the interactions between BMV particles in solution were studied as a function of pH, type of salt and size and concentration of polyethylene glycol. An unexpected result of these studies is that the precipitates obtained upon addition of PEG alone or PEG combined with salt were in fact made of microcrystals, which were all characterized by the same series of diffraction peaks, with positions close to those of a centered cubic space group. A phase diagram of the virus as a function of PEG concentration was established by means of microbatch experiments. From the precipitation zones, conditions for crystallization were tested from 5 to 40 mg ml−1 virus with 3−10%(w/v) PEG 8000 or PEG 20 000. Small crystals were obtained in several conditions after a few days and continued growing for several weeks.
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    Conditional optimization: a new formalism for protein structure refinement (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1820-1828 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Conditional optimization allows unlabelled loose-atom refinement to be combined with extensive application of geometrical restraints. It offers an N-particle solution for the assignment of topology to loose atoms, with weighted gradients applied to all possibilities. For a simplified test structure consisting of a polyalanine four-helical bundle, this method shows a large radius of convergence using calculated diffraction data to at least 3.5 Å resolution. It is shown that with a new multiple-model protocol to estimate σA values, this structure can be successfully optimized against 2.0 Å resolution diffraction data starting from a random atom distribution. Conditional optimization has potentials for map improvement and automated model building at low or medium resolution limits. Future experiments will have to be performed to explore the possibilities of this method for ab initio phasing of real protein diffraction data.
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    A twinned monoclinic crystal form of human peroxiredoxin 5 with eight molecules in the asymmetric unit (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1829-1835 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The monoclinic crystal form of human peroxiredoxin 5 with eight molecules in the asymmetric unit was obtained under exactly the same conditions as the tetragonal form with one molecule in the asymmetric unit, except that the latter was briefly cryosoaked with halide for derivatization. A merohedral twinning was observed, which is rather unusual in the monoclinic system and only possible with particular unit-cell dimensions. After detwinning the native and a mercury derivative, the structure was solved by the SIR method with the help of the non-crystallographic symmetry. The packing of the monoclinic and tetragonal forms are compared, with special attention to the role of bromide ions in the change of space group after crystallization. The availability of nine (eight monoclinic plus one tetragonal) independent molecules allows an analysis of the mobility. The two Cys residues implicated in the peroxide-reduction mechanism are located in rigid regions but are covered by mobile loops.
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    Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-α-cellopentoside highlights the alternative binding modes targeted by substrate mimics (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1739-1742 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Many three-dimensional structures of retaining β-D-glycoside hydrolases have been determined, yet oligosaccharide complexes in which the ligand spans the catalytic centre are rare. Those that have been reported so far have revealed two modes of binding: those in which the substrate adopts a distorted skew-boat or envelope conformation in the −1 subsite, reflecting the distortion observed during the catalytic cycle, and those which bypass the true catalytic centre and thus lie in a non-productive manner across the −1 subsite. The three-dimensional structure of a retaining endocellulase, Bacillus agaradhaerens Cel5A, in complex with methyl 4,4II,4III,4IV-tetrathio-α-cellopentoside falls into this latter category. The 1.1 Å structure reveals the binding of five pyranosides, all in the 4C1 chair conformation, occupying the −3, −2, +1 and +2 subsites whilst evading the catalytic machinery located in the true −1 subsite. Such binding is in marked contrast to the structure of another retaining endocellulase, the Fusarium oxysporum Cel7B, the identical ligand in which displayed a distorted skew-boat conformation at the active centre. These two binding modes may reflect different steps in the binding and catalytic process.
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    Streptococcus pneumonia YlxR at 1.35 Å shows a putative new fold (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1747-1751 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 Å. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 Å from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer α/β sandwich with the overall shape of a cylinder and shows no structural homology to proteins of known structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the α–β plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.
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    Automated data processing on beamline FIP (BM30A) at ESRF (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1752-1753 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Automation of protein crystallography synchrotron beamlines is becoming necessary to face challenging structural genomics projects. In this context, a program has been developed that processes diffraction frames using popular software but analyzes statistics and makes choices the way crystallographers usually do. This program includes the classical peak search, indexing, integration, scaling and anomalous signal analysis. The result, comparable with that obtained by standard users, is rapidly available, providing the required information for a more efficient use of the beam time.
