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  • International Union of Crystallography (IUCr)
  • American Meteorological Society
  • Annual Reviews
  • 2000-2004  (17,322)
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  • 1
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 229-231 
    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.
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  • 2
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 280-286 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Chymotrypsin is a member of the trypsin family of serine proteases and is one of the first proteins successfully studied by X-ray crystallography. It is secreted into the intestine as the inactive precursor chymotrypsinogen; four sequential cleavages of the peptide bonds following residues 13, 15, 146 and 148 occur to generate the active π, δ, κ and α forms of chymotrypsin. 13C NMR has shown [O'Connell & Malthouse (1995). Biochem. J. 307, 353–359] that when the δ form of chymotrypsin is inhibited by 2-13C-enriched benzyloxycarbonylglycylglycylphenylalanyl chloromethane, a tetrahedral adduct is formed which is thought to be analogous to the tetrahedral intermediate formed during catalysis. This inhibitor complex has been crystallized as a dimer in space group P41212. The structure has been refined at 2.14 Å resolution to an R value of 21.2% (free R = 25.2%). Conformational differences between δ-chymotrypsin and chymotrypsinogen in the region of the flexible autolysis loop (residues 145–150) were observed. This is the first crystal structure of δ-chymotrypsin and includes two residues which are disordered in previous crystal structures of active chymotrypsin. A difference of 11.3 Å2 between the average B values of the monomers within the asymmetric unit is caused by lattice-disordering effects approximating to rotation of the molecules about a crystallographic screw axis. The substrate-binding mode of the inhibitor was similar to other chymotrypsin peptidyl inhibitor complexes, but this is the first published chymotrypsin structure in which the tetrahedral chloromethyl ketone transition-state analogue is observed. This structure is compared with that of a similar tetrahedral transition-state analogue which does not alkylate the active-site histidine residue.
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  • 3
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 322-327 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In a previous communication [Weckert et al. (1999). Acta Cryst. D55, 1320–1328], the feasibility of the measurement of a large set of triplet phases by three-beam interference was demonstrated. This paper reports the methodology for the calculation of an electron-density map from this limited amount of experimental phase information and the map's properties with respect to model building and refinement. The tetragonal form of hen egg-white lysozyme (HEWL) was chosen as a test structure for the development of this method. The quality of the electron-density map obtained from all measured triplet phases allows a straightforward and nearly complete interpretation. The starting model was refined to a final R value of 17.4%. In a second step, the minimum number of phased reflections needed for the interpretation of an electron-density map was investigated, applying criteria based on |F| and resolution.
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 342-343 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: β-Mannosidase from Trichoderma reesei, a 105 kDa glycoprotein, has been crystallized. The crystals belong to the space group P41212 or P43212, with unit-cell dimensions a = b = 165.86, c = 122.46 Å, and diffract beyond 2.75 Å resolution. X-ray diffraction data were collected from a frozen crystal on a synchrotron X-ray source.
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  • 5
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 351-353 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pectate lyase A is secreted by Erwinia chrysanthemi and is a virulence factor for soft rot diseases in plants. Crystals of pectate lyase A were obtained by vapor-diffusion techniques in the presence of polyethylene glycol. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 48.96, b = 148.86, c = 78.61 Å, β = 97.32°. The crystals contain two protein molecules of 38 kDa per asymmetric unit and diffract to 2.4 Å using Cu Kα radiation.
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  • 6
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 359-362 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Adenylate cyclases (ACs) are involved in signal transduction by generating the second messenger, cAMP. In Trypanosoma brucei, 3′,5′-cyclic adenosine monophosphate (cAMP) controls the life cycle of this unicellular parasite. cAMP is generated by a class of adenylate cyclases which are either constitutively (GRESAG4.1–4.3) or transiently expressed (ESAG4) during the life cycle. Unlike mammalian ACs, the trypanosomal ACs have a simple topology comprising of a large extracellular region, a transmembrane helix and a cytosolic catalytic region. Two orthorhombic crystal forms of the catalytic AC domain of GRESAG4.1 (residues Ala884–Thr1132) were generated by the hanging-drop vapour-diffusion method. X-ray diffraction data from GRESAG4.1 crystals were collected at 1.9 Å resolution using synchrotron radiation. Furthermore, two heavy-metal derivative data sets were collected from crystal form A; heavy-atom sites were subsequently located in difference Patterson maps.
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  • 7
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cinnamomin (CIN) belongs to a family of 10 kDa proteins designated as elicitins. Some of these proteins induce a hypersensitive response in diverse plant species, leading to resistance against fungal and bacterial plant pathogens. CIN was crystallized by the vapour-diffusion method using either ammonium sulfate or polyethyleneglycol (PEG) as precipitants in solutions buffered at around pH 7. These crystals are isomorphous and belong to the triclinic space group, with unit-cell parameters a = 31.69, b = 36.99, c = 44.09 Å, α = 76.86, β = 84.41, γ = 80.26°. A frozen crystal diffracted X-rays beyond 1.45 Å resolution on a synchrotron-radiation source.
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  • 8
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant non-phosphorylating NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) of the hyperthermophilic crenarchaeote Thermoproteus tenax has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion technique. Crystals of different habits were obtained from several precipitant solutions (salts and polyethylene glycols). Preliminary X-ray analysis was performed with crystals grown in ammonium formate, which belonged to the primitive hexagonal space group P622, and had unit-cell parameters a = b = 184.8, c = 133.0 Å, γ = 120°. Assuming a molecular weight of 55 kDa, a Matthews parameter of 3.3 Å3 Da−1 is calculated assuming two molecules per asymmetric unit. The diffraction limit of these crystals is 2.5 Å resolution.
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  • 9
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 406-410 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Ser195Ala mutant of human α-thrombin was complexed with fibrinopeptide A(7–22) (FPA) in an effort to describe the (P1′–P6′) post-cleavage binding subsites of the fibrinogen-recognition exosite and define more clearly the nature of the Michaelis complex and the scissile peptide bond bound at the catalytic site. The thrombin mutant, however, has residual catalytic activity and proteolysis occurred at the Arg16–Gly17 bond. Thus, the structure of the thrombin complex determined was that of FPA(7–16) bound at the active site, which is very similar to the ternary FPA(7–16)cmk–human thrombin–hirugen complex (r.m.s.d. ∼ 0.4 Å; Stubbs et al., 1992). It is further shown by subsidiary experiments that the cleavage is the result of residual catalytic activity of the altered catalytic machinery.
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  • 10
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The NADP-dependent β-keto acyl-carrier protein reductase (BKR) from Brassica napus has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol of average molecular weight 1500 as the precipitant. The crystals belong to the hexagonal space group P6422, with unit-cell parameters a = b = 129.9, c = 93.1 Å, α = β = 90, γ = 120°. Calculated values for Vm, the use of rotation and translation functions and consideration of the packing suggest that the asymmetric unit contains a monomer. The crystals diffract to beyond 2.8 Å resolution and are more amenable to X-ray diffraction analysis than those reported previously for the Escherichia coli enzyme. The structure determination of B. napus BKR will provide important insights into the catalytic mechanism of the enzyme and into the evolution of the fatty-acid elongation cycle by comparisons with the other oxidoreductase of the pathway, enoyl acyl-carrier protein reductase (ENR).
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  • 11
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Liposarcus anisitsi is an armoured catfish that presents accessorial air oxygenation through a modified stomach, which allows this species to survive in waters with very low oxygen content. Analysis of its haemolysate has shown the presence of four haemoglobins; this work focuses on the main component, haemoglobin I. It has been crystallized in two different forms and X-ray diffraction data have been collected to 2.77 and 2.86 Å resolution using synchrotron radiation. Crystals were determined to belong to the space groups C2 and P21 and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit in both crystal forms. The structure was determined using a standard molecular-replacement technique.
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  • 12
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 509-511 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Periplasmic Escherichia coli L-asparaginase II with an Ser58Ala mutation in the active-site cavity has been crystallized in a new orthorhombic form (space group P21212). Crystals of this polymorph suitable for X-ray diffraction have been obtained by vapour diffusion using two sets of conditions: (i) 1% agarose gel using MPD as precipitant (pH 4.8) and (ii) liquid droplets using PEG-MME 550 (pH 9.0). The crystals grown in agarose gel are characterized by unit-cell parameters a = 226.9, b = 128.4, c = 61.9 Å and diffract to 2.3 Å resolution. The asymmetric unit contains six protein molecules arranged into one pseudo-222-symmetric homotetramer and an active-site competent dimer from which another homotetramer is generated by crystallographic symmetry.
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  • 13
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 512-515 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Shikimate dehydrogenase from Escherichia coli has been crystallized by the vapour-diffusion method using ammonium sulfate as a precipitant. Mass spectrometry confirmed the purity of the enzyme and dynamic light scattering was used to find the appropriate additives to yield a monodisperse enzyme solution. The crystals are monoclinic, space group C2, with unit-cell parameters a = 110.0, b = 139.8, c = 102.6 Å, β = 122.2° (at 100 K). Native crystals diffract to 2.3 Å in-house on a rotating-anode X-ray source. The asymmetric unit is likely to contain four molecules, related by 222 symmetry, corresponding to a packing density of 2.86 Å3 Da−1.
