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  • International Union of Crystallography (IUCr)  (2,258)
  • 2015-2019
  • 1995-1999  (2,258)
  • 1999  (2,258)
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  • 2015-2019
  • 1995-1999  (2,258)
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  • 1
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 4-4 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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  • 2
    Electronic Resource
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 5-7 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Significant improvement in the resolution and quality of the X-ray diffraction of crystals of MTCP-1 protein was observed on post-crystallization soaking. The MTCP-1 crystals grown from 1.5 M ammonium sulfate diffracted to only 3.0 Å resolution with some disorder in the diffraction. After post-crystallization soaking in a solution containing 2.0 M ammonium sulfate, the disorder was eliminated and diffraction extended to better than 2.0 Å resolution. Both native and selenomethionine-enriched crystals demonstrated better diffraction after soaking for several months. This simple technique may be useful to improve the diffraction quality of protein crystals generally.
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  • 3
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 25-30 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of a bifunctional inhibitor of α-amylase and trypsin from the seeds of ragi (Indian finger millet, Eleusine coracana Gaertneri) has been determined by an X-ray diffraction method. The inhibitor consists of 122 amino acids with five disulfide bridges and belongs to the plant α-amylase/trypsin-inhibitor family. This is the first crystal structure determination of a member of this family. The protein, purified from the seeds of ragi, has a molecular mass of 13300 Da with a pI of 10.3. Crystals were grown by a microdialysis method using ammonium sulfate as precipitant. The improved purification protocol and the modified crystallization conditions enabled reproducible growth of the crystals. The cell parameters are a = 41.2, b = 47.4, c = 55.9 Å. The intensity data were collected to 2.9 Å resolution, and the crystal structure was determined using the molecular-replacement method. The structure was refined using the X-PLOR and CCP4 program packages to a conventional R factor of 21%. The structure contains four α-helices between residues 19–29, 37–51, 56–65 and 90–95, and two short antiparallel β-strands between residues 67–70 and 73–75.
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  • 4
    Electronic Resource
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 8-24 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As isolated from Escherichia coli, the enzyme is an \alpha,β-heterodimer consisting of a small subunit that hydrolyzes glutamine and a large subunit that catalyzes the two required phosphorylation events. Here the three-dimensional structure of carbamoyl phosphate synthetase from E. coli refined to 2.1 Å resolution with an R factor of 17.9% is described. The small subunit is distinctly bilobal with a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. As observed in those enzymes belonging to the \alpha/\beta-hydrolase family, the active-site nucleophile, Cys269, is perched at the top of a tight turn. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain. Both the carboxyphosphate and carbamoyl phosphate synthetic components bind Mn2+ADP. In the carboxyphosphate synthetic component, the two observed Mn2+ ions are both octahedrally coordinated by oxygen-containing ligands and are bridged by the carboxylate side chain of Glu299. Glu215 plays a key allosteric role by coordinating to the physiologically important potassium ion and hydrogen bonding to the ribose hydroxyl groups of ADP. In the carbamoyl phosphate synthetic component, the single observed Mn2+ ion is also octahedrally coordinated by oxygen-containing ligands and Glu761 plays a similar role to that of Glu215. The carboxyphosphate and carbamoyl phosphate synthetic components, while topologically equivalent, are structurally different, as would be expected in light of their separate biochemical functions.
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  • 5
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of bovine heart cytochrome c oxidase has been determined at 2.8 Å resolution by the multiple isomorphous replacement (MIR) method with three heavy-atom derivatives. An asymmetric unit of the crystal has a molecular weight of 422 kDa. Eight heavy atoms as main sites of a CH3HgCl derivative were clearly located by solving the difference Patterson function. The electron density obtained by the MIR method was refined by density modification, consisting of solvent flattening, histogram matching and non-crystallographic symmetry averaging. The enzyme exhibits a dimeric structure in the crystal. Out of 3606 amino-acid residues in 26 subunits in the dimer, 3560 residues were located in the electron-density map. The structure was refined by X-PLOR. The final R factor and the free R factor were 0.199 and 0.252 at 2.8 Å resolution, respectively. One monomer in the dimeric structure with a stronger packing interaction has a lower averaged temperature factor than the other, by 16 Å2. The region \pm12 Å from the centre of the transmembrane part is almost 100% \alpha-helix, despite the glycine residue content being as high as 7.1% in the transmembrane region. The residues around haem a of animals have evolved away from those of bacteria in contrast with the residues of the haem a3. The hierarchy of the structural organization of the enzyme complex has been proposed on the basis of intersubunit interactions.
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  • 6
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 46-50 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The X-ray structure of recombinant bovine pancreatic phospholipase A2 (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Å resolution. The crystal belongs to the space group P212121 with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Å similar to the native enzyme reported previously by Dijkstra et al. [J. Mol. Biol. (1981), 147, 97–123]. The refinement converged to an R value of 18.4% (Rfree = 22.8%) for 16 374 reflections between 10.0 and 1.5 Å resolution. The surface-loop residues (60–70) are ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis. The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion. In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.
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  • 7
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 60-66 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two complexes between rainbow trout lysozyme (RBTL) and 4-methylumbelliferyl chitobioside, 4MeU-(GlcNAc)2, and chitotrioside, 4MeU-(GlcNAc)3, were produced by co-crystallization and soaking, respectively, and the crystal structures were solved at 2.0 Å resolution. The results show that 4-MeU-(GlcNAc)3 binds in subsites A–D and that 4-MeU-(GlcNAc)2 binds in subsites B–D in the active-site cleft of RBTL. This agrees well with earlier crystallographic studies on the binding of oligosaccharides of chitin to RBTL, which showed that (GlcNAc)3 binds to sites B–D in RBTL and not to A–C as seen in the human and turkey egg-white lysozymes. For both complexes the 4-MeU moiety in site D has diffuse electron density and is flexible, as it is only bound to water molecules and not to the protein. Since no electron density was observed in site E, the solved structures give views of nonproductive enzyme–substrate complexes.
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  • 8
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 67-76 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A multiple-wavelength anomalous diffraction (MAD) experiment was performed on an iridium derivative of hen egg-white lysozyme. Diffraction data were measured at five wavelengths on the X31 EMBL beamline on the DORIS III storage ring and at two further wavelengths on the X11 beamline. Four iridium-binding sites were located from the dispersive anomalous differences between two wavelengths at the rising and falling inflection points of the Ir LIII-edge white line using direct methods. All other attempts to determine the heavy-atom positions failed. The results demonstrate an experimental method whereby systematic error in MAD data due to sample absorption can be reduced where a white line is present in the absorption spectrum of a heavy atom.
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  • 9
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 279-280 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Hexitol nucleic acids are oligonucleotides built up from natural nucleobases and a phosphorylated 1,5-anhydrohexitol backbone. The anhydrohexitol oligonucleotide h(GTGTACAC) was synthesized using phosphoramidite chemistry and standard protecting groups. Crystals of h(GTGTACAC) were obtained at either 279 or 289 K by the hanging-drop vapour-diffusion technique using a 24-matrix screen for nucleic acid fragments. The crystals diffract beyond 2.0 Å resolution and belong to the hexagonal space group P6222 (or P6422) with unit-cell parameters a = 36.42 and c = 63.33 Å.
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  • 10
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 285-286 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The ATP-binding protein, MalK, of the bacterial ABC (ATP-binding-cassette) transport complex MalFGK2 provides the energy for the translocation of maltose and maltodextrins across the cytoplasmic membrane. The MalK protein from Salmonella typhimurium was overexpressed in Escherichia coli and crystallized by the hanging-drop method using (NH4)2SO4 as a precipitant. The crystals belong to space group P6x22 (most probably x = 1 or 5) with cell dimensions a = 181.8 and c = 182.5 Å, corresponding to three or four molecules per asymmetric unit. They diffract to a resolution of about 3 Å on a synchrotron X-ray source and are suitable for structure determination.
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  • 11
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 287-290 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pyrimidine nucleoside phosphorylase (PYNP) from B. stearothermophilus has been cloned and purified for crystallization. Crystals of a potential protein–inhibitor complex have been prepared by co-crystallization techniques using the substrate analog pseudouridine. These crystals provide good-quality diffraction images to 2.7 Å and belong to space group P21. The asymmetric unit contains the dimer structure of PYNP with unit-cell parameters a = 53.9, b = 71.9, c = 123.3 Å and β = 96.9°.
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  • 12
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 291-293 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: YPD1 is a yeast osmoregulatory protein that functions in a phosphorelay signal-transduction pathway. YPD1 has been expressed in Escherichia coli, purified to homogeneity and crystallized. The crystals were obtained by hanging-drop vapor-diffusion using PEG 4000 as a precipitant. Preliminary X-ray diffraction analysis indicates that the crystals belong to tetragonal space group P43212 or P41212 with unit-cell dimensions a = b = 52.71, c = 244.02 Å. X-ray data to 2.7 and 3.0 Å have been collected from native crystals and a heavy-atom derivative, respectively. Positions for two Hg atoms have been located by analysis of difference Patterson maps.
