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September 1995 issue
Cover illustration: Active site of purine nucleoside phosphorylase with the electrostatic potential surface and dipole of guanine. Rendered with Ribbons++ and SPARTAN.
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The advantages of difference refinement of a macromolecular structure in the case where a closely related structure had previously been determined are discussed.
The three-dimensional structure of a mutant human lysozyme, C77A-a, in which the residue Cys77 is replaced by alanine, has been refined to an R value of 0.125 using 8230 reflections in the resolution range 10.0-1.8 Å.
PDB reference: 1hnl
Under suitable conditions direct methods can be applied successfully to solve proteins with more than 800 independent atoms in the asymmetric unit.
The structure of the diferric form of the human iron-binding protein lactoferrin has been refined by restrained least-squares methods, using synchrotron data to 2.2 Å resolution.
PDB reference: 1lfg
The X-ray structure of a monomeric hemichrome hemoglobin is described. Hemichromes are low-spin ferrihemoglobins which have the sixth iron coordination site filled with a nitrogenous base, usually the imidazole of the distal histidine.
PDB reference: 1hlb
The structure provides direct evidence for the mode of thiocyanate binding to arginine residues and suggests a possible mechanism for the efficiency of thiocyanate in crystallizing basic proteins.
PDB reference: 1tew
Unrestrained full-matrix refinement of the small protein crambin reveals some differences from restrained refinement and gives an estimate of error from structure-factor data.
TEM1 β-lactamase structure solved by molecular replacement and refined structure of the S235A mutant
Limitation of the molecular-replacement methodology was tested in the case of enzymes that exhibit a wide variety of amino-acid sequences. A new class A β-lactamase as well as one active-site mutant have been solved.
A simple method has been developed for the ab initio calculation of low-resolution solvent envelopes for macromolecular structures. The derived phases can be used to generate low-resolution electron-density molecular envelopes.
The structures of two low-humidity crystal forms of rihonulease A have been determined at high resolution. When compared with other relevant forms, they provide information on the mobility of the enayme, the invariant features in its hydration shell and the possible relation between dehydration and enzyme action.
The crystal structure of azurin mutant nickel-Trp48Met from P. aeruginosa has been solved to a final crystallographic R value of 17.0% to 2.2 Å resolution. The mutation was performed at residue Trp48 to investigate its suggested role in the long-range electron-transfer pathway.
PDB reference: 1nzr
Crystal structure of turkey egg lysozyme complex with di-N-acetylchitobiose demonstrated that the sugar was bound in a manner not assumed in the catalytic reaction.
PDB reference: 1lzy
The structure of anionic salmon trypsin in a second crystal form has been refined at 1.83 Å. The structure agrees with that of the first form, but a sulfate ion and a second benzamidine molecule, not present in the former, have been located in the latter in well defined density.
PDB reference: 1bit
A practical method for bioincorporation of tellurornethionine into proteins is described. Unexpected selectivity of the process is discussed.
The direct rotation function includes all self-Patterson vectors of the search model. It produces a better signal-to-noise ratio than the other rotation functions for two difficult molecular replacement test cases.
Electron-density averaging. fast Fourier synthesis and fast Fourier atialysis programs have been adapted for parallel-compuflng systems. These have been linked to perform iterative phase improvement and extension utilizing non-crystallographic symmetry and solvent flattening.
The structure of liganded dimeric hemoglobin from a sea cucumber has close heme-heme contacts similar to those observed for clam hemoglobin.
PDB reference: 1hlm
The X-ray structure of bovine ribonuclase A cocrystallized with the dinucleotide deoxycytidylyl-3',5 -guanosine has been determined at 1.9 Å resolution and refined by restrained least squares to R = 0.218 for 7807 reflections. The structure established that the recently observed retrobound mode of attachment of substeate analogues cytidylyl-2'-5'-guanosine and deoxycytidylyl-3'~5'-guanosine found in soaked RNase A crystals is also present in the cocrystallized complex.