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  • 14
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The aromatic monooxygenase ActVA-Orf6 from Streptomyces coelicolor A3(2) that catalyses an unusual oxidation on the actinorhodin biosynthetic pathway has been crystallized. The crystals diffract to 1.73 Å and belong to space group P212121, with unit-cell parameters a = 46.95, b = 59.29, c = 71.67 Å. Solvent-content (44%) and self-rotation function calculations predict the presence of two molecules in the asymmetric unit. Structure determination should provide further insight into the enzyme mechanism and aid in the design of biosynthetic pathways to produce new polyketide natural products with novel functionality.
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  • 15
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 498-500 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Thermus flavus 5S rRNA with a molecular weight of about 40 kDa was modified at the 5′ and 3′ ends. Crystals were obtained under earth and microgravity conditions. The best crystals were obtained during NASA space mission STS 94. For the first time, it was possible to collect a complete data set from 5S rRNA crystals to 7.8 Å resolution and to assign the space group as R32, with unit-cell parameters a = b = 110.3, c = 387.6 Å, α = β = 90, γ = 120°.
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  • 16
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 506-508 
    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.
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  • 17
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 115-128 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The porphobilinogen synthase (PBGS) family of enzymes catalyzes the first common step in the biosynthesis of the essential tetrapyrroles such as chlorophyll and porphyrin. Although PBGSs are highly conserved at all four levels of protein structure, there is considerable diversity in the use of divalent cations for the catalytically essential and allosteric roles. Assumptions regarding commonalities among the PBGS proteins coupled with the diversity of usage of metal ions has led to a confused literature. The recent publication of crystal structures for three PBGS proteins coupled with more than 50 individual PBGS sequences allows an evaluation of these assumptions. This topical review focuses on the usage of metals by the PBGS family of proteins. It raises doubt concerning a dogma that there has been an evolutionary shift between ZnII and MgII at one or more of the divalent metal-binding sites. It also raises the possibility that there may be up to four specific divalent metal ion-binding sites, each serving a unique function that can be alternatively filled by amino acids in some of the PBGSs.
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  • 18
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 589-594 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The dispersion of the main-chain and side-chain conformations in the φ, ψ, χ1 space for all residues have been estimated in terms of three parameters corresponding to the entropy (S) of the distribution, the volume (DV) and the area (DA) the points are enclosed in. These parameters are inversely correlated with Chou and Fasman β-sheet propensities, Pβ (Gly and Pro excluded), suggesting that residues with greater dispersion in the conformational space are weak β-sheet formers. It was also found that different residues have different relative populations in the bridging region (intervening between the helical and β-sheet regions) which may lie on the pathway for interconversion between α and β conformations. The energy barrier for this transformation, as obtained from the population of residues in the bridging region relative to the β region, is directly correlated to Pβ. Residues with high Pβ have branched side chains, which have greater steric interactions with the main-chain atoms resulting in a shrinking of the available conformational space (first correlation) and a steeper energy gradient beyond the allowed space (second correlation) compared with linear residues. It is proposed that if residues exist in an extended conformation when the polypeptide chain is synthesized, a stretch of residues with high Pβ, because of the high energy barrier for their conversion into the α conformation, will continue to remain in the extended conformation and will ultimately constitute a β-strand in the folded structure.
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  • 19
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 618-624 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The wavelet transform is a powerful technique in signal processing and image analysis and it is shown here that wavelet analysis of low-resolution electron-density maps has the potential to increase their resolution. Like Fourier analysis, wavelet analysis expresses the image (electron density) in terms of a set of orthogonal functions. In the case of the Fourier transform, these functions are sines and cosines and each one contributes to the whole of the image. In contrast, the wavelet functions (simply called wavelets) can be quite localized and may only contribute to a small part of the image. This gives control over the amount of detail added to the map as the resolution increases. The mathematical details are outlined and an algorithm which achieves a resolution increase from 10 to 7 Å using a knowledge of the wavelet-coefficient histograms, electron-density histogram and the observed structure amplitudes is described. These histograms are calculated from the electron density of known structures, but it seems likely that the histograms can be predicted, just as electron-density histograms are at high resolution. The results show that the wavelet coefficients contain the information necessary to increase the resolution of electron-density maps.
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  • 20
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 643-644 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An archaeal Rieske iron–sulfur protein has been crystallized for the first time. The genetically constructed soluble form of the soxF protein was expressed in E. coli. It contains a correctly inserted [2Fe–2S] cluster. The authentic soxF protein is part of a terminal oxidase complex in the respiratory chain of the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius (DSM 639). The enzyme crystallizes in the space group P61 or P65, with unit-cell parameters a = b = 80.19, c = 75.69 Å. A complete data set has been collected to 1.64 Å resolution at 100 K.
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  • 21
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 581-588 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Bdellastasin is a 59-amino-acid, cysteine-rich, antistasin-type inhibitor of sperm acrosin, plasmin and trypsin, isolated from the medicinal leech Hirudo medicinalis. The complex formed between bdellastasin and porcine β-trypsin has previously been crystallized in the presence of PEG in a tetragonal crystal form of space group P43212 and has now been found to crystallize under high-salt conditions in the enantiomorphic space group P41212. These structures have been solved and refined to 2.8 and 2.7 Å resolution, respectively. Bdellastasin turns out to have an antistasin-like fold exhibiting a bis-domainal structure. In the second new crystal form, the flexible N-terminal subdomain is rotated with respect to the C-terminal subdomain by about 90°, fitting into a cavity formed by symmetry-related trypsin molecules. The canonical inhibitor–proteinase interaction is restricted to the primary binding loop comprising residues Leu31–Lys36 of bdellastasin. During the refinement, a bound sodium ion occupying the calcium-binding site of the porcine β-trypsin component was discovered. This sodium ion is coordinated in a tetragonal–pyramidal manner, with the geometry of the enclosing loop slightly changed compared with the loop in the presence of calcium. In the crystal form of space group P43212, the electron density for residue 115 of porcine β-trypsin clearly indicates the presence of a β-isomerized L-aspartic acid, which is placed in spatial proximity to segment Thr144–Gly148 of a symmetry-related trypsin molecule. This is the first structurally observed example of an L-isoaspartate in β-trypsin originating from Asn. A comparison with other known crystal structures of porcine β-trypsin–macromolecular inhibitor complexes suggests that the deamidation, isomerization and racemization of Asn115 is the key step in crystallization.
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  • 22
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of recombinant mouse L-chain apoferritin were obtained by the hanging-drop technique using ammonium sulfate as precipitant. Two crystal forms were observed in the same drop. The crystals belong to either the P2 monoclinic or to the P4212 tetragonal space group. The monoclinic crystals diffracted to beyond 2.4 Å resolution but were systematically twinned, while the tetragonal crystals diffracted to beyond 2.9 Å. These crystallization conditions in the absence of metal salts should facilitate the study of the interaction between L-chain ferritins and heavy metals, particularly the iron core.
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  • 23
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 648-649 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pk-REC is a protein which binds to DNA and catalyzes the central step of recombination and repair. The protein was crystallized using the hanging-drop vapour-diffusion method with PEG as a precipitant. Two orthorhombic crystal forms I and II with the same space group P212121 were obtained at pH 8.0 using PEG 3000 and PEG 550 monomethylether, respectively. The unit-cell parameters were a = 151, b = 174, c = 241 Å for form I and a = 151, b = 176, c = 300 Å for form II, indicating that the asymmetric unit contains more than 20 molecules.
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  • 24
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 665-666 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cucurmosin, a ribosome-inactivating protein purified from pumpkin, the sarcocarp of Cucurbita moschata, has been crystallized using polyethylene glycol as a precipitant. The crystals belong to space group P212121 and have unit-cell parameters a = 41.91, b = 59.48, c = 98.78 Å. There is one molecule in the asymmetric unit. The diffraction data to 3.0 Å resolution were collected on a MAR Research image-plate detector.
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  • 25
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 749-750 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pel-15, a high-alkaline pectate lyase (pectate transeliminase; E.C. 4.2.2.2) from Bacillus sp. strain KSM-P15, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Two different crystal forms were obtained and preliminary X-ray diffraction data were collected from each crystal form at 100 K. Both forms belong to the orthorhombic space group P212121 and contain one molecule per asymmetric unit. The unit-cell parameters of form I are a = 43.2 (2), b = 60.2 (2), c = 82.2 (2) Å and those of form II are a = 42.9 (1), b = 43.4 (1), c = 105.9 (3) Å. Diffraction data to a resolution of 1.5 Å were collected from form II crystals using a synchrotron-radiation source.