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  • 13
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 281-284 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The genomic RNA of all retroviruses is encapsidated in virions as a dimer of single-stranded chains held together near their 5′-end. For HIV-1, the initial site of dimerization has been shown to be a hairpin with a nine-residue loop containing a self-complementary sequence of six residues. This structure is proposed to promote dimerization by loop–loop interaction and formation of a so-called `kissing complex'. A 23-nucleotide RNA strand containing the loop enclosed by a seven base-pair stem has been synthesized. This oligomer was crystallized by the vapour-diffusion method at 310 K, pH 6.5, with methyl-pentanediol as the precipitant agent in the presence of MgCl2, KCl and spermine. Quasi-complete diffraction data were obtained at 2.7 Å resolution with a conventional X-ray source and at 2.3 Å resolution on a synchrotron beamline. The space group is P3121 or its enantiomorph P3221, with cell parameters a = b = 60.1, c = 65.9 Å at ambient temperature, or a = b = 59.0, c = 64.3 Å in a nitrogen-gas stream. There are two oligomers per asymmetric unit as determined from absorbance measurements of a dissolved crystal whose volume was carefully determined. In some cases, either perfectly or partially twinned crystals were obtained. Perfect twinning is detected by an apparent hexagonal symmetry and yields unusable crystallographic data, whilst partial twinning yields usable data after adequate processing. Structure solution is under way by searching for heavy-atom derivatives and systematically substituting bromo- or iodo-uridines for uridines.
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  • 14
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 294-296 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A highly thermostable xylose isomerase from Thermus caldophilus has been expressed in Escherichia coli. The purified enzyme has an optimum temperature of 363 K. It has been crystallized at room temperature using ammonium sulfate as a precipitant. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 84.35, b = 123.60, c = 140.24 Å. The presence of one molecule of tetrameric xylose isomerase in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.1 Å3 Da−1 and a solvent content of 41% by volume. The crystals initially showed diffraction to 1.7 Å Bragg spacing with synchrotron X-rays, and a set of native data extending to 2.3 Å resolution has been collected.
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  • 15
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Until now, wild-type bacteriophage λ lysozyme had been impossible to crystallize. This difficulty could be overcome by the replacement of the four tryptophan residues by aza-tryptophans. Analysis of the intermolecular and intramolecular contacts in this modification allows understanding of the differences in behaviour between the native and modified molecules. Furthermore, this mutation was very useful for the creation of new heavy-atom binding sites and for the solution of the non-crystallographic symmetry, which is extremely important for phase improvement. This procedure seems to be generally applicable, at least in the search for new possibilities for heavy-atom binding sites.
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  • 16
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 436-442 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Re-examination of the known data on crystalline forms of polyglycine reveals that the crystal modification `polyglycine I' has two different three-dimensional structures depending on the molecular weight. Structural models for both low molecular weight (LMW) and high molecular weight (HMW) polyglycine I crystals are described. In the LMW crystal model, the molecules have an unusual extended conformation generated by alternation of two mirror-symmetrical residual conformations along the chain. The molecules are parallel and each chain forms interpeptide hydrogen bonds with four adjacent chains. The structural model for the HMW crystal represents a composition of twinning crystallites. The crystallites themselves consist of antiparallel enantiomorphous chains united by hydrogen bonds to form rippled sheets. Calculations of the diffraction patterns and packing energy show that these polyglycine I structures have a higher level of conformity with the experimental data than previously suggested models. New insight into the structure of the polyglycine associates opens up the possibility of designing improved silk-like and nylon materials.
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  • 17
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 443-447 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 Å resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.
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  • 18
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 448-457 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The investigation of the structure of the four conformers of the nonapeptide described here has an additional purpose: to illustrate a method for combining isomorphous replacement information with anomalous dispersion information within the linear equations that have found use in the analysis of multiple-wavelength anomalous dispersion data. In the present application, isomorphous replacement data were obtained from the replacement of naturally occurring S atoms in the nonapeptide with Se atoms. Only one wavelength was used for the analysis: Cu Kα radiation. Details of the analysis are presented, as well as the structural results obtained. It was found that the four independent molecules in the structure have similar, but not identical, conformations. The backbones fold into predominantly α-helices with one or two 310-type hydrogen bonds and have extended side chains. Three to four water molecules are associated with each of the four head-to-tail regions between the peptides. Optimal packing between hydrophobic surfaces may account for the existence of four molecules in an asymmetric unit.
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  • 19
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 458-463 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An algorithm is described which utilizes the solvent mask generated by the solvent-flattening technique to calculate a monomer molecular envelope. In the case where non-crystallographic symmetry (NCS) is present in the crystal and self-rotation angles are known from a self-rotation function, the resultant monomer envelopes can be used to search for the translation component of the NCS element by a three-dimensional search in real space. In the absence of self-rotation angles, the monomer envelope may be used to derive the NCS operators by reciprocal-space techniques. Thus, an automatic procedure for averaging directly from the solvent-flattening stage can be implemented. The procedure was instrumental in the structure solution of fibrinogen fragment D, which is presented as an example.
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  • 20
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 464-468 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.
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  • 21
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 473-478 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases – an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.
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  • 22
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 469-472 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A procedure, called PBR (phase-bias reduction), has been developed to properly refine heavy-atom derivatives and to generate less biased heavy-atom phases when these derivatives contain common heavy-atom sites. Two independent events are obtained by splitting the refinement and phasing calculations into two stages, the first in which one of the derivatives having common sites is used together with the native amplitudes and the second in which both derivatives with common sites are used simultaneously, with one of them being used as the native data set. Improved centroid phases and the corresponding figures of merit are obtained by phase combination. This procedure has been used in the structure determination of the iron-cluster-containing protein pyruvate–ferredoxin oxidoreductase. When the common heavy-atom sites are properly treated by the PBR procedure, the resulting calculated centroid phases are improved with respect to classical heavy-atom refinement centroid phases where all derivatives are refined together. This leads to improved electron-density distributions, since anomalous difference Fourier maps calculated with the PBR-refined centroid phases and corresponding figures of merit show more clearly the positions of the iron sites.
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  • 23
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 149-156 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Aspartyl-tRNA synthetase (AspRS) extracted from yeast is heterogeneous owing to proteolysis of its positively charged N-terminus; its crystals are of poor quality. To overcome this drawback, a rational strategy was developed to grow crystals of sufficient quality for structure determination. The strategy is based on improvement of the protein homogeneity and optimization of crystallization, taking advantage of predictions from crystal-growth theories. An active mutant lacking the first 70 residues was produced and initial crystallization conditions searched. The shape and habit of initial crystals were improved by establishing a phase diagram of protein versus crystallizing-agent concentrations. Growth of large well faceted crystals takes place at low supersaturations near the isochronic supersolubility curve. Further refinement led to reproducible growth of two crystalline forms of bipyramidal (I) or prismatic (II) habit. Both diffract X-rays better than crystals previously obtained with native AspRS. Complete data sets were collected at 3 Å resolution for form I (space group P41212) and form II (space group P3221) and molecular-replacement solutions were found in both space groups.
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  • 24
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 168-172 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program MULTAN88 has been applied to a known protein, ribonuclease (RNAP1), containing 808 non-H atoms, including five S atoms, plus 83 ordered solvent water molecules. Phase sets with mean phase errors between 69 and 75° were selected by modified figures of merit for trials with the full data at 1.17 Å resolution and also with restricted data at 1.25 and 1.5 Å resolution. These figures of merit had previously only been applied to protein structures containing heavy atoms, and this is the first demonstration of their usefulness with no heavy atom present. An initial set of 1091 phases from a 1.17 Å trial was developed by an objective procedure to give the full structure with a residual of 0.21, which agrees well with the published structure.
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  • 25
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 157-167 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A previous article [Fourme et al. (1995). J. Synchrotron Rad. 2, 36–48] presented the theoretical foundations of MASC, a new contrast-variation method using multiwavelength anomalous scattering, and reported the first experimental results. New experiments have been conducted both at the ESRF (Grenoble, France) and at LURE-DCI (Orsay, France), using cryocooled crystals of three proteins of known structures and very different molecular weights. Amplitudes of \{\Gamma_T({\bf h})\}, the `normal' structure factors of the anomalously scattering part of the crystal including the solvent zone and the ordered anomalous scattering sites (if any), have been extracted from multiwavelength data. In the very low resolution range (d \ge 20 Å), the agreement between experimental \{|\Gamma_T({\bf h})|\} and model values calculated from the bulk solvent is all the more satisfactory since the molecular weight of the protein is high. For spacings between 10 and 20 Å, the agreement between experimental \{|\Gamma_T({\bf h})|\} and model values is also satisfactory if one takes into account ordered anomalous scatterer sites. Such sites have been found in the three cases.
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  • 26
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    Acta crystallographica 55 (1999), S. 386-398 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of Bacillus amyloliquefaciens ribonuclease (barnase), an extracellular 110-residue enzyme initially solved at 2.0 Å resolution, has been refined at 1.5 Å using synchrotron radiation and an imaging-plate scanner. Refinement with anisotropic atomic displacement parameters resulted in increased accuracy of the structure. The final model has a crystallographic R factor of 11.5% and an Rfree of 17.4%. The three independent molecules in the asymmetric unit, referred to as A, B and C, allowed detailed analysis of this final model and meaningful comparison with structures of barnase complexed either with nucleotide inhibitors or with its natural intracellular inhibitor, barstar. The analysis of the overall solvent structure revealed a similar number of water molecules associated with each barnase molecule; among these were 16 equivalent buried solvent molecules, the locations of which are discussed in detail and classified on the basis of their structural role. The importance of the water molecules' contribution to the barnase–barstar interaction is also highlighted. The high accuracy of the present analysis revealed the presence of a Zn2+ ion mediating the contacts between pairs of symmetry-related A, B or C molecules; such an ion had previously only been identified for pairs of C molecules.