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    The high-mosaicity illusion: revealing the true physical characteristics of macromolecular crystals. Erratum (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1754-1754 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the paper by Bellamy et al. [Acta Cryst. (2000), D56, 986–995] there is an error in equation (2). The denominator should contain a plus sign and not a minus sign as in the published paper.
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    Crystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADP (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1870-1871 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Shikimate kinase (SK) from Mycobacterium tuberculosis (Mt) was overexpressed in Escherichia coli, purified and cocrystallized with MgADP in hanging drops using the vapor-diffusion procedure with PEG 4000 and 2-propanol as precipitants at pH 7.5. The crystal of MtSK–MgADP, which diffracted to 2.2 Å resolution, belonged to space group P3221 or P3121, with unit-cell parameters a = b = 64.01, c = 92.41 Å. There was one MtSK molecule in the asymmetric unit. Molecular-replacement trials with the crystal structure of SK from Erwinia chrysanthemi (PDB code 1shk) and adenylate kinase (PDB code 1ake) as search models were not successful. Heavy-atom derivative screening is in progress.
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    The X-ray structure of a recombinant major urinary protein at 1.75 Å resolution. A comparative study of X-ray and NMR-derived structures (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1863-1869 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Major urinary proteins belong to the lipocalin family and are present in the urine of rodents as an ensemble of isoforms with pheromonal activity. The crystal structure of a recombinant mouse MUP (rMUP) was solved by the molecular-replacement technique and refined to an R factor and Rfree of 20 and 26.5%, respectively, at 1.75 Å resolution. The structure was compared with an NMR model and with a crystallographic structure of the wild-type form of the protein. The crystal structures determined in different space groups present significantly smaller conformational differences amongst themselves than in comparison with NMR models. Some, but not all, of the conformational differences between the crystal and solution structures can be explained by the influence of crystallographic contacts. Most of the differences between the NMR and X-ray structures were found in the N-terminus and loop regions. A number of side chains lining the hydrophobic pocket of the molecule are more tightly packed in the NMR structure than in the crystallographic model. Surprisingly, clear and continuous electron density for a ligand was observed inside the hydrophobic pocket of this recombinant protein. Conformation of the ligand modelled inside the density is coherent with the results of recent NMR experiments.
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    Crystallization and preliminary X-ray diffraction analysis of two homologous antigen-binding fragments in complex with different carbohydrate antigens (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1872-1876 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The antigen-binding fragments (Fab) of two murine monoclonal antibodies (mAb) S25-2 and S45-18, specific for carbohydrate epitopes in the lipopolysacchaide of the bacterial family Chlamydiaceae, have been crystallized in the presence and absence of synthetic oligosaccharides corresponding to their respective haptens. Crystals of both Fabs show different morphology depending on the presence of antigens. The sequence of mAb S45-18 was determined and shows a remarkable homology to that reported for mAb S25-2. These crystals offer an unparalleled opportunity to compare the structure and modes of binding of two homologous antibodies to similar but distinct carbohydrate epitopes.
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    Expression and preliminary X-ray diffraction studies of cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1877-1880 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Active cytosolic (CT) Cu,Zn superoxide dismutase from Schistosoma mansoni (SmCTSOD) was recovered after thrombin cleavage of a glutathione-S-transferase linked fusion protein (GST-SmCTSOD) expressed in the presence of the active-site metals. Crystals have been obtained in two space groups, P212121 and P21. The former have unit-cell parameters a = 74.64, b = 78.24, c = 95.18 Å and typically diffract to 2.2 Å. The monoclinic crystals have unit-cell parameters a = 39.27, b = 95.08, c = 78.41 Å, β = 103.55° and diffract to at least 1.55 Å. The calculated solvent content of the crystals is compatible with two dimers of SmCTSOD in the asymmetric unit in both cases. Molecular-replacement solutions have been obtained for both crystal forms and show that slight distortions in the crystal packing relate one form to the other.