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  • 26
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 705-713 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods. Despite all crystals being merohedrally twinned, an accurate structural model with an R value of 13.4% has been obtained at atomic resolution. With six molecules in the asymmetric unit and no atom heavier than sulfur, the structure corresponds to a protein of 120 amino acids and is the largest approximately equal-atom unknown structure solved by direct methods. In the crystal, the molecule assumes a compact fold different from that found by NMR in solution. Comparison of the NCS-related molecules reveals regions of variable flexibility. The region highly homologous to the related antibiotic actagardine is very rigid and possibly defines an essential building block of this class of new antibacterial substances.
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  • 27
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    Acta crystallographica 56 (2000), S. 769-771 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: p73 is a recently discovered homologue of the tumour suppressor p53 and contains all three functional domains of p53. The α-splice variant of p73 (p73α) contains an additional structural domain near its C-terminus that has sequence homology with the sterile α-motif (SAM) domain. This domain is considered to be responsible for mediating protein–protein interactions. Pyramidal crystals of human p73α SAM domain were obtained by the hanging-drop vapour-diffusion method with ammonium dihydrogen orthophosphate as the precipitant. The crystals diffract to 2.54 Å resolution and belong to the tetragonal space group P41212, with unit-cell parameters a = b = 32.02, c = 133.84 Å. The structure was solved by molecular replacement using the NMR structure of the same protein as the search model.
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  • 28
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    Acta crystallographica 56 (2000), S. 187-188 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes has been expressed in Escherichia coli and crystallized in a form suitable for X-ray crystallographic study. Crystals were grown using a salting-in technique. Crystals have a tetragonal plate shape and belong to the C2 space group, with unit-cell parameters a = 163.9, b = 106.5, c = 93.5 Å, β = 95.5°. The crystals diffract to 2.8 Å resolution.
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  • 29
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    Acta crystallographica 56 (2000), S. 772-774 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant human grancalcin, a calcium-binding protein from leukocytes, has been crystallized in the presence or absence of Ca2+ by the vapor-diffusion method. Two crystal forms of apo grancalcin were obtained: space group P21, with unit-cell parameters a = 48.4, b = 81.1, c = 46.6 Å, β = 111.3°, diffracting to 1.9 Å, and space group C2, with unit-cell parameters a = 97.0, b = 51.9, c = 75.9 Å, β = 108.5°, diffracting to 2.4 Å. Crystals were also grown in the presence of 5 mM Ca2+. They also belong to space group C2, with unit-cell parameters a = 97.4, b = 50.3, c = 77.6 Å, β = 108.2°, which are very similar to the second apo grancalcin form. These crystals diffract to 2.5 Å.
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  • 30
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ygr203p, a 148-residue protein encoded by the ygr203w gene of Saccharomyces cerevisiae, is a homologue of the yeast Acr2 arsenate reductase encoded by the acr2 (or ypr200c) gene. It also shows significant sequence similarity to the human cell-cycle control Cdc25 phosphatase family. It has been overexpressed in soluble form in Escherichia coli with a His6 tag at its C-terminus. The recombinant protein has been crystallized at 296 K using sodium chloride as precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 40.48, b = 50.95, c = 91.95 Å. The asymmetric unit contains a monomer, giving a crystal volume per protein mass (Vm) of 2.61 Å3 Da−1 and a solvent content of 53.8%. The crystals diffract to better than 1.9 Å resolution with Cu Kα X-rays. They are therefore suitable for high-resolution structure determination.
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  • 31
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the quest to develop drugs against traveller's diarrhoea and cholera, the structure of the B pentamer of heat-labile enterotoxin (LT) complexed with a new receptor-binding antagonist, m-carboxyphenyl-α-D-galactopyranoside, has been determined. The high resolution obtained for this structure allowed anisotropic refinement of the model. It was also now possible to confirm at a near-atomic resolution the structural similarity between the B subunits of LT and the closely related cholera toxin (CT), including the similarity in deviations of planarity of the same peptide unit in LT and CT. The structure of the LT complex clearly revealed different conformations for the m-carboxyphenyl moiety of the ligand in the five B subunits of LT, while the binding modes of the well defined galactopyranoside moieties were identical. In two binding sites the m-carboxyphenyl moiety displayed no significant electron density, demonstrating significant flexibility of this moiety. In a third binding site the m-carboxyphenyl moiety could be modelled unambiguously into the density. The two remaining binding sites were involved in crystal packing contacts and the density for the ligands in these two binding sites clearly revealed different binding modes, of which one conformation was identical to and one completely different from the conformation of m-carboxyphenyl-galactopyranoside in the third subunit. The multiple binding modes observed in the crystal may represent the ensemble of conformations of m-carboxyphenyl-α-D-galactopyranoside complexed to LT in solution.
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  • 32
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    Acta crystallographica 56 (2000), S. 842-856 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The eigenvalues and eigenvectors of the least-squares normal matrix for the full-matrix refinement problem contain a great deal of information about the quality of a model; in particular the precision of the model parameters and correlations between those parameters. They also allow the isolation of those parameters or combinations of parameters which are not determined by the available data. Since a protein refinement is usually under-determined without the application of geometric restraints, such indicators of the reliability of a model offer an important contribution to structural knowledge. Eigensystem analysis is applied to the normal matrices for the refinement of a small metalloprotein using two data sets and models determined at different resolutions. The eigenvalue spectra reveal considerable information about the conditioning of the problem as the resolution varies. In the case of a restrained refinement, it also provides information about the impact of various restraints on the refinement. Initial results support conclusions drawn from the free R factor. Examination of the eigenvectors provides information about which regions of the model are poorly determined. In the case of a restrained refinement, it is also possible to isolate places where X-ray and geometric restraints are in disagreement, usually indicating a problem in the model.
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  • 33
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant amylosucrase from Neisseria polysaccharea was crystallized by the vapour-diffusion procedure in the presence of polyethylene glycol 6000. The crystals belong to the orthorhombic space group P21212, with unit-cell parameters a = 95.7, b = 117.2, c = 62.1 Å, and diffract to 1.6 Å resolution. A p-chloromercuribenzene sulfonate (pcmbs) derivative has been identified and a selenomethionine-substituted protein has been produced and crystallized.
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  • 34
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    Acta crystallographica 56 (2000), S. 206-209 
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    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.
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  • 35
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    Acta crystallographica 56 (2000), S. 210-211 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The β-carbonic anhydrase from the red alga Porphyridium purpureum was heterologously expressed, purified and crystallized. The crystals belong to space group P21 (unit-cell parameters a = 63.8, b = 113.9, c = 73.8 Å, β = 104.1°) with two subunits per asymmetric unit and diffract to 2.5 Å resolution.
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  • 36
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    Acta crystallographica 56 (2000), S. 212-214 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Dishevelled (Dsh) protein is an important component of the Wnt signal-transduction pathway. It has three relatively conserved domains: DIX, PDZ and DEP. The PDZ domain of the Xenopus laevis homolog of Dsh, which consists of residues 254–348, was overexpressed as a soluble protein in Escherichia coli, purified and crystallized. The crystals were obtained by the vapor-diffusion method, using 1.4 M sodium formate as a precipitant. The crystals diffracted to 2.3 Å resolution. The space group was determined to be P6122 or P6522, with unit-cell dimensions a = b = 95.9, c = 93.9 Å.
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  • 37
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    Acta crystallographica 56 (2000), S. 973-985 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Laue data reduction has now reached a level of sophistication that allows nearly automated processing to be performed. The software described enables complete reduction of the data with essentially no user intervention, making Laue processing almost as straightforward as monochromatic data processing. Interactive work is limited to the indexing of only one Laue pattern. More importantly, it is shown that the data quality is substantially enhanced when soft-limited predictions are used. Further improvement obtained by taking advantage of the structure-factor amplitudes from a known closely related structure is described. To determine the most suitable type of insertion device to be used for time-resolved Laue crystallography, the technique described was applied to Laue data sets collected from photoactive yellow protein under identical conditions but with three different insertion devices: a wiggler, a broad-bandpass undulator and a single-line undulator. Although the optimal choice may ultimately be dictated by sample parameters (such as mosaic spread) and by the type of experiment (repeatable or non-repeatable reactions), the results here show that the use of single-line undulators will generally yield by far the best compromise between data quality, acquisition time and radiation damage.
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  • 38
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    Acta crystallographica 56 (2000), S. 1015-1016 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Rop protein is the paradigm of a highly regular four-α-helix bundle and as such has been subject to numerous structural and mutagenesis studies. Crystals of a designed Rop variant which establishes a continuous heptad pattern through the bend region have been obtained by a combination of vapour-diffusion and seeding techniques. The crystals diffract to ultrahigh (0.8 Å) resolution using synchrotron radiation and cryogenic conditions.