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  • 27
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    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 403-407 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human lactoferrin (hLf) has considerable potential as a therapeutic agent. Overexpression of hLf in the fungus Aspergillus awamori has resulted in the availability of very large quantities of this protein. Here, the three-dimensional structure of the recombinant hLf has been determined by X-ray crystallography at a resolution of 2.2 Å. The final model, comprising 5339 protein atoms (residues 1–691, 294 solvent molecules, two Fe3+and two CO_3^{2-} ions), gives an R factor of 0.181 (free R = 0.274) after refinement against 32231 reflections in the resolution range 10–2.2 Å. Superposition of the recombinant hLf structure onto the native milk hLf structure shows a very high level of correspondence; the main-chain atoms for the entire polypeptide can be superimposed with an r.m.s. deviation of only 0.3 Å and there are no significant differences in side-chain conformations or in the iron-binding sites. Dynamic properties, as measured by B-value distributions or iron-release kinetics, also agree closely. This shows that the structure of the protein is not affected by the mode of expression, the use of strain-improvement procedures or the changes in glycosylation due to the fungal system.
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  • 28
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    Acta crystallographica 55 (1999), S. 414-421 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the `blue' copper protein plastocyanin from the cyanobacterium Phormidium laminosum has been solved and refined using 2.8 Å X-ray data. P. laminosum plastocyanin crystallizes in space group P43212 with unit-cell dimensions a = 86.57, c = 91.47 Å and with three protein molecules per asymmetric unit. The final residual R is 19.9%. The structure was solved using molecular replacement with a search model based on the crystal structure of a close homologue, Anabaena variabilis plastocyanin (66% sequence identity). The molecule of P. laminosum plastocyanin has 105 amino-acid residues. The single Cu atom is coordinated by the same residues – two histidines, a cysteine and a methionine – as in other plastocyanins. In the crystal structure, the three molecules of the asymmetric unit are related by a non-crystallographic threefold axis. A Zn atom lies between each pair of neighbouring molecules in this ensemble, being coordinated by a surface histidine residue of one molecule and by two aspartates of the other.
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  • 29
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Agrobacterium radiobacter CCRC 14924 N-carbamyl-D-amino-acid amidohydrolase, the enzyme used for production of D-amino acids, was overexpressed in Escherichia coli JM109. The expressed protein was crystallized by vapour diffusion using lithium sulfate as precipitant. It crystallizes in space group P21 with unit-cell parameters a = 69.8, b = 67.9 and c = 137.8 Å and β = 96.4°. There are four molecules per asymmetric unit. Crystals diffract to 2.8 Å resolution using a rotating-anode source at cryogenic (113 K) temperatures.
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  • 30
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: ADP-L-glycero-D-mannoheptose 6-epimerase is a 240 kDa NAD-dependent nucleotide diphosphosugar epimerase from Escherichia coli K12 which catalyzes the interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose. ADP-L-glycero-D-mannoheptose is a required intermediate for lipopolysaccharide inner-core and outer-membrane biosynthesis in several genera of pathogenic and non-pathogenic Gram-negative bacteria. ADP-L-glycero-D-mannoheptose 6-epimerase was overexpressed in E. coli and purified to apparent homogeneity by chromatographic methods. Three crystal forms of the epimerase were obtained by a hanging-drop vapor-diffusion method. A native data set for crystal form III was collected in-house on a Rigaku R-AXIS-IIC image plate at 3.0 Å resolution. The form III crystals belong to the monoclinic space group P21. The unit-cell parameters are a = 98.94, b = 110.53, c = 180.68 Å and β = 90.94°. Our recent results show that these crystals diffract to 2.0 Å resolution at the Cornell High Energy Synchrotron Source. The crystal probably contains six 40 kDa monomers per asymmetric unit, with a corresponding volume per protein mass (Vm) of 4.11 Å3 Da−1 and a solvent fraction of 70%.
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  • 31
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    Acta crystallographica 55 (1999), S. 801-809 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Protein HU is a ubiquitous prokaryotic protein which controls the architecture of genomic DNA. It binds DNA non-specifically and promotes the bending and supercoiling of the double helical structure. HU is involved in many DNA-associated cellular processes, including replication, transcription and the packaging of DNA into chromosome-like structures. Originally determined at medium resolution, the crystal structure of HU has now been refined at 2.0 Å resolution. The high-resolution structure shows that the dimeric molecule is essentially a compact platform for two flexible and basic arms which wrap around the DNA molecule. To maximize the protein's stability, non-secondary structural regions are reduced to a minimum, there is an extensive aromatic hydrophobic core and several salt bridges and hydrogen-bonded water molecules knit together crucial regions. Based on the original medium-resolution structure of HU, several proposals were made concerning the structural basis of HU's ability to bind, bend and supercoil DNA. Each of these proposals is fully supported by the high-resolution structure. Most notably, the surfaces of the molecule which appear to mediate protein–DNA and protein–protein interactions have the ideal shapes and physicochemical properties to perform these functions.
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  • 32
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    Acta crystallographica 55 (1999), S. 810-819 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end-to-end interactions. Phosphate–phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end-to-end interactions and the average conformation of DNA. Dodecamers must have a B-form average conformation with 10 ± 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7–10.6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.
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  • 33
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    Acta crystallographica 55 (1999), S. 820-825 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program SAYTAN has been applied successfully to a known protein, rubredoxin, which contains 52 amino-acid residues including an FeS4 unit, a sulfate ion and 102 solvent water molecules. Starting with initially random phases, useful sets can be obtained from multiple trials and selected by figures of merit at different resolutions. Phase extension followed by weighted Fourier recycling reveals a recognizable structure of rubredoxin. The model is refined against 1 Å resolution data to an R factor of 14.5% using the program SHELXL93.
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  • 34
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant human glucose 6-phosphate dehydrogenase (G6PD) has been crystallized and its structure solved by molecular replacement. Crystals of the natural mutant R459L grow under similar conditions in space groups P212121 and C2221 with eight or four 515-residue molecules in the asymmetric unit, respectively. A non-crystallographic 222 tetramer was found in the C2221 crystal form using a 4 Å resolution data set and a dimer of the large β + α domains of the Leuconostoc mesenteroides enzyme as a search model. This tetramer was the only successful search model for the P212121 crystal form using data to 3 Å. Crystals of the deletion mutant ΔG6PD grow in space group F222 with a monomer in the asymmetric unit; 2.5 Å resolution data have been collected. Comparison of the packing of tetramers in the three space groups suggests that the N-terminal tail of the enzyme prevents crystallization with exact 222 molecular symmetry.
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  • 35
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    Acta crystallographica 55 (1999), S. 243-246 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Solving the phase problem is the crucial and quite often the most difficult and time-consuming step in crystallographic structure determination. The traditional methods of isomorphous replacement (MIR or SIR) and molecular replacement require the availability of an isomorphous heavy-atom derivative or the structure of a homologous protein, respectively. Here, a method is presented which utilizes the low-resolution molecular shape determined from solution X-ray scattering data for the molecular search. The molecular shape of a protein is an important structural property and can be determined directly by the small-angle scattering technique. The idea of locating this molecular shape in the crystallographic unit cell has been tested with experimental diffraction data from nitrite reductase (NiR). The conventional Patterson search proved to be unsuccessful, as the intra-envelope vectors are uniformly distributed and do not match those of intra-molecular (atom-to-atom) vectors. A direct real-space search for orientation and translation was then performed. A self-rotation function using 2.8 Å crystallographic data yielded the polar angles of the non-crystallographic threefold axis. Knowledge of the orientation of this axis reduces the potential six-dimensional search to four (Eulerian angle γ and three translational parameters). The direct four-dimensional search within the unit cell produced a clear solution. The electron-density map based on this solution agrees well with the known structure, and the phase error calculated from the map was 61° within 20 Å resolution. It is anticipated that the low-resolution envelope can be used as a starting model for phase extension by the maximum-entropy and density-modification method.
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  • 36
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: We have crystallized and performed preliminary X-ray characterization of the complex between the DNAase domain of the E9 colicin and its cognate immunity protein Im9. The dissociation constant for this complex, Kd = 1 × 10−16 M, reveals it to be one of the highest affinity protein–protein interactions known. Single crystals of the 1:1 complex were grown from microseeding experiments using PEG 4K as precipitant. The space group is P212121 with one molecule of complex in the asymmetric unit, and crystals contain approximately 43% solvent. These crystals are inherently non-isomorphous and so selenomethionine-derivatized protein has been prepared and crystals grown for MAD phasing experiments.
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  • 37
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A truncated soluble form of the murine class I major histocompatibility antigen complex H–2Dd was cloned using an Escherichia coli based system. It was expressed, refolded in vitro and crystallized in a complex with murine β2 microglobulin and the peptide RGPGRAFVTI from the V3-loop of the gp160 HIV-1 protein. Crystals belonging to the space group P212121 with cell dimensions a = 51.3, b = 92.5, c = 108.8 Å were obtained using two different crystallization conditions. The crystals contain one complex per asymmetric unit and diffract to at least 2.4 Å resolution.
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  • 38
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    Acta crystallographica 55 (1999), S. 263-265 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: During homologous recombination in Escherichia coli the RuvA, B and C proteins interact specifically with the Holliday junction formed by the action of RecA to promote the strand-exchange reaction. RuvA, a homotetrameric protein of molecular weight 88 kDa, has been overexpressed in E. coli, purified and co-crystallized with a synthetic Holliday junction substrate made from four 18-base deoxyoligonucleotides. Crystals were grown using the hanging-drop vapour-diffusion method with sodium acetate as the precipitant. The crystals diffract to a resolution of 6 Å and belong to the monoclinic system, space group C2, with cell parameters a = 148, b = 148, c = 106 Å and β = 123°. The X-ray analysis of these crystals should reveal the structure of the Holliday junction and its mode of binding to RuvA, providing new insights into the molecular mechanism of genetic recombination.
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  • 39
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    Acta crystallographica 55 (1999), S. 865-868 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.
