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  • 1
    Electronic Resource
    Electronic Resource
    Expression, crystallization and preliminary characterization of methylmalonyl coenzyme A epimerase from Propionibacterium shermanii (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 706-708 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Methylmalonyl-CoA epimerase (MMCE) is an enzyme that interconverts the R and S epimers of methylmalonyl-CoA in the pathway that links propionyl-CoA with succinyl-CoA. This is used for both biosynthetic and degradative processes, including the breakdown of odd-numbered fatty acids and some amino acids. The enzyme has been expressed in Escherichia coli both as the native enzyme and as its selenomethionine (SeMet) derivative. Crystals of both forms have been obtained by vapour diffusion using monomethylether PEG 2000 as precipitant. The native MMCE crystals are orthorhombic, with unit-cell parameters a = 56.0, b = 114.0, c = 156.0 Å, and the SeMet-MMCE crystals are monoclinic, with unit-cell parameters a = 43.6, b = 78.6, c = 89.4 Å, β = 92.0°; both diffract to better than 2.8 Å resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901002050
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  • 2
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray analysis of native and recombinant human bile-salt dependent lipase: strategies for improvement of diffraction quality (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 478-480 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human bile-salt dependent lipase (BSDL), secreted into both the digestive tract and human milk, is integral to the effective absorption of dietary lipids. In attempts to obtain crystals suitable for high-resolution X-ray crystallographic studies, various forms of the enzyme have been crystallized, including native and desialidated human milk BSDL and both intact recombinant BSDL and a truncated form lacking the heavily glycosylated C-terminal repeat region. Trigonal crystals of native BSDL, with unit-cell parameters a = b = 90.0, c = 156.1 Å, were obtained using 15–20%(w/v) PEG 8000 as precipitant. These crystals diffract to 3.5 Å along the unique axis, but to only 5–7 Å in orthogonal directions. Crystals of recombinant truncated BSDL grown from 15–20%(w/v) PEG 6000 are orthorhombic, space group P212121, with unit-cell parameters a = 59.2, b = 90.0, c = 107.7 Å, and diffract to 2.6 Å resolution. These are suitable for structural analysis by X-ray crystallography.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900000986
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  • 3
    Electronic Resource
    Electronic Resource
    Subunit dissociation and reassociation leads to preferential crystallization of haemoglobin Bart's (γ4) from solutions of human embryonic haemoglobin Portland (ζ2γ2) at low pH (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 921-924 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A variety of human haemoglobins (Hbs) are produced at different stages of human development, including three embryonic Hbs, foetal Hb and adult Hb. All are heterotetramers. During crystallization experiments on human embryonic Hb Portland (ζ2γ2), it was discovered by crystallographic and biochemical analysis that the homotetramer Hb Bart's (γ4) preferentially crystallizes from ζ2γ2 solutions below pH 5. This results from dissociation of Hb Portland into γ2 dimers and ζ monomers and has interesting implications for subunit interactions and tetramer stability in Hbs. It also makes possible a full crystallographic analysis of Hb Bart's, which is of considerable medical significance because of its presence in the red blood cells of millions of people worldwide who suffer from α-thalassaemia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901004516
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  • 4
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray diffraction analysis of the Saccharomyces cerevisiae Ran-binding protein Mog1p (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 229-231 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mog1p binds the Ras-family GTPase Ran/Gsp1p, which has a central role in nucleocytoplasmic transport and cell-cycle progression. Overexpression of MOG1 is able to suppress temperature-sensitive gsp1 mutants in yeast; Δmog1 null mutants display temperature-sensitive defects in nuclear trafficking. Orthorhombic crystals of bacterially expressed Mog1p that diffract to beyond 2 Å resolution using synchrotron radiation have been obtained. The crystals have P212121 symmetry, with unit-cell parameters a = 39.67, b = 51.96, c = 112.23 Å, a Matthews coefficient of 2.44 Å3 Da−1, an estimated solvent content of 49.5% and one chain in the asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999016856
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  • 5
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray diffraction studies of mutants of B1 IgG-binding domain of protein L from Peptostreptococcus magnus (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 506-508 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The small 62-residue IgG-binding domain B1 of protein L from Peptostreptococcus magnus (Ppl-B1) has proven to be a simple system for the study of the thermodynamics and kinetics of protein folding. X-ray diffraction studies have been initiated in order to determine how the thermostability, folding and unfolding rates of a series of point mutations spanning Ppl-B1 correlate with the high-resolution structures. To this end, a tryptophan-containing variant of Ppl-B1 (herein known as wild type) and two mutants, Lys61Ala and Val49Ala, have been crystallized. Full data sets have been collected for the wild type and the Lys61Ala and Val49Ala mutants to resolutions of 1.7, 2.3 and 1.8 Å, respectively. Interestingly, all three crystallize using different precipitants and in different space groups. This may be a consequence of the relatively large effects of single-site mutations on surface-charge distribution or structural conformation, which might affect crystal contact sites.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900002195
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 206-209 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Phosphonoacetaldehyde hydrolase, a C—P bond-cleaving enzyme which utilizes an unusual bicovalent catalytic strategy, has been crystallized by the hanging-drop vapor-diffusion method using PEG 4000 as the precipitant. The crystals belong to the monoclinic system and belong to space group C2, with unit-cell parameters a = 210.5, b = 45.5, c = 64.7 Å, β = 105.0°. The asymmetric unit contains a dimer related by a non-crystallographic dyad. In addition to a 2.7 Å native data set, the following data sets have been collected: a 2.4 Å data set from crystals complexed with the intermediate analog vinyl sulfonate, a 3.0 Å three-wavelength MAD data set from crystals complexed with the product analog WO_{4}^{2-}, as well as several heavy-atom data sets to 3.0 Å or better, of which only three have proven useful for MIR calculations. Examination of the native Patterson map revealed NCS that made previously uninterpretable derivative data useful. Independent phase sets were first calculated and refined for the MAD and MIR experiments separately and were then combined. The combined phase set was further improved by solvent flattening, histogram matching and NCS averaging. Interpretation of the resulting electron-density map is currently under way.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999015899
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  • 7
    Electronic Resource
    Electronic Resource
    Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothermophilus (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 165-167 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) is a 39.5 kDa molecular weight metalloenzyme which catalyzes the oxidation of glycerol to dihydroxyacetone with the concomitant reduction of NAD+ to NADH. Despite its classification as a member of the `iron-containing' polyol dehydrogenase family, studies on recombinant B. stearothermophilus GlyDH have shown this enzyme to be Zn2+-dependent. Crystals of a S305C GlyDH mutant were obtained by the hanging-drop vapour-diffusion method, using ammonium sulfate and PEG 400 as precipitating agents, in the presence and absence of NAD+. The crystals belong to space group I422, with approximate unit-cell parameters a = b = 105, c = 149 Å and one subunit in the asymmetric unit, corresponding to a packing density of 2.6 Å3 Da−1. The crystals diffract X-rays to at least 1.8 Å resolution on a synchrotron-radiation source. Determination of the structure will provide insights into the key determinations of catalytic activity of this class of enzymes, for which no structures are currently available.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900014918
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  • 8
    Electronic Resource
    Electronic Resource
    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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  • 9
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901008642
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  • 10
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901015189
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