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    Crystallization and preliminary X-ray analysis of W120K mutant of streptavidin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1885-1886 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Bacterial streptavidin and chicken avidin are homotetrameric proteins that share an exceptionally high affinity towards the vitamin biotin. The biotin-binding sites in both proteins contain a crucial tryptophan residue contributed from an adjacent subunit. This particular tryptophan (W110 in avidin and W120 in streptavidin) plays an important role in both biotin binding and in the quaternary stabilities of the proteins. An intriguing naturally occurring alteration of tryptophan to lysine was previously described in the C-terminal domain of sea-urchin fibropellins, which share a relatively high sequence similarity with avidin and streptavidin. Avidin (Avm-W110K) and streptavidin (Savm-W120K) mutations show substantially reduced affinities towards biotin as well as the dissociation of their tetrameric structure into stable avidin and streptavidin dimers. Savm-W120K was crystallized at 293 K using the hanging-drop vapour-diffusion method. The crystals diffract to 1.7 Å resolution using synchrotron radiation and belong to the monoclinic space group P21, with unit-cell parameters a = 50.43, b = 100.41, c = 52.51 Å, β = 112.12°. The asymmetric unit contains four molecules of Savm-W120K, with a corresponding VM of 2.3 Å3 Da−1 and a solvent content of 46%.
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    Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Haloferax mediterranei (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1887-1889 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glucose dehydrogenase (E.C 1.1.1.47; GlcDH) from Haloferax mediterranei has been overexpressed in Escherichia coli, solubilized by the addition of 8 M urea and refolded by rapid dilution. The protein has been purified by conventional techniques and crystallized by the hanging-drop vapour-diffusion method using sodium citrate as the precipitant. Two crystal forms representing the free enzyme and the binary complex with NADP+ grow under these conditions. Crystals of form I diffract to beyond 3.5 Å resolution and belong to the hexagonal space group P622, with unit-cell parameters a = b = 89.1, c = 214.6 Å, α = β = 90, γ = 120°. Crystals of form II diffract to greater than 2.0 Å and belong to the orthorhombic space group I222 or I212121, with unit-cell parameters a = 61.8, b = 110.9, c = 151.7 Å, α = β = γ = 90°. Calculated values for VM and consideration of the packing for both crystal forms suggests that the asymmetric units in both crystal forms contain a monomer.
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    Crystallization and preliminary X-ray study of the edema factor exotoxin adenylyl cyclase domain from Bacillus anthracis in the presence of its activator, calmodulin (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1881-1884 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Edema factor from Bacillus anthracis is a 92 kDa secreted adenylyl cyclase exotoxin and is activated by the host-resident protein calmodulin. Calmodulin is a ubiquitous intracellular calcium sensor in eukaryotes and activates edema factor nearly 1000-fold upon binding. While calmodulin has many known effectors, including kinases, phosphodiesterases, motor proteins, channels and type 1 adenylyl cyclases, no structures of calmodulin in complex with a functional enzyme have been solved. The crystallization and initial experimental phasing of crystals containing a complex of edema factor adenylyl cyclase domain and calmodulin are reported here. The edema factor–calmodulin complex crystallizes in three different space groups. A native data set in the I222 space group has been collected to 2.7 Å and the self-rotation function solution suggests three edema factor–calmodulin complexes in each asymmetric unit. Initial 4 Å phases were obtained by selenomethionyl MAD in combination with two heavy-atom derivatives. These phases were successfully extended to 2.7 Å using NCS averaging.
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    Preliminary crystallographic studies of the double-stranded DNA-binding protein Sso10b from Sulfolobus solfataricus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1893-1894 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of Sso10b from the hyperthermophilic archaeon Sulfolobus solfataricus have been grown that diffract to 2.6 Å resolution. The protein is a highly abundant non-specific double-stranded DNA-binding protein, conserved throughout the archaea, that has been implicated in playing a role in the architecture of archaeal chromatin.
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    Crystallization and preliminary crystallographic data of the PAS domain of the NifL protein from Azotobacter vinelandii (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1895-1896 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Azotobacter vinelandii NifL protein is a redox-sensing flavoprotein which inhibits the activity of the nitrogen-specific transcriptional activator NifA. The N-terminal PAS domain has been overexpressed in Escherichia coli and crystallized by the hanging-drop vapour-diffusion method. The crystal belongs to the rhombohedral space group R32, with unit-cell parameters a = b = 65.0, c = 157.3 Å, and has one molecule in the asymmetric unit. Native data were collected to 3.0 Å on the BW7B synchrotron beamline at the EMBL Hamburg Outstation.