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  • 40
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    Acta crystallographica 55 (1999), S. 736-744 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the FKBP12–rapamycin–FRB ternary complex has now been refined at 2.2 Å resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12–rapamycin binding (FRB) domain of FKBP12–rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity. The conformation of rapamycin in the ternary complex is very similar to that observed in the FKBP12–rapamycin binary complex, with an r.m.s. difference of only 0.30 Å. However, a slight (9°) rotation repositions the FRB-binding face of rapamycin in the ternary complex. There are extensive rapamycin–protein interactions and relatively few interactions between the two protein partners FKBP12 and FRB, these interactions mainly involving residues in the 40s and 80s loops of FKBP12 and α1 and α4 of FRB. The high-resolution refinement has revealed the crucial role of several buried waters in the formation of the ternary complex.
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  • 41
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    Acta crystallographica 55 (1999), S. 869-872 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: α-D-Glucuronidases cleave the α-1,2-glycosidic bond of the 4-O-methyl-α-D-glucuronic acid side chain in xylan. Of the xylan-debranching hydrolases, these enzymes are the least studied and characterized. The α-glucuronidase gene (aguA) from Bacillus stearothermophilus T-6 has been cloned, sequenced and overproduced in Escherichia coli. The gene encodes for a protein of 679 amino acids with a calculated molecular weight of 78480 and a pI of 5.42. α-Glucuronidase T-6 shows high homology to the α-glucuronidases of Thermotoga maritima (60% identity) and of Trichoderma reesei (44% identity). Based on the amino-acid sequence similarity, it is likely that these enzymes represent a new class of glycosyl hydrolases. Crystallographic studies of α-glucuronidase T-6 were initiated to study the mechanism of catalysis, as well as to provide a structural basis for rational introduction of enhanced thermostability by site-specific mutagenesis. In this report, the crystallization and preliminary crystallographic characterization of the native α-glucuronidase T-6 enzyme is described. Two crystal forms were found suitable for detailed crystal structure analysis. The T1 form was obtained by the vapour-diffusion method using PEG 4000 as a precipitant and 2-propanol as an organic additive. The crystals belong to a primitive tetragonal crystal system (space group P41212 or P43212) with unit-cell dimensions a = b = 76.1 and c = 331.2 Å. These crystals are mechanically strong, are stable in the X-ray beam and diffract X-rays to better than 2.4 Å resolution. A full 3.0 Å resolution diffraction data set (97.3% completeness, Rmerge 9.8%) has recently been collected on one crystal at room temperature using a rotating-anode X-ray source and an R-AXIS IIc imaging-plate detector. The M1 form was obtained and characterized by similar techniques. The best crystallization occurred at a slightly lower pH and a lower concentration of 2-propanol. The crystals belong to a primitive monoclinic crystal system (space group P21) with unit-cell dimensions a = 65.8, b = 127.4, c = 96.6 Å and β = 97.9°. These crystals are also quite strong and stable, and diffract to better than 2.8 Å resolution. A full 2.8 Å resolution diffraction data set (96.2% completeness, Rmerge 7.6%) has recently been collected on one crystal at room temperature using the same R-AXIS IIc setup. Both forms are currently being used to obtain crystallographic phasing via isomorphous heavy-atom derivatives and selenomethionine MAD experiments.
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  • 42
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    Acta crystallographica 55 (1999), S. 877-879 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Periplasmic nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 contains two molybdopterin guanine dinucleotide cofactors and one [4Fe–4S] cluster as prosthetic groups and catalyzes the conversion of nitrate to nitrite. Crystals of the oxidized form of this enzyme were obtained using PEG as precipitant and belong to space group P3121 or P3221, with unit-cell dimensions a = b = 106.3, c = 135.1 Å. There is one monomer of 80 kDa in the asymmetric unit, which corresponds to a Matthews ratio of 2.75 Å3 Da−1. Using cryo-cooling procedures and X-rays from a rotating-anode generator, diffraction was observed to beyond 3.0 Å resolution.
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  • 43
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    Acta crystallographica 55 (1999), S. 883-884 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two orthorhombic forms of crystals of the haptoglobin–hemoglobin complex were obtained using polyethylene glycol as precipitant. These crystals did not diffract well enough for data collection and work on the complex is no longer continued. However, the description of the crystallization conditions may be useful in future endeavors to obtain suitable crystals.
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  • 44
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    Acta crystallographica 55 (1999), S. 542-543 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molybdenum-responsive ModE regulatory protein from Escherichia coli has been purified and used in crystallization trials. Two crystal forms have been observed. Form I is tetragonal, P41212 (or enantiomorph), with a = b = 72.3, c = 246.2 Å and diffracts to medium resolution. Form II is orthorhombic, P21212, with a = 82.8, b = 127.9, c = 64.0 Å and diffraction has been observed beyond 2.8 Å resolution. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure–activity relationship in regulating the uptake of molybdate in bacteria.
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  • 45
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    Acta crystallographica 55 (1999), S. 544-546 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of 1,5-α-arabinanase A from Pseudomonas fluorescens subspecies cellulosa have been obtained by vapour diffusion. The crystals belong to the space group P6122 with unit-cell parameters a = b = 91.6, c = 179.4 Å with one molecule in the asymmetric unit. The native crystals and, to a much greater extent, heavy-atom soaked crystals are sensitive to radiation which necessitates cryocooling. Suitable cryocooling conditions have been established, though a shrinkage of the unit cell is observed, with a = b = 88.8 and c = 176.9 Å.
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  • 46
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    Acta crystallographica 55 (1999), S. 547-548 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Blasticidin S deaminase from Aspergillus terreus was crystallized with polyethylene glycol 8000. Two types of crystals were grown under the same crystallization conditions. One type grew as thin plates, while the other had a rhombic shape. The rhombic shaped crystal was suitable for high-resolution crystal structure analysis. Precession photographs and diffraction data showed that the crystal belonged to orthorhombic space group P212121, with unit-cell dimensions a = 70.33, b = 146.56 and c = 56.48 Å. The calculated Vm value was acceptable when a tetramer of the enzyme was contained in an asymmetric unit. Preliminary diffraction data were collected to a resolution of 2.0 Å with good statistics.
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  • 47
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    Acta crystallographica 55 (1999), S. 552-553 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Single crystals of ferritin extracted from Listeria innocua have been obtained by the vapour-diffusion method using PEG 1000 as precipitant. The crystals are orthorhombic, space group P212121, with unit-cell dimensions a = 87.7, b = 137.5, c = 173.1 Å. The crystals diffract to 2.9 Å resolution on a rotating-anode X-ray source and to 2.35 Å resolution on a synchrotron X-ray source. The asymmetric unit contains one molecule formed by 12 subunits, corresponding to a packing density of 2.41 Å3 Da−1
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  • 48
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    Acta crystallographica 55 (1999), S. 549-551 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The flavoenzyme L-aspartate oxidase from Escherichia coli was crystallized using the hanging-drop vapour-diffusion technique with PEG 4000 as precipitant. The crystals belong to space group P3121 (or P3221) with unit-cell parameters a = b = 84.9, c = 159.9 Å. A solvent content of 42% corresponds to a monomer (60 kDa) in the asymmetric unit. A complete 2.8 Å resolution data set was collected using a rotating-anode X-ray generator.
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  • 49
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant constructs encoding the fibrinogen-binding domains of ClfA and ClfB from Staphylococcus aureus have been crystallized. ClfA was crystallized in the orthorhombic space group P212121 with unit-cell parameters a = 39.58, b = 81.39 and c = 112.65 Å. A complete data set was recorded to 2.1 Å resolution and had a Vm of 2.3 Å3 Da−1 with 46.5% solvent, suggesting one molecule per asymmetric unit. Co-crystals of ClfA with the 17 amino-acid C-terminal peptide of fibrinogen γ-chain diffracted to 2.1 Å resolution and had unit-cell parameters a = 39.11, b = 81.39 and c = 109.51 Å in the space group P212121. ClfB was crystallized in the tetragonal space group P41212 or P43212 with unit-cell parameters a = 96.31, b = 96.31 and c = 84.13 Å and diffracted to 2.45 Å resolution. The estimated Vm of 2.6 Å3 Da−1 with 53% solvent indicated one molecule in the asymmetric unit.
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  • 50
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    Acta crystallographica 55 (1999), S. 1023-1035 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Previous atomic force microscopy (AFM) studies and periodic bond-chain (PBC) analyses of tetragonal lysozyme crystals have suggested that the (110) face consists of chains of molecules related to one another by 43 axes parallel to the crystal face. In this study, high-resolution AFM images of the (110) face were obtained and analyzed in order to verify this prediction. A computer program was employed which constructs the theoretical AFM image corresponding to a specific crystallographic molecular-packing arrangement and AFM tip shape. The packing arrangement and tip shape were varied in order to obtain the maximum possible correlation between experimental and theoretical images. The prediction from PBC analysis of an arrangement involving 43 helices was confirmed in this manner, while the alternate arrangement, consisting of molecules related to one another by 21 axes, was not observed. However, the surface structure was found to differ significantly even from this crystallographic arrangement. The molecules were found to pack slightly closer about what will become the 43 axes within the interior of the crystal, suggesting the occurrence of surface reconstruction or rearrangement on the tetragonal lysozyme (110) face. This study represents a new approach for more precise determination of the molecular-packing arrangements on protein crystal faces employing AFM.
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  • 51
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    Acta crystallographica 55 (1999), S. 1046-1047 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the 52 kDa monomeric Escherichia coli cysteinyl-tRNA synthetase complexed with ATP and cysteine have been grown by hanging-drop vapor diffusion from solutions containing ammonium sulfate as the precipitating agent. The crystals form long hexagonal rods in the space group P321 with unit-cell dimensions a = b = 82.3, c = 168.9 Å. There is one enzyme molecule in the asymmetric unit. A complete native data set has been collected from a rotating-anode source to a resolution of 2.7 Å at 103 K, with an Rmerge of 6.7%.