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  • 39
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    Acta crystallographica 56 (2000), S. 986-995 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Typical measurements of macromolecular crystal mosaicity are dominated by the characteristics of the X-ray beam and as a result the mosaicity value given during data processing can be an artifact of the instrumentation rather than the sample. For physical characterization of crystals, an experimental system and software have been developed to simultaneously measure the diffraction resolution and mosaic spread of macromolecular crystals. The contributions of the X-ray beam to the reflection angular widths were minimized by using a highly parallel, highly monochromatic synchrotron source. Hundreds of reflection profiles over a wide resolution range were rapidly measured using a charge-coupled device (CCD) area detector in combination with superfine φ-slicing data collection. The Lorentz effect and beam contributions were evaluated and deconvoluted from the recorded data. Data collection and processing is described. From 1° of superfine φ-slice data collected on a crystal of manganese superoxide dismutase, the mosaicities of 260 reflections were measured. The average mosaicity was 0.0101° (s.d. 0.0035°) measured as the full-width at half-maximum (FWHM) and ranged from 0.0011 to 0.0188°. Each reflection profile was individually fitted with two Gaussian profiles, with the first Gaussian contributing 55% (s.d. 9%) and the second contributing 35% (s.d. 9%) of the reflection. On average, the deconvoluted width of the first Gaussian was 0.0054° (s.d. 0.0015°) and the second was 0.0061° (s.d. 0.0023°). The mosaicity of the crystal was anisotropic, with FWHM values of 0.0068, 0.0140 and 0.0046° along the a,  b and c axes, respectively. The anisotropic mosaicity analysis indicates that the crystal is most perfect in the direction that corresponds to the favored growth direction of the crystal.
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  • 40
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    Acta crystallographica 56 (2000), S. 1012-1014 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Three insect neurotoxins from the scorpion Buthus martensii Karsch, named BmK I1, BmK I4 and BmK I6, have been purified and crystallized. BmK I1 and BmK I4 show strong toxicity to insects, while BmK I6 is relatively weaker. They all exhibit an evident analgesic effect on mice; this is a novel biological function for scorpion insect toxins. Their crystals diffract to at least 3.5 (BmK I1), 2.8 (BmK I4), 2.8 (BmK I6 crystal form I) and 2.2 Å (of BmK I6 crystal form II) resolution on an ordinary X-ray source. Crystals of BmK I1 belong to space group P6, with unit-cell parameters a = b = 66.2, c = 176.7 Å. BmK I4 crystallized in the tetragonal space group I4, with unit-cell parameters a = b = 134.5, c = 60.6 Å. BmK I6 has been crystallized in two forms: form I belongs to space group C2, with unit-cell parameters a = 46.5, b = 85.2, c = 32.6 Å, β = 110.5°; form II belongs to space group R3, with the hexagonal unit-cell parameters a = b = 44.5, c = 164.7 Å.
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  • 41
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    Acta crystallographica 56 (2000), S. 1027-1029 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Feruloyl esterases cleave ferulic acid from arabinoxylan and pectin. Feruloyl groups are believed to crosslink the polysaccharide chain within the polymer and to link hemicellulose to lignin, which may play a role in controlling the growth of plants. The Clostridium thermocellum cellulosome xylanase Z feruloyl esterase was expressed in Escherichia coli, purified and crystallized. The crystals diffract to 2.4 Å resolution and belong to the orthorhombic space group P212121, with unit-cell parameters a = 43.14, b = 63.77, c = 79.57 Å. Assuming one molecule per asymmetric unit, the Matthews coefficient is calculated to be 1.87 Å3 Da−1, which corresponds to a solvent content of 34%.
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  • 42
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    Acta crystallographica 56 (2000), S. 1042-1044 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Rho-kinase binds to a small GTPase Rho in a GTP-dependent manner and regulates many cytoskeletal events in the cell. The minimum region of bovine Rho-kinase sufficient for Rho-binding was expressed as a fusion protein with glutathione S-transferase. After removal of the glutathione S-transferase, thin plate crystals were obtained. The selenomethionine-substituted protein was introduced and crystallized, as was the native protein. The crystals of the Rho-binding domain of Rho-kinase belong to the space group C2, with unit-cell parameters a = 148.0 (2), b = 26.1 (1), c = 39.6 (1) Å, β = 90.3 (1)°. The crystals diffract to a resolution beyond 1.5 Å.
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  • 43
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    Acta crystallographica 56 (2000), S. 344-347 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A DNA–multiple drug complex, d(ACGTAGCTACGT)2:[actinomycin D, (echinomycin)2] has been crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 85.6, b = 72.8, c = 56.6 Å, β = 101.5° at 93 K and Z = 8. The crystal diffracted to 3.0 Å resolution along the DNA fiber axis and to 3.5 Å resolution in other directions. The Patterson maps indicate that all complexes in the crystal are oriented along their helical axes in the [10\bar 1] direction.
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  • 44
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    Acta crystallographica 56 (2000), S. 348-350 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The conversion of glucose 6-phosphate to 1-L-myo-inositol 1-phosphate (MIP) by 1-L-myo-inositol 1-phosphate synthase (MIP synthase) is the first committed and rate-limiting step in the de novo biosynthesis of inositol in all eukaryotes. The importance of inositol-containing molecules both as membrane components and as critical second messenger signal-transduction species make the function and regulation of this enzyme important for a host of biologically important cellular functions including proliferation, neurostimulation, secretion and contraction. MIP synthase has been overexpressed in Esherichia coli and purified to homogeneity by chromatographic methods. Two crystal forms of MIP synthase were obtained by the hanging-drop vapor-diffusion method. Native data sets for both crystal forms were collected in-house on a Rigaku R-AXIS IIC imaging-plate detector. Crystal form I belongs to space group C2, with unit-cell parameters a = 153.0, b = 96.6, c = 122.6 Å, β = 126.4°, and diffracts to 2.5 Å resolution. Crystal form II belongs to space group P21, with unit-cell parameters a = 94.5, b = 186.2, c = 86.5 Å, β = 110.5°, and diffracts to 2.9 Å resolution.
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  • 45
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome bo3 ubiquinol oxidase has been successfully purified for crystallization. Single crystals of this integral membrane protein diffract X-rays to 3.5 Å resolution and belong to the orthorhombic space group C2221. From the diffraction data, the unit-cell parameters were determined to be a = 91.3, b = 370.3, c = 232.4 Å. The crystals have a solvent content of 59% and contain two molecules per asymmetric unit. A search model generated from the structures of cytochrome c oxidase from Paracoccus denitrificans and the extrinsic domain of cytochrome bo3 ubiquinol oxidase from Escherichia coli was used for molecular-replacement studies, resulting in a solution with sensible molecular packing.
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  • 46
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    Acta crystallographica 56 (2000), S. 1096-1099 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of jack bean chitinase was solved at 1.8 Å resolution by molecular replacement. It is an α-helical protein with three disulfide bridges. The active site is related in structure to animal and viral lysozymes. However, unlike in lysozyme, the architecture of the active site suggests a single-step cleavage. According to this mechanism, Glu68 is the proton donor and Glu90 assists in the reaction by moving towards the substrate and recruiting a water molecule that acts as the nucleophile. In this model, a water molecule was found in contact with Glu90 Oε1 and Thr119 Oγ at a distance of 3.0 and 2.8 Å, respectively. The model is in accordance with the observed inversion mechanism.
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  • 47
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    Acta crystallographica 56 (2000), S. 1137-1147 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 Å) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage (∼5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized α-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.
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  • 48
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    Acta crystallographica 56 (2000), S. 1173-1175 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: CYP119 is a cytochrome P450 with a molecular weight of 43 kDa which has been isolated from the thermophilic archaeon Sulfolobus solfataricus. This enzyme is extremely stable to high temperature and high pressure. The first crystallization and preliminary crystallographic study of CYP119 is reported here. Crystals of CYP119 were obtained by the sitting-drop vapour-diffusion method using a precipitant solution containing 20%(w/v) PEG 4000 and 0.2 M sodium thiocyanate at pH 6.4. Using synchrotron radiation, the CYP119 crystal diffracted to 1.84 Å resolution. It belongs to the tetragonal space group P43212, with unit-cell parameters a = b = 86.17 (0.07), c = 221.11 (0.04) Å, in which the numbers in parentheses describe the standard deviations. Assuming two molecules of the CYP119 per asymmetric unit, the calculated molar volume (Vm) is 2.38 Å3 Da−1. Bijvoet and dispersive anomalous difference Patterson maps show a clear peak corresponding to the haem irons. The complete crystallographically defined structure is currently in progress using MIR (multiple isomorphous replacement) and MAD (multiwavelength anomalous diffraction) techniques.
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  • 49
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mammalian cytosolic thioredoxin reductase is a homodimer of 55 kDa subunit containing an essential penultimate selenocysteine residue. An active analogue of the rat enzyme in which cysteine replaces selenocysteine has been expressed in Escherichia coli cells at high levels and purified to homogeneity. The pure enzyme contains one FAD per subunit and shows spectral properties identical to that of the wild-type thioredoxin reductase. The isolated enzyme in its oxidized and reduced forms or the enzyme complexed with NADP+ was crystallized by the hanging-drop vapour-diffusion method. The diffraction pattern extends to 3 Å resolution. The crystals are monoclinic, space group P21, with unit-cell parameters a = 78.9, b = 140.5, c = 170.8 Å, α = 94.6°. There are three dimeric molecules in the asymmetric unit.