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    Crystallization and preliminary X-ray analysis of the periplasmic nitrate reductase (NapA–NapB complex) from Rhodobacter sphaeroides f. sp. denitrificans (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1900-1902 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The periplasmic nitrate reductase of Rhodobacter sphaeroides f. sp. denitrificans is a heterodimer responsible for the first step of reduction in the denitrification process by the conversion of nitrate to nitrite. It consists of a 91 kDa molybdenum-containing catalytic subunit (NapA) and a 17 kDa dihaem cytochrome c (NapB). Crystals of the NapA–NapB complex were obtained by the vapour-diffusion method using ammonium sulfate as precipitant. They belong to the P6122 space group, with unit-cell parameters a = b = 151.9, c = 255.8 Å, and contain a single complex in the asymmetric unit. A complete native data set was collected at a synchrotron source to 3.1 Å resolution.
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    Crystallization and preliminary X-ray analysis of neural haemoglobin from the nemertean worm Cerebratulus lacteus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1897-1899 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The nemertean worm Cerebratulus lacteus neural tissue haemoglobin (109 amino acids, the shortest known haemoglobin) has been overexpressed in Escherichia coli, purified and crystallized. A highly redundant native data set has been collected at the Cu Kα wavelength to 2.05 Å resolution. The crystals belong to the orthorhombic P212121 space group, with unit-cell parameters a = 42.5, b = 43.1, c = 60.2 Å and one molecule per asymmetric unit. The anomalous difference Patterson map clearly reveals the position of the haem Fe atom, thus paving the way for MAD/SAD structure determination.
    Type of Medium: Electronic Resource
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    Purification, crystallization and preliminary X-ray analysis of an acetylxylan esterase from Bacillus pumilus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1906-1907 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The gene encoding for acetylxylan esterase from Bacillus pumilus has been cloned and expressed in Escherichia coli. The recombinant protein has been purified to homogeneity and crystallized. The crystals obtained are of regular shape of dimensions 0.05 × 0.05 × 0.05 mm with R32 symmetry and diffract to 2.0 Å using synchrotron radiation.
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    Crystallization and preliminary X-ray study of two liver basic fatty acid-binding proteins (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1903-1905 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The fatty acid-binding proteins (FABPs) are a very well known protein family which includes the liver basic FABPs (Lb-FABPs), a subgroup so far characterized in several vertebrates but not in mammals. The most important difference recognized between the proteins in this subgroup and the better known mammalian liver FABPs (L-FABPs) is the stoichiometry of ligand binding: two fatty acid molecules in L-FABPs compared with one in Lb-FABPs. The only Lb-FABP with a known three-dimensional structure is that of chicken Lb-FABP, but the details of ligand binding are still unresolved as the crystals of the protein are grown at an acidic pH and the protein has been shown to lose its ligand under these conditions. The two proteins whose crystallizations are reported here are the second and third members of this subfamily to be crystallized. The crystals of axolotl Lb-FABP belong to either space group P41212 or P43212, with unit-cell parameters a = b = 65.38, c = 60.90 Å, and diffract to a resolution of 2.0 Å on a conventional source at room temperature. The crystals of toad Lb-FABP belong to either space group P4122 or P4322, with unit-cell parameters a = b = 48.14, c = 135.23 Å, and diffract to 2.5 Å resolution under the same conditions. It is expected that the solution of these two structures will help to clarify the structural differences between Lb-FABPs and L-FABPs and will possibly explain the different binding stoichiometries observed in these otherwise so similar protein subfamilies.
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    Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1908-1911 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A complex between interleukin-10 and the extracellular domain of its high-affinity receptor (sIL-10R1) has been crystallized from polyethylene glycol solutions. Crystals suitable for diffraction analysis required the modification of the NXS/T glycosylation sites on sIL-10R1 by site-directed mutagenesis and inclusion of the detergent cyclohexyl-methyl-β-D-maltopyranoside in the crystallization experiments. The crystals belong to space group P3212 or its enantimorph P3112, with unit-cell parameters a = b = 46.23, c = 307.78 Å, α = β = 90, γ = 120°, and diffract X-rays to ∼2.9 Å. The IL-10 dimer is positioned on a crystallographic twofold, resulting in one IL-10 chain and one sIL-10R1 chain in the asymmetric unit, which corresponds to a solvent content of approximately 44%.