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  • 52
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    Acta crystallographica 55 (1999), S. 564-565 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The acidic lectin (WBAII) from the winged bean (Psophocarpus tetragonolobus) binds to the H-antigenic determinant on human erythrocytes and to the T-antigenic disaccharide Gal-β1,3-GalNAc. Two crystal forms of WBAII were obtained in the presence of methyl-α-D-galactose. Form I belongs to space group R3 with unit-cell dimensions a = b = 182.11, c = 44.99 Å and has one dimer in the asymmetric unit. Form II belongs to space group C2 with unit-cell dimensions a = 135.36, b = 127.25, c = 139.98 Å, β = 95.9° and has four dimers in the asymmetric unit. Intensity data were collected to 3.0 Å and to 3.5 Å from crystals of form I and II, respectively. The structures were solved by the molecular-replacement method using the coordinates of the basic form of winged bean lectin.
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  • 53
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    Acta crystallographica 55 (1999), S. 566-567 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts has been crystallized by vapour diffusion in the pH range 7–8.5 in (NH4)2SO4 and Tris–HCl buffer or potassium phosphate buffer at room temperature. Crystals of the A4 isoform, grown at pH 8.5 in Tris–HCl buffer, diffract to 3.0 Å (at 100 K) using synchrotron radiation. The crystals belong to the orthorhombic C222 space group, with unit-cell dimensions a = 145.9, b = 185.9 and c = 106.3 Å, and probably contain one tetramer per asymmetric unit. Structure determination by molecular replacement is in progress.
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  • 54
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    Acta crystallographica 55 (1999), S. 568-570 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: DOPA decarboxylase is responsible for the synthesis of the key neurotransmitters dopamine and serotonin via decarboxylation of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan, respectively. The crystals of recombinant DOPA decarboxylase differ from those previously reported for the enzyme purified from pig kidney. They belong to space group P622 with unit-cell dimensions a = b = 302.6, c = 178.1 Å. Both the self-rotation function and the good diffraction quality of these crystals (2.5 Å on a synchrotron source) suggest that there should be at least three protein dimers in the asymmetric unit. Diffraction data sets have been collected for the native enzyme and a heavy-atom derivative.
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  • 55
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Golgi mannosidase IA is a class I α-mannosidase which catalyzes the conversion of Man9GlcNAc2 or Man8GlcNAc2 oligosaccharide substrates to Man5GlcNAc2 during the maturation of Asn-linked oligosaccharides. The enzyme is a type II membrane protein, and a recombinant form of mannosidase IA from mouse, lacking the transmembrane domain, has been expressed in Pichia pastoris, purified to homogeneity and crystallized by the hanging-drop vapor-diffusion method. The crystals grow as thin rods, with unit-cell dimensions a = 54.9, b = 135.01, c = 69.9 Å. The crystals exhibit the symmetry of space group P2221 and diffract to 2.8 Å resolution. The asymmetric unit contains one monomer (∼53 kDa) and has a solvent content of 59%.
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  • 56
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Deoxycytidylate hydroxymethylase from bacteriophage T4 is a homodimeric enzyme in which each polypeptide chain consists of 246 amino-acid residues. It has been crystallized in the presence of its substrate, deoxycytidine monophosphate, at room temperature using sodium citrate as precipitant. The crystals are monoclinic, belonging to space group C2, with unit-cell parameters a = 174.22, b = 53.12, c = 75.17 Å, β = 115.29°. The asymmetric unit contains one homodimer, with a corresponding Vm of 2.65 Å3 Da−1 and solvent content of 54%. Native diffraction data to 1.6 Å resolution have been collected from two crystals using synchrotron radiation.
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  • 57
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the catalytic core domain of a Trichoderma reesei β-mannanase belonging to glycoside hydrolase family 5 have been grown by the sitting-drop method at room temperature using ammonium sulfate as precipitant. The crystals grow as thin colourless plates and belong to space group P21, with unit-cell parameters a = 50.0, b = 54.3, c = 60.2 Å, β = 111.3°, and have a single monomer of mannanase in the asymmetric unit. Native data to 2.0 Å resolution have been collected at room temperature using synchrotron radiation. Data for a platinum derivative have been collected to 1.65 Å at 110 K in a very short time at the CCLRC Daresbury synchrotron source, using a charge-coupled device (CCD) as detector.
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  • 58
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    Acta crystallographica 55 (1999), S. 1064-1065 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 28 kDa heterodimeric complex from Taiwan viper (F4/F7 complex) is composed of a neurotoxic phospholipase A2 (F4) and a non-toxic PLA2-like component (F7). Despite a high sequence identity (65%), the biological and pharmacological activities of F4 and F7 are contrasting. The complex is a structural analogue of Vipoxin found in the venom of the Bulgarian viper Vipera ammodites meridionalis. It is unclear how and why such varied bioactivities are expressed in these similar components. The F4/F7 complex has been crystallized using hanging-drop vapour diffusion and macroseeding techniques. The space group is monoclinic P2_1 with unit-cell dimensions a=74.92, b=85.13, c=78.16 Å and \beta=95.12°. X-ray intensity data to 2.0 Å resolution have been collected at 120 K and the structure has been solved using the molecular-replacement method. There are four F4/F7 complex molecules in the asymmetric unit, which do not exhibit any local point-group symmetry.
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  • 59
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    Acta crystallographica 55 (1999), S. 1101-1104 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: TRAIL (also known as Apo-2L) belongs to the tumour necrosis factor (TNF) cytokine family and induces rapid apoptosis in a wide variety of tumour cell lines upon binding to the death-signalling receptors on the cell membrane. Normal cells are resistant to TRAIL, owing to the expression of decoy receptors which lack functional death domains and antagonize TRAIL-induced apoptosis. Soluble and functional human TRAIL, expressed in Escherichia coli and refolded into a functional form, has been crystallized. The crystals belong to space group P63 with unit-cell dimensions a = b = 65.61, c = 131.70 Å. The asymmetric unit contains two molecules of TRAIL, with a crystal volume per protein mass (Vm) of 2.41 Å3 Da−1 and a solvent content of about 42% by volume. A native and a platinum-derivative data set to 2.8 and 3.5 Å resolution, respectively, were obtained from frozen crystals. Structure determination by a combined molecular replacement and isomorphous replacement method is in progress.
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  • 60
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    Acta crystallographica 55 (1999), S. 1105-1107 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Hsp70 proteins are highly conserved proteins induced by heat shock and other stress conditions. An ATP-binding domain of human Hsp70 protein has been crystallized in two major morphological forms at pH 7.0 in the presence of PEG 8000 and CaCl2. Both crystal forms belong to the orthorhombic space group P212121, but show no resemblance in unit-cell parameters. Analysis of the crystal structures for both forms shows a 1–2 Å shift of one of the subdomains of the protein. This conformational change could reflect a `natural' flexibility of the protein which might be relevant to ATP binding and may facilitate the interaction of other proteins with Hsp70 protein.
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  • 61
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    Acta crystallographica 55 (1999), S. 1108-1108 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The coordinates and structure factors have now been deposited with the Protein Data Bank for the high-resolution structure described in the paper by Jameson, Anderson, Norris, Thomas & Baker [Acta Cryst. (1998). D54, 1319–1335]. The PDB reference code for this structure is 1cb6.
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  • 62
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    Notes: Cytochrome P450sca-2 from Streptomyces carbophilus catalyzes the hydroxylation of ML-236B sodium salt to pravastatin sodium, a tissue-selective inhibitor of 3-hydroxy-3-methylglutaryl-coenzymeA (HMG-CoA) reductase. HMG-CoA reductase is a key enzyme in cholesterol biosynthesis. Crystals of the protein were obtained by the vapour-diffusion method, using ammonium sulfate as a precipitant. The crystals belong to the trigonal space group P3121 (or its enantiomorph, P3221) with unit-cell dimensions a = 103.5, c = 79.8 Å. Assuming the presence of one molecule in the asymmetric unit, the calculated value of Vm is 2.68 Å3 Da−1. A native data set was collected to a resolution of 2.2 Å.
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  • 63
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    Acta crystallographica 55 (1999), S. 1212-1214 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 6-Phospho-α-glucosidase (GlvA) is the protein involved in the dissimilation of α-glycosides accumulated via a phosphoenolpyruvate-dependent maltose phosphotransferase system (PEP-PTS) in Bacillus subtilis. The purified enzyme has been crystallized in a form suitable for X-ray diffraction analysis. Thin rod-like crystals have been grown by the hanging-drop method in the presence of manganese and NAD. They diffract beyond 2.2 Å using synchrotron radiation and belong to the space group I222 (or its enantiomorph) with unit-cell dimensions a = 83.26, b = 102.56, c = 145.31 Å and contain a single molecule of GlvA in the asymmetric unit.
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  • 64
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: FixL is a transmitter protein in a two-component system which acts as an oxygen sensor when the symbiotic Rhizobia resides in root nodules of host plants. The oxygen-sensor domain of Rhizobium meliloti FixL (RmFixLH) was purified by His-tag affinity and isoelectronic focusing chromatographies, without the use of gel-filtration chromatography. Dynamic light-scattering measurements of RmFixLH thus obtained revealed it to be monodispersive and present as a homodimer in solution. A single crystal of RmFixLH in the met (Fe3+) form was grown in 100 mM acetic acid/NaOH buffer at pH 4.6 in the presence of 200 mM ammonium acetate, using 40%(w/v) PEG 4000 as a precipitant. A crystal of the ferrous CO form of RmFixLH was also prepared by reduction of the met crystal with Na2S2O4 in an atmosphere of CO. The crystals (0.2 × 0.05 × 0.01 mm) belong to the monoclinic system (C2) with unit-cell parameters a = 60.94, b = 37.44, c = 54.14 Å, β = 115.29° and diffract X-rays to 1.7 Å resolution at station BL44B2 of SPring-8, Japan. Bijvoet difference Patterson maps show a clear peak corresponding to the haem iron in RmFixLH.