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  • 50
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    Acta crystallographica 56 (2000), S. 1198-1200 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Aquaporin-1 (AQP1), a water channel from bovine red blood cells has been deglycosylated, purified to homogeneity and crystallized in a form suitable for X-ray crystallographic study. Crystals are grown using polyethylene glycol as precipitant and belong to the tetragonal space group I422, with unit-cell parameters a = b = 93.4, c = 180.4 Å. The crystals diffract beyond 2.2 Å resolution.
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    Acta crystallographica 56 (2000), S. 1205-1214 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The tools of modern direct methods are examined and their limitations for solving protein structures discussed. Direct methods need atomic resolution data (1.1–1.2 Å) for structures of around 1000 atoms if no heavy atom is present. For low-resolution data, alternative approaches are necessary and these include maximum entropy, symbolic addition, Sayre's equation, group scattering factors and electron microscopy.
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  • 52
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    Acta crystallographica 56 (2000), S. 1233-1244 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Direct phasing needs additional information of a non-specific kind in order to select the correct phase set from all possible ones. This paper analyses the use of constraints which can be formulated in terms of electron-density values. One- and multi-dimensional histograms and connectivity properties are implemented as such constraints in density-modification procedures. These approaches usually cannot unambiguously select the best solution from a set of alternative phase variants. Nevertheless, they do allow the rejection of wrong solutions and the use of cluster analysis and averaging on the remaining variants provide a good starting point for further phase-refinement procedures.
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  • 53
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    Acta crystallographica 56 (2000), S. 1253-1258 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Single-particle analysis using cryo-electron microscopy has emerged recently as a tool for elucidating the structure of biological macromolecules and their assemblies. A prerequisite for single-particle analysis is an ensemble of images of structurally identical particles in different orientations. There are a variety of techniques used for image processing of this type of object in electron microscopy. The paper gives an overview of the general philosophy of image analysis of single particles in electron microscopy. It has been shown that multivariate statistical analysis of large data sets in conjunction with angular reconstitution is capable of yielding a structural resolution approaching that of X-ray structural analysis of large macromolecules. Structure preservation during specimen preparation for electron microscopy is crucial for high-resolution studies. Nowadays, cryo-electron microscopy is a beneficial method for studying biological macromolecules in their natural environment, allowing their rapid freezing in a particular functional state. The processing of images of 50S Escherichia coli ribosomal subunits embedded in vitreous ice is used as an example of image analysis of single particles at 7.5 Å resolution.
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  • 54
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    Acta crystallographica 56 (2000), S. 1-1 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 55
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    Acta crystallographica 56 (2000), S. 595-603 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A significant improvement in the X-ray resolution of crystals of Escherichia coli inorganic pyrophosphatase at cryotemperature was obtained as a result of studying the relationship between the crystal order and cryosolution component concentrations. To perform the experiments, the ability to reverse the flash-cooling process and to return a crystal to ambient temperature was used. In each cycle, the crystal was transferred from a cold nitrogen-gas stream to a cryosolution with modified concentrations of the components. The crystal was then flash-cooled again and the diffraction quality checked. Such a technique allows the screening of a wide concentration range rather quickly without using a large number of crystals and allows the determination of optimal cryosolution component concentrations. The resolution limit for crystals of pyrophosphatase increased by almost 0.7 Å, from 1.8 to 1.15 Å.
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  • 56
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    Acta crystallographica 56 (2000), S. 625-633 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method to extend low-resolution phases has been developed using histogram matching not only of the electron density itself but also of histograms obtained from the different levels of detail provided by the wavelet transform of the electron density. It is shown that the method can extend phases from 10 Å to around 6–7 Å on a wide range of trial structures differing in size, space group and solvent content. This level of phase extension can improve the electron-density map from little more than a molecular envelope to one in which secondary structure can often be identified.
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  • 57
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    Acta crystallographica 56 (2000), S. 640-642 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The streptogramin A acetyltransferase from Enterococcus faecium (SWISS-PROT P50870) has been overexpressed in Escherichia coli, purified and crystallized. Crystallization conditions were screened using the hanging-drop vapor-diffusion method and resulted in two distinct crystal forms. Form I crystals diffract to 2.5 Å and belong to space group P212121, with unit-cell parameters a = 68.6, b = 102.6, c = 107.5 Å. Form II crystals diffract to 2.7 Å and belong to space group F222, with unit-cell parameters a = 185.8, b = 185.8, c = 186.5 Å. Rotation-function and packing analyses for both crystal forms indicate that the asymmetric unit may contain one and two copies of the trimeric enzyme for crystal forms I and II, respectively.
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  • 58
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    Acta crystallographica 56 (2000), S. 650-652 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Depending on pH, arylsulfatase A exists in solution as a dimer or as an octamer. The enzyme isolated from human placenta was crystallized at pH 5.4 in a new crystal form with space group C2, unit-cell parameters a = 154.0, b = 190.3, c = 112.5 Å, β = 122.4° and four subunits in the asymmetric unit. At pH 6.5–6.7, tetragonal crystals are obtained that are isomorphous to the known crystals of recombinant arylsulfatase A obtained at pH 5.0–5.4. The crystal structure of both forms was determined by the molecular-replacement method. The monoclinic crystals contain octamers of the same type as found in the tetragonal form.
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  • 59
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    Acta crystallographica 56 (2000), S. 656-658 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The high-potential iron–sulfur protein (HiPIP) is an electron carrier between the photosynthetic reaction centre and the cytochrome bc1 complex in the electron-transfer chain of photosynthesis. The purified HiPIP from Thermochromatium tepidum (formerly Chromatium tepidum) was crystallized in a solution of 1.4 M ammonium sulfate and 0.1 M sodium citrate pH 3.5. The crystals diffract X-rays beyond 1.4 Å resolution and belong to the orthorhombic space group P212121, with unit-cell parameters a = 47.12 (6), b = 59.59 (10), c = 23.62 (3) Å. The structure was preliminarily solved by the molecular-replacement method. The crystal structure of HiPIP from T. tepidum showed that the proteins exist as monomers, although HiPIPs from several other species can form dimers.
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  • 60
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mastoparans are tetradecapeptides found to be the major component of vespid venoms. A mastoparan toxin isolated from the venom of Anterhynchium flavomarginatum micado has been crystallized and X-ray diffraction data collected to 2.7 Å resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P6222 (P6422). This is the first mastoparan to be crystallized and will provide further insights into the conformational significance of mastoparan toxins with respect to their potency and activity in G-protein regulation.
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  • 61
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Ferredoxin-NADP+ reductase (FNR) and its physiological electron donor ferredoxin (Fd) from the cyanobacterium Anabaena PCC7119 have been co-crystallized. The unit-cell parameters are a = b = 63.72, c = 158.02 Å and the space group is P212121. The crystal structure has been solved with 2.4 Å resolution synchrotron data by molecular replacement, anomalous dispersion and Rmin search methods. For the computations, the crystal was treated as a merohedral twin. The asymmetric unit contains two FNR molecules and one ferredoxin molecule. The packing of the FNR molecules displays a nearly tetragonal symmetry (space group P43212), whereas the ferredoxin arrangement is orthorhombic. This study provides the first crystallographic model of a dissociable complex between FNR and Fd.
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  • 62
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    Acta crystallographica 56 (2000), S. 1421-1429 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An empirical function is developed to measure the protein-like character of electron-density maps. The function is based upon a systematic analysis of numerous local and global map properties or descriptors. Local descriptors measure the occurrence throughout the unit cell of unique patterns on various defined templates, while global descriptors enumerate topological characteristics that define the connectivity and complexity of electron-density isosurfaces. We examine how these quantitative descriptors vary as error is introduced into the phase sets used to generate maps. Informative descriptors are combined in an optimal fashion to arrive at a predictive function. When the topological and geometrical analysis is applied to protein maps generated from phase sets with varying amounts of error, the function is able to estimate changes in average phase error with an accuracy of better than 10°. Additionally, when used to monitor maps generated with experimental phases from different heavy-atom models, the analysis clearly distinguishes between the correct heavy-atom substructure solution and incorrect heavy-atom solutions. The function is also evaluated as a tool to monitor changes in map quality and phase error before and after density-modification procedures.
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  • 63
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the thermoactive recombinant F. pennivorans type I pullulanase, purified from the supernatant of a Bacillus subtilis culture, have been obtained by the vapour-diffusion method in the presence of the inhibitor β-cyclodextrin (2 mM) by mixing protein (15 mg ml−1) with an equal volume of crystallization solution containing 0.1 M bis–tris propane pH 6.5, 50 mM MgCl2 and 15% polyethylene glycol 3350. Crystals diffracted to 3.0 Å using conventional Cu Kα radiation and belong to space group P212121, with unit-cell parameters a = 76.8, b = 96.2, c = 98.5 Å. The asymmetric unit contains one monomer. A preliminary 26% complete data set has been collected at 2.2 Å resolution using synchrotron radiation.