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    Preparation and X-ray crystallographic analysis of recombinant obelin crystals diffracting to beyond 1.1 Å (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1919-1921 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of recombinant obelin, the Ca2+-regulated photoprotein from the marine hydroid Obelia longissima, have been grown from a solution containing PEG 8000 and potassium phosphate. Hexaminecobalt trichloride was used as an additive to increase the chance of crystallization. The crystals grow in a light yellow cubic form (0.5 × 0.5 × 0.45 mm) which diffracts to beyond 1.1 Å resolution. The crystals belong to the space group C2, with unit-cell parameters a = 83.43, b = 54.92, c = 52.99 Å, β = 112.00°. The asymmetric unit contains one molecule. Crystals exposed to calcium ion before and after X-ray irradiation emit light, confirming that the crystals consist of an active photoprotein.
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    Crystallization and preliminary X-ray analysis of maltose O-acetyltransferase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1915-1918 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Maltose O-acetyltransferase (Mac) is a member of the hexapeptide-repeat family of enzymes, which contains proteins with left-handed parallel β-helix architecture forming homotrimers. Diffraction data for four well diffracting crystal forms were collected. Crystal form I diffracted beyond 1.53 Å resolution but was perfectly merohedrally twinned with an apparent space group P622. Crystal forms II and III (space groups R3 and C2, respectively) could be obtained under very similar conditions by adjusting the buffer pH differently. Crystal forms II and III had several monomers in the asymmetric unit and were difficult to derivatize. However, during soaking with trimethyl lead acetate, the form III crystals dissolved and crystals with a different habit and space group grew in their place (form IV). In three of the crystal forms, a ladder of peaks was visible in the native Patterson maps along the c axis. These peaks were interpreted as corresponding to the vectors between the β-strands in the turns of the β-helix. Crystal form IV is suitable for structure determination of Mac exploiting the anomalous scattering of lead.
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    Crystallization and preliminary X-ray analysis of Citrobacter amalonaticus methylaspartate ammonia lyase (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1922-1924 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Methylaspartate ammonia lyase (MAL) catalyses the reversible α,β-elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to give mesaconic acid. Crystals of Citrobacter amalonaticus MAL have been obtained by the hanging-drop method of vapour diffusion using ammonium sulfate as the precipitant. Three crystal forms were obtained from identical crystallization conditions, two of which (forms A and B) diffract to high resolution, whilst the third form diffracted poorly. Crystals of form A diffract to beyond 2.1 Å and have been characterized as belonging to one of the enantiomorphic space groups P4122 or P4322, with unit-cell parameters a = b = 66.0, c = 233.1 Å, α = β = γ = 90° and a monomer in the asymmetric unit. Crystals of form B diffract to beyond 1.5 Å and belong to space group C222, with unit-cell parameters a = 128.3, b = 237.4, c = 65.8 Å, α = β = γ = 90° and a dimer in the asymmetric unit. Determination of the structure of MAL will be an important step in resolving current conflicts concerning the enzyme mechanism which differ between one which places MAL as a member of the superfamily of ammonia lyases whose catalytic activity requires a cofactor formed by post-translational modification of the enzyme and another which links MAL to the enolase superfamily.
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    Crystallization and preliminary crystallographic analysis of the proline dehydrogenase domain of the multifunctional PutA flavoprotein from Escherichia coli (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1925-1927 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The PutA flavoprotein from Escherichia coli is a multifunctional protein that plays pivotal roles in proline catabolism by functioning as both a membrane-associated bifunctional enzyme and a transcriptional repressor. Peripherally membrane-bound PutA catalyzes the two-step oxidation of proline to glutamate, while cytoplasmic PutA represses the transcription of its own gene and the gene for a proline-transporter protein. X-ray crystallographic studies on PutA have been initiated to determine how the PutA structural scaffold enables it to be both an enzyme and a repressor, and to understand the mechanism by which PutA switches between its enzymatic and DNA-binding functions. To facilitate crystallization, a recombinant protein (PutA669) corresponding to the N-terminal 669 amino-acid residues of the 1320 residues of PutA was engineered. Activity assays demonstrated that PutA669 catalyzes the first step of chemistry performed by PutA, the conversion of proline to Δ1-pyrroline-5-carboxylate. Crystals of PutA669 have been obtained from PEG 3000 buffered at pH 6–7. The crystals occupy an I-centered orthorhombic lattice with unit-cell parameters a = 72.5, b = 140.2, c = 146.8 Å; a 2.15 Å data set was collected using a rotating-anode source. Assuming one molecule per asymmetric unit, the Matthews coefficient VM is 2.5 Å3 Da−1, with a solvent content of 50%. The structure of PutA669 will be solved by multiple isomorphous replacement.