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  • 65
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    Acta crystallographica 55 (1999), S. 1516-1523 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Epidoxorubicin and daunorubicin are proposed to be cytotoxic to tumor cells by catalyzing production of formaldehyde through redox cycling and using the formaldehyde for covalent attachment to DNA at G bases. The crystal structure of epidoxorubicin covalently bound to a d(CGCGCG) oligomer was determined to 1.6 Å resolution. The structure reveals slightly distorted B-form DNA bearing two molecules of epidoxorubicin symmetrically intercalated at the termini, with each covalently attached from its N3′ to N2 of a G base via a CH2 group from the formaldehyde. The structure is analogous to daunorubicin covalently bound to d(CGCGCG) determined previously, except for additional hydrogen bonding from the epimeric O4′ to O2 of a C base. The role of drug–DNA covalent bonding in cells was investigated with synthetic epidoxorubicin–formaldehyde conjugate (Epidoxoform) and synthetic daunorubicin–formaldehyde conjugate (Daunoform). Uptake and location of drug fluorophore in doxorubicin-resistant human breast-cancer cells (MCF-7/ADR cells) was observed by fluorescence microscopy and flow cytometry. The fluorophore of Daunoform appeared more rapidly in cells and was released more rapidly from cells than the fluorophore of Epidoxoform over a 3 h exposure period. The fluorophore appeared predominantly in the nucleus of cells treated with both conjugates. The difference in uptake is explained in terms of the slower rate of hydrolysis of Epidoxoform to the species reactive with DNA and a proposed slower release from DNA based upon the crystal structures.
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  • 66
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    Acta crystallographica 55 (1999), S. 1524-1532 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of human insulin mutant B9 (Ser→Glu) was determined by an X-ray crystallographic method at 2.5 Å resolution with an R factor of 0.165 under non-crystallographic restraints. The crystals were grown at low pH (〈3.8) and belong to the orthorhombic P212121 space group with unit-cell dimensions a = 44.54, b = 46.40, c = 51.85 Å and one dimer per asymmetric unit without further aggregation. The structure in this crystal form can be regarded as a model for a discrete insulin dimer and displays the following features compared with the structure of 2Zn insulin. (i) The overall dimer is expanded and more symmetric. The two A chains are about 2 Å more distant from each other, while the two B chains are about 0.8 Å further apart. Both monomers are more similar to molecule 1 than molecule 2 of the 2Zn insulin dimer. (ii) The dimer structure is stabilized by protonation and neutralization of the carboxyl groups at lower pH and, in addition, by formation of a hydrogen-bond network among the side chains of residues GluB9, HisB13 and HisB10 on the dimer-forming surface of both monomers, resulting from a structural rearrangement. (iii) The B-chain amino-terminal segment is in an open state (O state), i.e. a state different from the well known R and T states found in the insulin hexamer. In the O state, the B-chain N-terminal segment is in an extended conformation and is detached from the rest of the molecule. This conformational state has also been observed in the monomeric crystal structure of despentapeptide (B26–B30) and desheptapeptide (B24–B30) insulin, as well as in the solution structure of an engineered insulin monomer. It suggests that the O state may be the characteristic conformation of insulin in lower aggregation forms and may be relevant to the formation of insulin fibrils. In addition, based on the crystallization process, the smallest possible building blocks of insulin crystal are also discussed.
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  • 67
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    Acta crystallographica 55 (1999), S. 1533-1538 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The 2.2 Å crystalline structure of an oxidized active-site variant of Escherichia coli thioredoxin (Trx) has been solved. Trx is a 12 kDa enzyme which catalyzes the oxidation of dithiols and the reduction and isomerization of disulfides in other proteins. Its active site contains the common structural motif CXXC. Protein-disulfide isomerase (PDI), a 57 kDa homolog of Trx, contains four Trx-like domains. The three-dimensional structure of PDI is unknown. PDI-deficient Saccharomyces cerevisiae are inviable. An active-site variant of Trx which complements PDI-deficient yeast has the active-site sequence Cys32-Val33-Trp34-Cys35 (CVWC). The reduction potential of oxidized CVWC Trx (E°′ = −0.230 V) is altered significantly from that of the wild-type enzyme (E°′ = −0.270 V). However, the structure of the oxidized CVWC enzyme is almost identical to that of wild-type Trx. The addition of valine and tryptophan in the active site is likely to increase the reduction potential, largely by decreasing the pKa of the Cys32 thiol in the reduced enzyme. Unlike in wild-type Trx, significant protein–protein contacts occur in the crystal. Protein molecules related by a crystallographic twofold axis form a dimer in the crystal. The dimer forms as an extension of the twisted mixed β-sheet which composes the backbone of each Trx structure.
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  • 68
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    Acta crystallographica 55 (1999), S. 1539-1545 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.
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  • 69
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    Acta crystallographica 55 (1999), S. 1546-1554 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the homodimeric 267 kDa pyruvate:ferredoxin oxidoreductase (PFOR) of Desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. Phases were obtained from multiwavelength anomalous dispersion (MAD), solvent flattening (SF), molecular replacement (MR) using a 5 Å resolution electron-density search model, multiple isomorphous replacement (MIR) and, finally, electron-density averaging (DA) procedures. It is shown how the combination of all these techniques was used to overcome problems arising from incompleteness of MAD data and weak phasing power of MIR data. A real-space refinement (RSR) procedure is described to improve MR solutions and obtain very accurate protein envelopes and non-crystallographic symmetry (NCS) transformations from 5 Å resolution phase information. These were crucial for the phase extension to high resolution by DA methods.
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    Acta crystallographica 55 (1999), S. 1555-1567 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: With the rise of Bayesian methods in crystallography, the error estimates attached to estimated phases are becoming as important as the phase estimates themselves. Phase improvement by density modification can cause problems in this environment because the quality of the resulting phases is usually overestimated. This problem is addressed by an extension of the γ correction [Abrahams (1997). Acta Cryst. D53, 371–376] to arbitrary density-modification techniques. The degree to which the improved phases are biased by the features of the initial map is investigated in order to determine the limits of the resulting procedure and the quality of the phase-error estimates.
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  • 71
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    Acta crystallographica 55 (1999), S. 1568-1577 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new highly automated heavy-atom search procedure combines a fast Fourier transform translation function, Patterson superposition functions and Patterson correlation refinement. The search procedure can be applied to various native and difference Patterson maps and their statistically weighted averages. The procedure was tested with diffraction data for several crystal structures with up to 30 heavy-atom sites in the asymmetric unit and with minimum Bragg spacings ranging from 3 to 4 Å. In all cases, the correct sites were found with modest computing time.
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    Acta crystallographica 55 (1999), S. 927-928 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Glutamate racemase catalyzes the reversible reaction of L-glutamate to D-glutamate, an essential component of the bacterial cell wall. Glutamate racemase from Aquifex pyrophilus has been crystallized by the hanging-drop vapor-diffusion method using polyethylene glycol 6000 as a precipitant. The crystals belong to space group P6122 or P6522 with unit-cell parameters a = b = 72.1, c = 185.02 Å. The asymmetric unit contains one molecule, corresponding to a Vm value of 2.35 Å3 Da−1. Complete data sets from a native and a mercury-derivative crystal have been collected at 2.0 and 2.3 Å resolution, respectively, using a synchrotron-radiation source.
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    Acta crystallographica 55 (1999), S. 929-930 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recombinant β-1,4-galactanase from Aspergillus aculeatus has been crystallized and characterized by X-ray diffraction. Crystals were obtained in hanging drops by vapour-diffusion under the conditions 30% PEG 400, 0.2 M CaCl2 and 0.1 M Na HEPES buffered to pH 7.5. The crystals diffract to 2.3 Å resolution and belong to one of the orthorhombic space groups I222 or I212121. The unit-cell dimensions are a = 60.42, b = 88.94 and c = 129.08 Å. With one molecule in the asymmetric unit, the corresponding solvent content is ∼48%.
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    Acta crystallographica 55 (1999), S. 921-924 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The arsenical resistance (ars) operon of the Escherichia coli plasmid R773 encodes a system for the active extrusion from cells of the toxic oxyanions arsenite (AsIIIO_{2}^{-}) and antimonite (SbIIIO_{2}^{-}) via an ATP-driven pump. The arsA and arsB genes of the operon encode the catalytic subunit (ATPase) and the membrane subunit of the pump, respectively. The arsC gene codes for a reductase that converts arsenate (AsVO_{4}^{3-}) to arsenite, thus extending bacterial resistance to the pentavalent state of arsenic. Crystals diffracting beyond 2.0 Å were obtained for the catalytic subunit of the pump (ArsA). These crystals belong to space group I222, with unit-cell parameters a ∼ 73, b ∼ 76, c ∼ 223 Å. A single molecule of ArsA, composed of two homologous halves, occupies the asymmetric unit of the I222 crystals with a predicted solvent content of 46%. Self-rotation function analysis suggests, however, that ArsA adopts a molecular packing corresponding to point group 422. One possible explanation of this result is that the two homologous halves of ArsA are related by a twofold axis of local symmetry and that the two halves of a `pseudo'-tetramer are related by a crystallographic twofold axis.