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  • 64
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    Acta crystallographica 56 (2000), S. 1479-1481 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A novel human factor CIB (CCG1-interacting factor B) has been isolated using the yeast two-hybrid system. The 22 kDa CIB protein has been expressed in Escherichia coli, purified to homogeneity and crystallized in a form suitable for crystallographic studies. The protein was crystallized in the orthogonal space group P212121, with unit-cell parameters a = 43.60 (2), b = 44.45 (1), c = 110.70 (5) Å and one molecule in the asymmetric unit. The crystal diffracted beyond 2.2 Å resolution using synchrotron radiation.
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  • 65
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    Acta crystallographica 56 (2000), S. 1488-1491 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: ATP-phosphoribosyltransferase (ATP-PRT) from Escherichia coli has been purified and crystals were obtained by the vapour-diffusion method using sodium tartrate as a precipitant. Dynamic light scattering was used to assess conditions for the monodispersity of the enzyme. The crystals are trigonal, space group R32, with unit-cell parameters a = b = 133.6, c = 114.1 Å (at 100 K), and diffract to 2.7 Å on a synchrotron X-ray source. The asymmetric unit is likely to contain one molecule, corresponding to a packing density of 2.9 Å3 Da−1. A model for the quaternary structure is proposed based on the crystallographic symmetry.
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  • 66
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    Acta crystallographica 56 (2000), S. 1495-1497 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Dihydroxybutanone phosphate synthase (DS) catalyzes a commitment step in riboflavin biosynthesis where ribulose 5-phosphate is converted to dihydroxybutanone phosphate and formate. DS was cloned from the pathogenic fungus Magnaporthe grisea (using functional complementation of an Escherichia coli DS knockout mutant) and expressed in E. coli. The purified protein crystallized in space group P21212. Diffraction data extending to 1.5, 1.0 and 1.8 Å resolution were collected from crystals that were divalent cation free, soaked in Zn2+ or soaked in Mg2+, respectively.
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  • 67
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    Acta crystallographica 56 (2000), S. 1505-1507 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new Escherichia coli L-asparaginase belonging to the class of Ntn amidohydrolases has been crystallized using the vapour-diffusion method and PEG 4000 as the precipitant. The crystals belong to the orthorhombic space group P212121 (unit-cell parameters a = 50.3, b = 77.6, c = 148.2 Å) and diffract to 1.65 Å resolution. The structure has been solved by molecular replacement using aspartylglucosaminidase from Flavobacterium meningosepticum as the search model. The asymmetric unit contains four protein chains composed into a dimer of αβ heterodimers, where the subunits α and β are the product of autoproteolytic cleavage of the immature protein.
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  • 68
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    Notes: Glucose-1-phosphate thymidylyltransferase (RmlA; E.C. 2.7.7.24) is the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, the precursor of L-rhamnose, a key component of the cell wall of many pathogenic bacteria. RmlA catalyses the condensation of thymidine triphosphate (dTTP) and α-D-glucose-1-phosphate (G1P), yielding dTDP-D-glucose. RmlA from Pseudomonas aeruginosa has been overexpressed and purified. Crystals of the enzyme have been grown using the sitting-drop vapour-diffusion technique with PEG 6000 and lithium sulfate as precipitant. Several diffraction data sets of single frozen crystals were collected to a resolution of 1.66 Å. Crystals belonged to space group P1, with unit-cell parameters a = 71.5, b = 73.1, c = 134.7 Å, α = 89.9, β = 80.9, γ = 81.1°. The asymmetric unit contains eight monomers in the form of two RmlA tetramers with a solvent content of 51%. Selenomethionine-labelled protein has been obtained and crystallized.
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  • 69
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    Notes: Neutral endopeptidase (NEP) is a mammalian zinc metalloprotease involved in the inactivation of a wide variety of regulatory peptides such as enkephalins and atrial natiuretic factor. The soluble extracellular domain of NEP (sNEP) was expressed in the methylotrophic yeast Pichia pastoris. The protein was purified to homogeneity and single crystals have been obtained. Enzymatic deglycosylation of the enzyme was essential for the production of crystals suitable for X-ray analysis for both the NEP–phosphoramidon binary complex and the apo enzyme.
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  • 70
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    Notes: Oligandrin is a 10 kDa acidic protein produced by the fungus micromycete Pythium oligandrum and is a member of the α-elicitin group, with sterol- and lipid-carrier properties. Oligandrin has been crystallized at 290 K using PEG 4000 as a precipitant. A cholesterol complex was obtained under the same conditions. The space group of the crystals at low temperature (100 K) is C222, with unit-cell parameters a = 94.0, b = 171.1, c = 55.3 Å. Four molecules are present in the asymmetric unit. Data from the free and cholesterol-complexed forms were recorded at synchrotron sources to resolutions of 2.4 (uncomplexed) and 1.9 Å (complexed), respectively.
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  • 71
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    Acta crystallographica 56 (2000), S. 1569-1576 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of cadmium/cadmium and zinc/calcium concanavalin A (con A) at pH 5.0 and pH 6.15, respectively, were determined. The structure of cadmium/cadmium con A confirms that the secondary Cd2+-binding site S3 is empty at pH 5. The metal-binding sites S1 and S2 are only very slightly affected by the substitution with cadmium. On the other hand, S1 and S2 and most of the protein surface of zinc/calcium con A at pH 6.15 differ from other fully metal-bound and carbohydrate-free structures. Most of these structural differences at the protein surface are a result of the interplay between metal binding, protonation and crystal packing. This interplay is expressed by relative rotations and translations of the con A units in alternative crystal packings and participation in space-group conversions inside crystals in situ. The particular crystal packing of zinc/calcium con A creates a novel zinc-binding site S4. The Zn2+ ion in S4 ligates two aspartates from one tetramer and a histidine from a symmetry-related tetramer.
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  • 72
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    Acta crystallographica 56 (2000), S. 1591-1611 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Building a protein model from the initial three-dimensional electron-density distribution (density map) is an important task in X-ray crystallography. This problem is computationally challenging because proteins are extremely flexible. The algorithm ConfMatch is a global real-space fitting procedure in torsion-angle space. It solves this `map-interpretation' problem by matching a detailed conformation of the molecule to the density map (conformational matching). This `best-match' structure is defined as one which maximizes the sum of the density at atom positions. ConfMatch is a practical systematic algorithm based on a branch-and-bound search. The most important idea of ConfMatch is an efficient method for computing accurate bounds. ConfMatch relaxes the conformational matching problem, a problem which can only be solved in exponential time, into one which can be solved in polynomial time. The solution to the relaxed problem is a guaranteed upper bound for the conformational matching problem. In most empirical cases, these bounds are accurate enough to prune the search space dramatically, enabling ConfMatch to solve structures with more than 100 free dihedral angles. Experiments have shown that ConfMatch may be able to automate the interpretation of density maps of small proteins.
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  • 73
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    Acta crystallographica 56 (2000), S. 1625-1629 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An AMPA-specific ionotropic glutamate receptor binding domain was overexpressed using the baculovirus system and purified by immunoaffinity and metal-affinity chromatography. Purified protein was enzymatically deglycosylated. Both glycosylated and deglycosylated proteins crystallized under the same conditions and in the same space group (P2). In both cases, it was observed that the use of MPD as a cryoprotectant induced a significant reduction in the unit-cell volume compared with glycerol or sucrose. For crystals of deglycosylated protein, cryoprotection with MPD also yielded a dramatic improvement in resolution.
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    Acta crystallographica 56 (2000), S. 1638-1640 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The A4 isoform of the bark lectin RPbAI from Robinia pseudoacacia has been crystallized in two different crystal forms. Crystal form I grows in the P21 space group with two tetramers in the asymmetric unit, whereas crystal form II grows in the I222 space group with a monomer in the asymmetric unit. Data sets were collected for both crystal forms to resolution limits of 2.55 and 1.81 Å, respectively, which will allow successful structure determinations.
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    Acta crystallographica 56 (2000), S. 1647-1651 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The tcm operon in Streptomyces glaucescens encodes a group of enzymes involved in the synthesis of the polyketide tetracenomycin (Tcm) C that exhibits both antitumor and antibiotic activities. Here, the crystallization and preliminary data characterization of the tcmG gene product, Tcm A2 oxygenase, which catalyzes the triple hydroxylation of Tcm A2 to form Tcm C, are reported. Tcm A2 oxygenase crystallizes in two different space groups, both with six monomers per asymmetric unit, resulting in large unit-cell parameters. Synchrotron data have been collected from both the hexagonal and tetragonal crystal forms to 4.5 and 4.2 Å, respectively. The self-rotation function searches in both space groups suggest the monomers assemble into a complex with D3 symmetry.