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    Crystallization and preliminary X-ray diffraction analysis of the 10 kDa C-terminal subdomain of 70 kDa heat-shock cognate protein (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1928-1930 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 70 kDa heat-shock cognate protein (Hsc70) is a cytosolic molecular chaperone. It is composed of a 44 kDa N-terminal nucleotide-binding domain, an 18 kDa peptide-binding subdomain and a 10 kDa C-terminal subdomain. Single crystals of recombinant 10 kDa subdomain of rat Hsc70 have been obtained using ammonium sulfate as a precipitant at room temperature. The crystals diffract beyond 3.5 Å using a synchrotron-radiation source at a wavelength of 1.0 Å. The crystals belong to the hexagonal space group P6122 or P6522, with unit-cell parameters a = b = 119.0, c = 166.4 Å.
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    Crystallization and preliminary crystallographic studies of antibacterial polypeptide LCI expressed in Escherichia coli (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1931-1932 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: LCI is a type of novel antibacterial polypeptide secreted by a Bacillus subtilis strain. It consists of 47 residues with a molecular weight of 5468 Da. Using bioengineering, LCI was expressed in Escherichia coli DH5α with recombinant plasmid pBVAB16. It was crystallized using PEG 4000 as a precipitant. The crystal belongs to space group P6222 or P6422, with unit-cell parameters a = b = 29.30, c = 187.09 Å, and diffracts to 2.44 Å. A set of diffraction data to 2.8 Å was collected.
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    Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB N-terminal domain (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1933-1935 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Escherichia coli Hsp100 ClpB plays critical roles in multi-chaperone systems in cell physiology. After the ATPase activity is stimulated by protein or peptide binding, ClpB disaggregates denatured polypeptides by employing ATP hydrolysis and allows other molecular chaperones such as Hsp70 DnaK and Hsp40 DnaJ to more efficiently refold the non-native polypeptides. The mechanisms by which the ClpB acts as a molecular chaperone to disaggregate non-native polypeptides are unknown. The N-terminal domain of ClpB has been proposed to interact with non-native polypeptides. To investigate whether the N-terminal domain participates in polypeptide recognition and binding or modulates the activity of ClpB, the ClpB N-terminal domain has been cloned, purified and crystallized. The ClpB N-terminal domain crystals diffract to 1.95 Å using a synchrotron X-ray source and belong to the space group P1, with unit-cell parameters a = 50.2, b = 52.6, c = 56.8 Å, α = 90.5, β = 111.8, γ = 107.1°. Structure determination by the multiple anomalous dispersion (MAD) method is under way.
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    Crystallization and preliminary crystallographic analysis of human alanine:glyoxylate aminotransferase and its polymorphic variants (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1936-1937 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The human hereditary disease primary hyperoxaluria type 1 is caused by a deficiency of the liver-specific peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). In this study, the crystallization and preliminary crystallographic analysis of C-terminal His-tagged human AGT expressed in Escherichia coli is reported. At least two crystal forms were obtained using similar conditions for three different polymorphic variants, namely AGT, AGT[P11L] and AGT[P11L, I340M]. Complete data have been collected for all three AGT variants. The crystals of AGT[P11L] belong to space group P41212 (or its enantiomorph), with unit-cell parameters a = b = 90.81, c = 142.62 Å, and diffract to a resolution of 2.8 Å.
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    Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1938-1944 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cry1Ac from Bacillus thuringiensis ssp. kurstaki HD-73 is a pore-forming protein specifically toxic to lepidopteran insect larvae. It binds to the cell-surface receptor aminopeptidase N in Manduca sexta midgut via the sugar N-acetyl-D-galactosamine (GalNAc). By using 1,3-diaminopropane (DAP) as the buffer throughout protoxin activation and chromatography on Q-Sepharose at pH 10.3, trypsin-activated Cry1Ac has been purified in a monomeric state, which was crucial to obtaining single crystals of Cry1Ac and of the Cry1Ac–GalNAc complex. Crystals of Cry1Ac alone are triclinic, with unit-cell parameters a = 51.78, b = 113.23, c = 123.41 Å, α = 113.11, β = 91.49, γ = 100.46°; those of the Cry1Ac–GalNAc complex show P21 symmetry, with unit-cell parameters a = 121.36, b = 51.19, c = 210.56 Å, β = 105.75°. Data sets collected to 2.36 and 2.95 Å resolution, respectively, show that both crystal forms contain four molecules of the 66 kDa toxin in the asymmetric unit and have related packing arrangements. The deaggregating effect of DAP may be explained by its capacity for bivalent hydrogen bonding and hydrophobic interactions at protein interfaces.