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  • 75
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    Acta crystallographica 55 (1999), S. 1459-1461 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Human rhinoviruses, the major cause of mild recurrent infections of the upper respiratory tract, are small icosahedral particles. Over 100 different serotypes have been identified. The majority (91 serotypes) use intercellular adhesion molecule 1 as the cell-attachment site; ten serotypes (the minor group) bind to members of the low-density lipoprotein receptor. Three different crystal forms of the minor-group human rhinovirus serotype 2 (HRV2) were obtained by the hanging-drop vapour-diffusion technique using ammonium sulfate and sodium/potassium phosphate as precipitants. Monoclinic crystals, space group P21, diffracted at least to 2.8 Å resolution, and two complete virus particles were located in the crystal asymmetric unit. A second type of crystals had a compact cubic like morphology and diffracted beyond 2.5 Å resolution. These crystals belong to a primitive orthorhombic space group, with unit-cell parameters a = 309.3, b = 353.5, c = 759.6 Å, and contain one virus particle in the asymmetric unit. A third type of crystals, with a prismatic shape and belonging to space group I222, was also obtained under similar crystallization conditions. These latter crystals, with unit-cell parameters a = 308.7, b = 352.2, c = 380.5 Å, diffracted to high resolution (beyond 1.8 Å) and contained 15 protomers per asymmetric unit; this requires that three perpendicular crystal twofold axes coincide with three of the viral particle's dyad axes.
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  • 76
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    Acta crystallographica 55 (1999), S. 1462-1464 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The oxidized form of purple acid phosphatase from pig allantoic fluid has been crystallized in the presence of phosphate using the hanging-drop technique. The crystals belong to the space group P212121 and have unit-cell parameters a = 66.8, b = 70.3, c = 78.7 Å. Diffraction data collected from a cryocooled crystal using a conventional X-ray source extend to 1.55 Å resolution. A knowledge of the three-dimensional structure of mammalian purple acid phosphatase will aid in understanding the substrate specificity of the enzyme and will be important in the rational design of inhibitors, with potential in the treatment of bone diseases.
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  • 77
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of rubredoxin oxygen oxidoreductase have been obtained and characterized. They belong to space group P21212, with unit-cell dimensions a = 88.24 (15), b = 101.25 (7), c = 90.80 (3) Å. The homodimer (86 kDa) in the asymmetric unit is related by a non-crystallographic twofold rotation axis parallel to the ab `diagonal' direction, as shown by the self-rotation maximum in the section with χ = 180°. This pseudo-crystallographic symmetry element was also found to be the twinning axis of pseudo-merohedrally twinned crystals, leading to apparent pseudo-tetragonal P4212 crystal symmetry.
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  • 78
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    Acta crystallographica 55 (1999), S. 1468-1470 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Applaggin (Agkistrodon piscivorus piscivorus platelet-aggregation inhibitor) is a potent inhibitor of blood platelet aggregation derived from the venom of the North American water moccasin. The protein consists of 71 amino acids, is rich in cysteines, contains the sequence-recognition site of adhesion proteins at positions 50–52 (Arg-Gly-Asp) and shares high sequence homology with other snake-venom disintegrins such as echistatin, kistrin and trigramin. Single crystals of applaggin have been grown and X-ray diffraction data have been collected to a resolution of 3.2 Å. The crystals belong to space group P41212 (or its enantiomorph), with unit-cell dimensions a = b = 63.35, c = 74.18 Å and two molecules per asymmetric unit. Molecular replacement using models constructed from the NMR structures of echistatin and kistrin has not been successful in producing a trial structure for applaggin.
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  • 79
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    Acta crystallographica 55 (1999), S. 1471-1473 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The rhdA gene identified in Azotobacter vinelandii codes for a protein, RhdA, which displays rhodanese (thiosulfate–cyanide sulfurtransferase) activity. RhdA was overexpressed and purified to homogeneity. The protein crystallized in the orthorhombic space group P21212 with unit-cell parameters a = 44.4, b = 150.8, c = 53.8 Å; on a synchrotron source the diffraction patterns could be collected to a resolution limit of 1.8 Å. Evaluation of the crystal density indicates that the crystal lattice accommodates one molecule per asymmetric unit and that the solvent content is 59% of the total volume.
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  • 80
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    Acta crystallographica 55 (1999), S. 1474-1477 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Tyrosine aminotransferase catalyzes transamination for both dicarboxylic and aromatic amino-acid substrates. The substrate-free Escherichia coli tyrosine aminotransferase (eTAT) bound with the cofactor pyridoxal 5′-phosphate (PLP) was crystallized in the trigonal space group P32. A low-resolution crystal structure of eTAT was determined by molecular-replacement methods. The overall folding of eTAT resembles that of the aspartate aminotransferases, with the two identical subunits forming a dimer in which each monomer binds a PLP molecule via a covalent bond linked to the ε-NH2 group of Lys258. Comparison of the structure of eTAT with those of the open, half-open or closed form of chicken or E. coli aspartate aminotransferases shows the eTAT structure to be in the open conformation.
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  • 81
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    Acta crystallographica 55 (1999), S. 1478-1480 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Sterol carrier protein 2 (SCP2) is a basic intracellular protein which facilitates the in vitro intermembrane transfer of cholesterol, phospholipids and glycolipids. SCP2 was expressed in Escherichia coli, purified to apparent electrophoretic homogeneity and crystallized. Single crystals were obtained by hanging-drop vapour diffusion using ammonium sulfate as precipitant. These crystals belong to space group P41212 or its enantiomorph, with unit-cell parameters a = b = 57.5, c = 86.5 Å, and have one molecule in the crystallographic asymmetric unit. Intensity data to 1.8 Å resolution were collected from native SCP2 crystals using synchrotron radiation, were processed and scaled with an Rlinear = 4.9%.
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  • 82
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    Acta crystallographica 55 (1999), S. 1481-1483 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A recombinant form of Enterococcus facieum BM4147 D-alanine-D-lactate ligase (VanA) has been prepared and crystallized. VanA was found to crystallize only in the presence of a phosphinate inhibitor analogue of D-alanine-D-alanine. The crystals grow in 40–45% ammonium sulfate, 0.1 M 3-(N-morpholino)-propanesulfonic acid pH 6.0 and reach dimensions of 0.4 × 0.2 × 0.1 mm. The crystals diffract to at least 2.5 Å and are in the centred orthorhombic space group C2221, with unit-cell dimensions a = 123.2, b = 225.4, c = 72.4 Å.
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  • 83
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    Acta crystallographica 55 (1999), S. 1484-1486 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The absolute requirement of Ca2+ for proteolytic activity is a feature unique to the calpains, a family of heterodimeric cysteine proteases. Conditions are described which give rise to diffraction-quality crystals of m-calpain in two crystal forms, P1 and P21. Data have been collected from native crystals of m-calpain in both P1 and P21 forms, to 2.6 and 2.15 Å, respectively. Selenomethionine-containing crystals have been grown in both forms, and anomalous data from the P21 selenomethionine enzyme provided the location of 17 of the 19 Se atoms in the protein.
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  • 84
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    Acta crystallographica 55 (1999), S. 1231-1233 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Haloalkane hydrolytic dehalogenase LinB from Sphingomonas paucimobilis UT26, an enzyme which releases chloride or bromide anion from n-halogenated alkanes and has a broad range of substrate specificity, was crystallized using the hanging-drop vapour-diffusion method at 278 K. The best crystals were obtained by microseeding with a precipitant containing 18–20%(w/v) PEG 6000, 0.2 M calcium acetate and 0.1 M Tris–HCl pH 8.9. The crystals diffract to at least 1.60 Å using synchrotron X-ray under cryogenic (100 K) conditions. They belong to the orthorhombic space group P21212 with unit-cell parameters a = 50.29, b = 71.70, c = 72.73 Å. The asymmetric unit contains one molecule of the enzyme.
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  • 85
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    Acta crystallographica 55 (1999), S. 1491-1494 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: To prevent crystals from moving in orbit and sedimenting upon their return to earth, the model protein thaumatin was crystallized in agarose gel in the Advanced Protein Crystallization Facility during the eight-day Space Shuttle mission STS-95 (November 1998). The quality of tetragonal crystals grown in microgravity was compared with that of controls prepared in parallel in the laboratory. On the basis of their diffraction properties, microgravity crystals were more ordered than crystals grown in gel on earth (the latter being, on average, better than reference crystals obtained in solution on earth). It is concluded that protein crystallization within a gel in microgravity may yield crystals of superior quality by combining the advantages of both environments. A possible explanation for the positive effect of microgravity on protein crystallization in gels involving the better quality of the nucleus is discussed.
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  • 86
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    Acta crystallographica 55 (1999), S. 1237-1239 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Botulinum neurotoxin (BoNT) is one of the most potent toxins known. BoNT is also a food poison, which means that the toxin must survive the protease action and acidity of the gut. A group of neurotoxin-associated proteins which are only beginning to be identified and characterized are believed to be responsible for this protection. Hn-33 is a 33 kDa polypeptide which is a major component of the type A botulinum neurotoxin complex. Crystals of Hn-33 have been grown by vapour-diffusion techniques. They belong to a primitive orthorhombic space group and diffract to a resolution of 2.6 Å, with unit-cell parameters a = 130.3, b = 122.2, c = 37.2 Å.
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  • 87
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    Acta crystallographica 55 (1999), S. 1242-1243 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Metallothionein II (Mw = 6.8 kDa), induced by cadmium and purified from rabbit liver, has been crystallized in space group P6222 or P6422. The unit-cell parameters were a = b = 113.4, c = 219.1 Å, α = β = 90.0, γ = 120.0° when crystallized from sodium citrate buffer and a = b = 113.4, c = 219.6 Å, α = β = 90.0, γ = 120.0° when crystallized from Tris–HCl buffer. There are 12 molecules per asymmetric unit and the solvent content is about 57%.