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    Acta crystallographica 56 (2000), S. 1659-1661 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Earthworm fibrinolytic enzyme component A, a protein which functions both as a direct fibrinolytic enzyme and a plasminogen activator, was purified from the earthworm Eisenia fetida. Diffraction-quality single crystals of the protein were grown by the hanging-drop vapour-diffusion technique with ammonium sulfate as a precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 40.6, b = 127.5, c = 129.2 Å and three molecules per asymmetric unit. The data set reached a resolution of 1.95 Å.
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  • 77
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Endopolygalacturonase SE1 from Trichosporon penicillatum has been crystallized by the hanging-drop method of vapour diffusion using ammonium sulfate as a precipitant. The crystals belong to the hexagonal space group P61 or P65, with unit-cell parameters a = b = 135.0, c = 70.7 Å, γ = 120°. The calculated VM based on one molecule per asymmetric unit is 3.09 Å3 Da−1. A native data set from a crystal has been collected to 2.0 Å resolution on a Cu Kα rotating-anode X-ray source.
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  • 78
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    Acta crystallographica 56 (2000), S. 1670-1672 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The recombinant Fab fragment of the anti-17β-oestradiol antibody 57-2 has been a target for several protein-engineering experiments. A method for production, purification and crystallization of the Fab fragment alone (apo form) and in complex with the major female sex hormone 17β-oestradiol is reported here. Diffracting apo-form crystals were only obtained with microseeding; crystals of the Fab–steroid complex were produced by co-crystallization in the presence of oestradiol and cross-seeding with the apo-form crystals. The crystals were grown using vapour-diffusion methods with reservoir solutions containing 10–14% PEG 4000 or 8–12% PEG 8000 and Tris–HCl buffer at high pH (9.0–9.5). Both the apo and complex crystals belong to space group P212121 and diffract to 2.0 Å resolution. High-resolution X-ray data sets suitable for structure determination were collected from flash-cooled crystals using 25% glycerol as the cryoprotectant.
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  • 79
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    Notes: A recombinant form of Yersinia pestis YopM with a C-terminal polyhistidine affinity tag has been overproduced in Escherichia coli, purified to homogeneity and crystallized using the hanging-drop vapor-diffusion technique. Several different crystal forms were obtained. The most suitable crystals for X-ray diffraction belonged to space groups P4222 (unit-cell parameters a = 109.36, b = 109.36, c = 101.50 Å) and C2221 (unit-cell parameters a = 71.73, b = 121.85, c = 189.79 Å). With a synchrotron-radiation source, these crystals diffracted to 2.4 and 1.9 Å resolution, respectively.
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    Acta crystallographica 56 (2000), S. 1691-1693 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Escherichia coli sn-glycerol 3-phosphate regulon contains the glpE gene coding for a 12 kDa protein which displays a sequence and a thiosulfate:cyanide sulfurtransferase activity similar to those of rhodanese enzymes. The GlpE protein was overexpressed, purified to homogeneity and crystallized in the trigonal space group P31 (or P32). The unit-cell parameters are a = b = 53.87, c = 30.52 Å, γ = 120°. Evaluation of the crystal packing parameter establishes the presence of one molecule per asymmetric unit, with a solvent content of 42%. The GlpE crystals display very high resolution diffraction; a 1.06 Å data set was collected using synchrotron radiation (λ = 0.9102 Å) with an overall completeness of 99.6%.
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  • 81
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    Acta crystallographica 56 (2000), S. 1699-1701 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cytochrome c2 from Rhodopseudomonas palustris has been crystallized in two different crystal forms: a monoclinic form I at pH 4.4 from both reduced and oxidized protein solution and a trigonal form II at pH 9.0 from reduced protein solution. Complete 1.7 and 1.4 Å resolution data sets were collected from the oxidized form I and from the form II, respectively. The preliminary structures show an important change in the iron coordination environment in the trigonal form obtained at basic pH arising from the substitution of the Met ligand by an ammonia molecule.
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  • 82
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    Acta crystallographica 57 (2001), S. 8-19 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 Å resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 Å resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1–S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's β-protein precursor, with some differences in the S1 site.
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  • 83
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    Acta crystallographica 57 (2001), S. 37-43 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of affinity-purified Thermomonospora fusca β-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.7% of the mannanase gene sequence was obtained from genomic T. fusca DNA by PCR. The structure-derived sequence was then compared with the DNA-derived sequence and corrected when necessary. Applying the presented protocol, there was no need to manually build a model at an early stage of structure determination, an erroneous and tedious process, especially in the absence of the amino-acid sequence. Using the DNA sequence information and the current version of ARP/wARP, 281 residues, or 93% of the polypeptide chain (including side chains), were built and refined to an R factor of 16.5% without any manual intervention.
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  • 84
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The dynamic response of tetragonal lysozyme crystals to dehydration has been characterized in situ using a combination of X-ray topography, high-resolution diffraction line-shape measurements and conventional crystallographic diffraction. For dehydration from 98% relative humidity (r.h.) to above 89%, mosaicity and diffraction resolution show little change and X-ray topographs remain featureless. Lattice constants decrease rapidly but the lattice-constant distribution within the crystal remains very narrow, indicating that water concentration gradients remain very small. Near 88% r.h., the c-axis lattice parameter decreases abruptly, the steady-state mosaicity and diffraction resolution degrade sharply and topographs develop extensive contrast. This transformation exhibits metastability and hysteresis. At fixed r.h. 〈 88% it is irreversible, but the original order can be almost completely restored by rehydration. These results suggest that this transformation is a first-order structural transition involving an abrupt loss of crystal water. The front between transformed and untransformed regions may propagate inward from the crystal surface and the resulting stresses along the front may degrade mosaicity. Differences in crystal size, shape and initial perfection may produce the observed variations in degradation timescale. Consequently, the success of more general post-growth treatments may often involve identifying procedures that either avoid lattice transitions, minimize disorder created during such transitions or maintain the lattice in an ordered metastable state.
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  • 85
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    Acta crystallographica 57 (2001), S. 95-100 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The low-density elimination method, which was developed for phase extension and refinement, has been investigated regarding its power to solve crystal structures starting from completely random phase sets. The method employs a multi-solution strategy. Low-symmetry structures are easily solvable where phase restrictions are only applied to a few reflections. Even with high-symmetry structures, a reasonable solution was obtained regarding centric reflections as general reflections. It is also shown that the structure of a small protein ribonuclease Ap1 is solvable if the positions of the five S atoms in the protein are known.
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  • 86
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    Acta crystallographica 56 (2000), S. 1156-1165 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A protein sequence can be classified into one of four structural classes, namely α, β, α + β and α/β, based on its amino-acid composition. The present study aims at understanding why a particular sequence with a given amino-acid composition should fold into a specific structural class. In order to answer this question, each amino acid in the protein sequence was classified to a particular neighbor density based on the number of spatial residues surrounding it within a distance of 6.5 Å. Each of the four structural classes showed a unique preference of amino acids in each of the neighbor densities. Residues which show a high compositional bias in a structural class are also found to occur in high neighbor densities. This high compositional bias towards specific residues in the four different structural classes of proteins appears to be caused by structural and functional requirements. The distribution of amino acids in different neighbor densities is graphically presented in a novel logo form which incorporates several features such as composition, the frequency of occurrence and color code for amino acids. The spatial neighbors of the residues in different neighbor densities and their secondary structural location are also represented in the form of logos. This representation helped in the identification of specific details of the whole data which may otherwise have gone unnoticed. It is suggested that the data presented in this study may be useful in knowledge-based structure modelling and de novo protein design.
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  • 87
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    Acta crystallographica 56 (2000), S. 1176-1179 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Carbonic anhydrases are zinc metalloenzymes that fall into three distinct evolutionary and structural classes, α, β and γ. Although α-class enzymes, particularly mammalian carbonic anhydrase II, have been the subject of extensive structural studies, for the β class, consisting of a wide variety of prokaryotic and plant chloroplast carbonic anhydrases, the structural data is quite limited. A member of the β class from E. coli (CynT2) has been crystallized in native and selenomethionine-labelled forms and multiwavelength anomalous dispersion techniques have been applied in order to determine the positions of anomalous scatterers. The resulting phase information is sufficient to produce an interpretable electron-density map. A crystal structure for CynT2 would contribute significantly to the emerging structural knowledge of a biologically important class of enzymes that perform critical functions in carbon fixation and prokaryotic metabolism.
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  • 88
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The head–tail connector of bacteriophage φ29, an oligomer of gene product 10 (gp10), was crystallized into various forms. The most useful of these were an orthorhombic P22121 form (unit-cell parameters a = 143.0, b = 157.0, c = 245.2 Å), a monoclinic C2 form (a = 160.7, b = 143.6, c = 221.0 Å, β = 97.8°) and another monoclinic C2 form (a = 177.0, b = 169.1, c = 185.2 Å, β = 114.1°). Frozen crystals diffracted to about 3.2 Å resolution. There is one connector per crystallographic asymmetric unit in each case. Rotation functions show the connector to be a dodecamer. Translation functions readily determined the position of the 12-fold axis in each unit cell. The structure is being determined by 12-fold electron-density averaging within each crystal and by averaging between the various crystal forms.