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    Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1945-1949 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Acyl-homoserine-L-lactones (AHLs) are diffusible chemical signals that are required for virulence of many Gram-negative bacteria. AHLs are produced by AHL synthases from two substrates, S-adenosyl-L-methionine and acyl-acyl carrier protein. The AHL synthase EsaI, which is homologous to the AHL synthases from other pathogenic bacterial species, has been crystallized in the primitive tetragonal space group P43, with unit-cell parameters a = b = 66.40, c = 47.33 Å. The structure was solved by multiple-wavelength anomalous diffraction with a novel use of the rhenium anomalous signal. The rhenium-containing structure has been refined to a resolution of 2.5 Å and the perrhenate ion binding sites and liganding residues have been identified.
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    Notes for authors (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. e3-e8 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Structure Reports Online: the birth of a new journal (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. e1-e2 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
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    1,1,1,2,2-Pentaiododiphosphanium tetraiodogallate(III) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. i1-i2 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 1,1,1,2,2-Pentaiododiphosphanium tetraiodogallate(III), (P2I5)[GaI4], crystallizes in the orthorhombic space group Pbca. The structure is isotypic with (P2I5)[AlI4]. Short I...I interatomic distances indicate weak interactions between cations and anions.
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    Bis[1,2-bis(diphenylphosphino)ethane-P,P′](dithioformato-S,S′)technetium tris(benzene) solvate (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. m1-m2 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two Tc-containing products were isolated from the reaction between CS2 and the electron-deficient complex TcCl(dppe)2. The title dithioformate complex, [Tc(S2CH)(dppe)2]·3C6H6, where dppe is 1,2-bis(diphenylphosphino)ethane (C26H24P2), exhibits Tc—P bond lengths ranging from 2.3566 (14) to 2.3884 (14) Å, which are little shorter than normally found. The other product is [TcCl(CS)(dppe)2], and is the first reported Tc–thiocarbonyl complex.
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    A new reduced molybdenum oxide with a hollandite-type structure, PrMo6O12 (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. i3-i5 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The title compound, praeseodymium hexamolybdenum dodecaoxide, PrMo6O12, crystallizes in the tetragonal space group I4/m and is isostructural with NdMo6O12. Both compounds adopt a hollandite-related structure with a tripled c axis compared to the mineral hollandite. Within the double chains of edge-sharing MoO6 octahedra, the Mo atoms form infinite chains of Mo3 triangular clusters. Another dominant feature of the structure is the ordering of the Pr3+ cations within the square-shaped channels delimited by the Mo—O double strings.
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    A linear supramolecular array of {[Mn(H2O)2(15-crown-5)]Br2}n (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. m3-m4 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Diaqua(1,4,7,10,14-pentaoxacyclopentadecane)manganese(II) dibromide, [Mn(C10H20O5)(H2O)2]Br2, prepared in a search for emissive MnII ions in unusual coordination environments, contains the metal ion encircled by the crown ether ligand, with the water molecules in trans axial positions. Hydrogen bonding between these and the Br− counter-ions forms chains of cations running approximately parallel to a.
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    Dibromo(N,N,N′,N′-tetramethylethane-1,2-diamine)zinc(II) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. m5-m6 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the title compound, [ZnBr2(C6H16N2)], which is interesting from the metal coordination point of view, was determined by direct methods on 15672 observed reflections with Mo Kα radiation. The asymmetric unit contains two molecules on general positions.
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  • 200
    Electronic Resource
    Electronic Resource
    trans-Tetraaquabis(pyridine-4-carboxylate-κN)nickel(II) (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. m7-m8 
    Details
    ISSN: 1600-5368
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The title complex, [Ni(C6H4NO2)2(H2O)4], consists of Ni atoms coordinated to two trans pyridylcarboxylate ligands, coordinated through the N atoms, and four water ligands. The Ni atom lies on a centre of symmetry. Extensive inter-complex hydrogen bonding occurs between the water ligands and the carboxylate groups, resulting in a three-dimensional network.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S1600536800018730
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