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  • 88
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    Acta crystallographica 55 (1999), S. 1247-1249 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The effect of fractal surfaces on protein crystallization has been investigated. A super-water-repellent fractal surface consisting of alkylketene dimers was formed on microscope cover slips. Crystallization experiments with hen egg-white lysozyme using the sitting-drop vapour-diffusion method have been undertaken on the fractal and conventionally siliconized surfaces. The size of the crystals obtained on the fractal surface is significantly larger than on the conventionally siliconized surface. The number of crystals on the fractal surface is markedly smaller than on the conventionally siliconized surface. The results clearly indicate that the fractal surface is very effective and promising in the crystallization of macromolecules using the sitting-drop vapour-diffusion method.
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  • 89
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    Acta crystallographica 55 (1999), S. 1251-1256 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the purple membrane of Halobacterium salinarium, bacteriorhodopsin trimers are arranged in a hexagonal lattice. When purple membrane sheets are incubated at high temperature with neutral detergent, membrane vesicularization takes place, yielding inside-out vesicles with a diameter of 50 nm. The vesicular structure becomes unstable at low temperature, where successive fusion of the vesicles yields a crystal which is composed of stacked planar membranes. X-ray crystallographic analysis reveals that the bacteriorhodopsin trimers are arranged in a honeycomb lattice in each membrane layer and that neighbouring membranes orient in opposite directions. The native structure of the trimeric unit is preserved in the honeycomb lattice, irrespective of alterations in the in-plane orientation of the trimer. One phospholipid tightly bound to a crevice between monomers in the trimeric unit is suggested to act as a glue in the formation of the trimer.
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  • 90
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    Acta crystallographica 55 (1999), S. 1273-1290 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 Å resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conventional R factor of 10.51% for all reflections in the 15–1.15 Å resolution range. The estimated r.m.s. errors of the model are 0.026 and 0.038 Å for protein atoms and all atoms, respectively. The structure comprises all 310 amino acids, with 28 side chains and two peptide bonds in multiple conformations, two covalently linked Pb atoms, 601 water molecules, seven glycerol molecules, one sulfate ion and two chloride ions. Water molecules accounting for alternative solvent structure are modelled with a fixed occupancy of 0.5. The structure is described in detail and compared with previously reported dehalogenase structures refined at 1.9–2.3 Å resolution. An analysis of the protein's geometry and stereochemistry reveals eight mean values of bond lengths and angles which deviate significantly from the Engh & Huber parameters, a wide spread in the main-chain ω torsion angle around its ideal value of 180 (6)° and a role for C—H\cdotsO interactions in satisfying the hydrogen-bond acceptor capacity of main-chain carbonyl O atoms in the central β-sheet.
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  • 91
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    Acta crystallographica 55 (1999), S. 1291-1300 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The three-dimensional structures of the deoxy- and carbonmonoxyhaemoglobin (Hb) from Dasyatis akajei, a stingray, have been determined at 1.6 and 1.9 Å resolution, respectively. This is one of the most distantly related vertebrate Hbs to human HbA. Both structures resemble the respective forms of HbA, indicating that the α2β2-type tetramer and the mode of the quaternary structure change are common to Hbs of jawed vertebrates. Larger deviations between D. akajei Hb and human HbA are observed in various parts of the molecule, even in the E and F helices. Significant mutations and/or conformational changes are also observed around the haems, in the C-terminal region of the β subunit, in the α1β2 interface and in the organic phosphate-binding site of HbA. Despite these structural differences, the oxygen affinity, haem–haem interaction, Bohr effect and organic phosphate effect of D. akajei Hb are all only moderately reduced. Compared with human HbA, the overall r.m.s. deviation of main-chain atoms in the helical regions of bony fish Hbs is smaller than that of D. akajei Hb.
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  • 92
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    Acta crystallographica 55 (1999), S. 1309-1319 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Three investigators, with varying levels of experience, independently built and refined the structure of Escherichia coli ribokinase at 2.6 Å resolution. At the end of the refinement/rebuilding processes the models had essentially converged, although each had its own particular pattern of remaining errors. The subsequent refinement of the same structure at 1.8 Å resolution allowed an overall quality check of each of the lower resolution models, and an analysis of which graphics-based tools were generally most efficient in locating these errors. Criteria which are useful in the application of Ramachandran, main-chain and side-chain database and real-space fit analyses are presented.
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  • 93
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    Acta crystallographica 55 (1999), S. 1340-1341 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A monoclinic crystal form of a recombinant major urinary protein, (MUP) from mouse, has been obtained. MUP is a member of the lipocalin family whose biological function relates to olfaction and sexual communication. Crystals were grown by the vapour-diffusion technique against a mother liquor containing CdCl2. Crystals belong to the monoclinic space group P21 with the cell parameters a = 37.14, b = 55.79, c = 37.67 Å, and β = 93.24°. The crystals diffract to beyond 1.4 Å resolution at a synchrotron beamline.
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  • 94
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    Acta crystallographica 55 (1999), S. 1345-1347 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The R2 subdomain of the mouse c-Myb DNA-binding domain and its V103L mutant have been crystallized by the vapour-diffusion method using highly concentrated sodium citrate at pH 6.8 as a precipitant. Using ammonium sulfate as precipitant in MES buffer only produced crystals for the mutant R2. All crystals are isomorphous and belong to space group P212121. The unit-cell dimensions for wild-type R2 crystals grown from sodium citrate precipitant are a = 28.83, b = 40.18, c = 49.23 Å. Crystals contain one R2 molecule per asymmetric unit. They are stable during 3 d exposure to X-rays and diffract to 1.37–1.45 Å resolution.
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  • 95
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    Notes: EST2, a thermophilic carboxylesterase from Alicyclobacillus acidocaldarius, belonging to the HSL group of the esterase/lipase superfamily, has been crystallized for the first time. Ammonium sulfate was used as a precipitant and the crystallization proceeded at pH 7.8. The crystals belong to space group P41212 or its enantiomorph P43212, with unit-cell parameters a = b = 78.8, c = 106.4 Å. A complete data set has been collected at the synchrotron source Elettra in Trieste to 2.4 Å resolution, using a single frozen crystal.
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  • 96
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    Notes: The gene for Escherichia coli N-acetyl-L-glutamate kinase (NAGK) was cloned in a plasmid and expressed in E. coli, allowing enzyme purification in three steps. NAGK exhibits high specific activity (1.1 µmol s−1 mg−1), lacks Met1 and forms dimers (shown by cross-linking). Crystals of unliganded NAGK diffract to 2 Å and belong to space group P6122 or its enantiomorph P6522 (unit-cell parameters a = b = 78.6, c = 278.0 Å) with two monomers in the asymmetric unit. Crystals of NAGK with acetylglutamate and the ATP analogue AMPPNP diffract to 1.8 Å and belong to space group C2221 (unit-cell parameters a = 60.0, b = 71.9, c = 107.4 Å), with one monomer in the asymmetric unit. NAGK crystallization will allow the determination of proposed structural similarities to carbamate kinase.
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  • 97
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    Acta crystallographica 55 (1999), S. 1356-1358 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of the molbindin ModG (subunit Mr = 14359 Da), a cytoplasmic molybdate-binding protein from Azotobacter vinelandii, were grown by vapour diffusion. Both apo and tungstate-bound forms were crystallized and X-ray data were collected at 100 K. Apo-ModG crystallizes in space group P6322, with unit-cell dimensions a = b = 90.62, c = 79.46 Å. Native data to a resolution of 2.5 Å were collected from a single crystal, which showed a marked improvement in diffraction quality after annealing. Data from a single-site gold derivative were also collected at 2.7 Å resolution. Crystals of the ligand-bound form of ModG belong to space group P321, with unit-cell parameters a = b = 50.57, c = 79.29 Å. X-ray data to a resolution of 2.0 Å were collected.
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  • 98
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    Acta crystallographica 55 (1999), S. 1359-1361 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Endo-polygalacturonases catalyze the fragmentation and solubilization of the homogalacturonan of the plant cell wall. These enzymes are extracellularly targeted glycoproteins produced by a number of organisms such as fungi, bacteria and plants, and are involved in both pathological and physiological processes. Single crystals of the endo-polygalacturonase from the phytopathogenic fungus Fusarium moniliforme were obtained by the vapour-diffusion method at 294 K. The starting material as well as the crystal consist of three forms with different degrees of glycosylation. The crystals belong to the orthorhombic space group P212121 and diffract to 1.9 Å resolution on a synchrotron-radiation source under cryocooling conditions.
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  • 99
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    Acta crystallographica 55 (1999), S. 1362-1364 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The proteolytically defined Z-DNA binding domain Za of human adenosine deaminase type 1 (hADAR1) has been crystallized in complex with the DNA oligomer d(TCGCGCG). The crystals were obtained from a solution containing ammonium sulfate as precipitating agent and belong to the tetragonal space group P4212. A complete diffraction data set has been collected to a resolution of 2.4 Å. The unit-cell dimensions are a = b = 85.9, c = 71.3 Å. A Raman spectrum of the complex indicates that the DNA in the complex adopts the left-handed Z conformation.
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    Acta crystallographica 55 (1999), S. 1606-1607 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26, one of the Z-prenyl chain-elongating enzymes, was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate and lithium sulfate as precipitants. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 127.2, b = 60.2, c = 75.7 Å, β = 105.6°. The crystals diffract X-rays to at least 2.2 Å resolution using synchrotron radiation and are suitable for high-resolution crystal structure analysis.
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