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  • 89
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    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.
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  • 90
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    Acta crystallographica 57 (2001), S. 181-186 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human stuttering is a simple example of the repetition of sounds or symbols, sometimes associated with single letters, and may be used to illustrate the amazing repetition of amino acids (symbolized by a letter, e.g. W) in proteins. A survey of available databases with highly improbable strings of single amino acids is tabulated. This paper concludes with a challenge to the crystallographic community to probe the structural origins of the structure–function relationship in this neglected area. When nature stutters, we should pay attention.
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  • 91
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structures of hydroxynitrile lyase from Manihot esculenta (MeHNL) complexed with the native substrate acetone and substrate analogue chloroacetone have been determined and refined at 2.2 Å resolution. The substrates are positioned in the active site by hydrogen-bond interactions of the carbonyl O atom with Thr11 OG, Ser80 OG and, to a lesser extent, Cys81 SG. These studies support a mechanism for cyanogenesis as well as for the stereospecific MeHNL-catalyzed formation of (S)-cyanohydrins, which closely resembles the base-catalyzed chemical reaction of HCN with carbonyl compounds.
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  • 92
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    Acta crystallographica 57 (2001), S. 145-147 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Dimeric (R)-specific enoyl-coenzyme A (CoA) hydratase from Aeromonas caviae catalyzes the hydration of trans-2-enoyl-CoAs with carbon lengths of 4–6 to yield their corresponding (R)-3-hydroxyacyl-CoAs and is essential for polyhydroxyalkanoate (PHA) biosynthesis. The enzyme has been crystallized by vapour diffusion against a reservoir solution containing 20% polyethylene glycol 4000, 5% 2-propanol and 20 mM HEPES pH 7.0 at 298 K. Crystals belong to the monoclinic space group C2, with unit-cell parameters a = 111.54 (3), b = 59.29 (1), c = 47.27 (4) Å, β = 113.04 (2)° and contain a dimeric molecule in the asymmetric unit. Flash-cooling of a crystal at 100 K alters its unit-cell parameters to a = 109.82 (7), b = 57.98 (6), c = 46.84 (2) Å, β = 112.71 (3)°. Native data to a resolution of 1.7 Å have been collected with 94.5% completeness and an Rmerge of 4.0% under cryogenic (100 K) conditions using synchrotron radiation.
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  • 93
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    Acta crystallographica 57 (2001), S. 279-280 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The enzyme 3-dehydroquinase catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate. The enzymes are classified into two groups, type I and type II, which have different biochemical and biophysical properties and act with different mechanisms. The type II dehydroquinase of Helicobacter pylori, a dodecameric enzyme, was overexpressed in Escherichia coli. The recombinant protein has been crystallized at 296 K using polyethylene glycol (PEG) 4000 as a precipitant. Native X-ray diffraction data have been collected to 2.5 Å resolution using synchrotron radiation. The crystals are cubic and belong to the space group P4232, with unit-cell parameters a = b = c = 98.91 Å. The asymmetric unit contains one subunit of recombinant type II dehydroquinase, with a corresponding VM of 2.18 Å3 Da−1 and a solvent content of 43.6%.
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  • 94
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Cystathionine β-synthase (CBS) is a unique heme enzyme that catalyzes a PLP-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an autosomal recessively inherited disease of sulfur metabolism. A truncated form of CBS in which the C-terminal amino-acid residues have been deleted has been prepared. The truncated CBS subunits form a dimer, in contrast to the full-length subunits which form tetramers and higher oligomers. The truncated CBS yielded crystals diffracting to 2.6 Å which belong to space group P31 or P32. This is the first comprehensive structural investigation of a PLP and heme-containing enzyme.
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  • 95
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    Acta crystallographica 57 (2001), S. 301-303 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A [2Fe–2S] ferredoxin found in the photosynthetic bacterium Rhodobacter capsulatus has been purified in recombinant form from Escherichia coli. This protein, called FdVI, resembles ferredoxins involved in iron–sulfur cluster biosynthesis in various prokaryotic and eukaryotic cells. Purified recombinant FdVI was recovered in high yields and appeared to be indistinguishable from the genuine R. capsulatus ferredoxin based on UV–visible absorption and EPR spectroscopy and mass spectrometry. FdVI has been crystallized in the oxidized state by a sitting-drop vapour-diffusion technique using sodium formate as precipitant. Seeding larger drops from a previous hanging-drop-grown small crystal resulted in the formation of long red–brown prismatic needles. Preliminary X-ray diffraction analysis indicated that FdVI crystals are orthorhombic and belong to the space group P212121, with unit-cell parameters a = 45.87, b = 49.83, c = 54.29 Å.
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  • 96
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    Acta crystallographica 57 (2001), S. 310-313 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Fructose-1,6-bisphosphate aldolase (E.C. 4.1.2) catalyses the reversible cleavage of fructose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde-3-phosphate in the glycolytic pathway of prokaryote and eukaryote organisms. The enzyme was obtained from the extreme thermophile Thermus aquaticus and, in contrast to mesophilic aldolases, expresses maximal activity in the presence of Co2+ as cofactor instead of Zn2+. The purified recombinant protein was monodisperse according to dynamic light-scattering measurements. Crystals of recombinant native class II fructose-1,6-bisphosphate aldolase from T. aquaticus were obtained from two different starting conditions at low protein concentrations. Condition I, using the sitting-drop vapour-diffusion method, yielded monoclinic crystals having space group P2 and unit-cell parameters a = 99.5, b = 57.5, c = 138.6 Å, β = 90.25°. Diffraction data were collected to 2 Å resolution at beamline X8-C of the NSLS synchrotron-radiation source. Native and selenomethionine-substituted protein crystals were obtained from condition II by hanging-drop vapor diffusion. The tetragonal crystals of the native protein belong to the space group P41, with unit-cell parameters a = b = 88.8, c = 163.1 Å, while those of the SeMet protein have space group I41, with unit-cell parameters a = b = 88.6, c = 164.1 Å. A data set suitable for MAD phasing was collected to 2.6 Å resolution at beamline X8-C of the NSLS synchrotron source.
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  • 97
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    Acta crystallographica 57 (2001), S. 260-262 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: CysB is a positive regulator of transcription of genes involved in cysteine biosynthesis in Gram-negative bacteria and belongs to the large family of LysR-type transcriptional regulators. The full-length protein from Klebsiella aerogenes has been crystallized from solutions containing PEG 8000 in the presence and in the absence of the inducer N-acetylserine by the method of vapour diffusion in hanging drops. For the complexed protein different crystal forms appear in the same drops.
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  • 98
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    Acta crystallographica 57 (2001), S. 272-275 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The gene encoding the highly thermostable arginyl-tRNA synthetase (ArgRS) from Thermus thermophilus was cloned and overexpressed in Escherichia coli under the control of the T7 promoter. The recombinant ArgRS was purified by two chromatographic steps and was crystallized by the hanging-drop vapour-diffusion method using PEG 8000 and ethylene glycol as precipitants. The crystals belong to the hexagonal space group P65, with unit-cell parameters a = b = 156.04 (7), c = 87.17 (4) Å. X-ray data to 2.8 Å resolution were collected at room temperature from a native crystal using an in-house X-ray source. Uranium, platinum and selenomethionine derivatives were found to be useful for phasing by the multiple isomorphous replacement method with anomalous scattering. The flash-frozen crystals diffracted beyond 2.3 Å resolution using synchrotron radiation from the beamline 41XU at SPring-8 (Harima).
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  • 99
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    Acta crystallographica 57 (2001), S. 284-286 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An enzyme from Comomonas acidovorans has been isolated that is specific for the stereospecific hydrolysis of (+)γ-lactam. This so-called (+)γ-lactamase has important applications in biotransformation reactions. The enzyme has been crystallized by vapour-phase diffusion using polyethylene glycol 4000 as a precipitant. Addition of a detergent, β-octylglucoside, was found to be essential for obtaining diffraction-quality crystals. The crystals grow in the space group P1, with unit-cell parameters a = 63.0, b = 93.2, c = 152.4 Å, α = 104.3, β = 92.6, γ = 108.5°, and diffract to 2 Å resolution using synchrotron radiation. Native data from these crystals have been collected to 2.4 Å.
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  • 100
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    Acta crystallographica 57 (2001), S. 296-297 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of Escherichia coli GlmU, a bifunctional enzyme catalyzing the acetylation of glucosamine-1-phosphate and uridylylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc, have been prepared in complex with coenzyme A and UDP-GlcNAc. These crystals belong to space group R32, with unit-cell parameters a = 104.5, c = 648.2 Å, diffract to at least 2.1 Å resolution and may contain two subunits of the trimeric enzyme per asymmetric unit.
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