PDB reference: 1rca
Concentrations of polyethylene glycol 8000 that are equivalent with respect to the vapor pressure of water were measured for salts at known concentrations. The results have practical consequences when PEG is used as a crystallizing agent in vapor-diffusion experiments.
In vapor-diffusion experiments employing polyethylene glycol as the sole crystallizing agent, droplets may be quite slow to equilibrate with their reservoirs. The addition of modest amounts of salts to both droplet and reservoir can greatly speed the equilibration process.
The rate of water equilibration in a sitting-drop vapor-diffusion experiment is sensitive to the residual pressure of air in the vapor space suggesting that transit of water across the vapor space is the rate-limiting step in vapor-diffusion crystallizations.
The coat protein subunits of Pf1 Inovirus are gently curved α-helices held close together in the virion by a polar interactions.
PDB reference: 4ifm
Active-site metal-substituted alcohol dehydrogenase (LADH) is frequently used in functional studies of this enzyme. Insertion of CuII ion gives a blue protein with spectroscopic properties siinilar to cupredoxins. Copper in the ternary LADH-NADH-DMSO complex has a trigonal geometry with CuII almost in the NS2-liganded plane and DMSO about 3.2 Å from the metal.
PDB reference: 2oxi
Mercury derivatives of a cysteine mutant of Dictyostelium nucleoside diphosphate kinase and of lobster enolase were used for data collection at wavelengths below the Hg LIII absorption edge. SIRAS phases yielded electron-density maps that were interpretable after solvent flattening.
PDB reference: 1npk
This publication introduces a method for deconvoluting twinned data in cases of hemihedry if a Patterson-search solution or other kind of phases are available.
PDB reference: 1pyt
short communications
The extracellular form of glutathione peroxidase from human plasma has been crystallized. The preliminary X-ray diffraction analysis shows the possible (222) symmetry for the tetramers of this enzyme.
Carbamoyl phosphate synthetase from E. coli has been crystallized at pH 8 in the presence of L-omithine, MnCl2 and ADP using PEG 8000 in combination with NEt4Cl and KCl.
Crystals have been grown of the NAD+-linked glycerol dehydrogenase from B. stearothermophilus. Analysis of these crystals will provide a structural framework for the class of polyol dehydrogenases to which this enzyme belongs.
Crystallization experiments with E. coli class II aldolase have produced new orthorhombic and monoclinic forms to assist structure solution.
A glutamic acid-specific proteinase from Bacillus licheniformis has been crystallized as a complex with the inhibitor Z-Leu-Glu-CH2Cl.
The NADP-linked glutamate dehydrogenase from Neurospora crassa has been crystallized and a full structure determination will lead to an understanding of the molecular basis of inter-allelic complementation observed with hybrid hexamers of naturally occuring mutants.
Crystals of arginase from an extreme thermophile, Bacillus caldevelox, have been prepared tn a form suitable for high-resolution structure determination by X-ray crystallography.
Chleroperoxidase. the most diverse of the known heme enzyme catalysts, has been crystallized in two space groups, both of which are suitable for high-resolution X-ray studies. Heavy-atom derivatives have been obtained and the active site located in the initial electron-density map.
Crystallization and light-scattering studies have shown that the enzyme imidazoleglycerol phosphate dehydratase undergoes a manganese-dependent assembly to a particle whose quaternary structure is a 24-mer based on 432 symmetry.
Crystallization and preliminary X-ray analysis of maize ZBPl4 protein. a member of a new family of zinc-binding proteins.
A series of novel aromatic inhibitors were designed based on crystal structure of influenza virus neuraminadase. These inhibitors can potentially be orally active anti-influenza drugs.
A simple modification to a standard translation function can reduce systematic error for partial search model cases.
PDB reference: 1trr
Chitosanase from Bacillus circulans MH-K I was crystallized using ammonium sulfate as a precipitant. The orthorhombic crystals diffract X-rays at least 2.3 Å resolution and are suitable for high-resolution structure analysis.
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