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January 1996 issue
Cover illustration: NMR solution structure of an Antennapedia homeodomain complex with a 14-base pair operator DNA duplex. The dotted surface outlines a hydrated cavity in the protein-DNA interface.
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research papers
This paper reports the first structure determination of a family 45 glycosyl hydrolase. This made use of optimized wavelength data collection and anisotropic modelling of the atomic displacement parameters.
PDB reference: 2eng
At 125 K, the crystal structure of BPTI is much less disordered than at room temperature. In particular, the previously badly disordered C terminus and several side chains are completely resolved.
PDB reference: 1bpi
The structure of bovine mitochondrial F1 ATPase (372 kDa) was solved to 2.8 Å resolution using only one derivative compound. The structure solution depended on careful data collection and processing in conjunction with `solvent flipping'.
Current phase-combination procedures are applied inappropriately in many density-modification calculations. Some of the problems are investigated.
A multi-dimensional histogram is proposed as a generalized representation of stereochemical information characterizing the shape of a macromolecular electron-density distribution. One dimension, the magnitude of the electron-density gradient, has a significantly enhanced sensitivity to phase errors.
The construction of an X-PLOR dictionary for nucleic acids is described. The results of refinement trials with this dictionary are presented.
The cytochrome b5 structure has been refined at high resolution using the programs PROFFT and X-PLOR. The latter refinement allowed identification of and additional three residues and refinement of alternate side-chain conformations.
The three-dimensional structure of flavoprotein FP390 from a luminescent bacterium, Photobacterium phosphoreum, was refined to an R factor of 24.0% at 2.7 Å resolution.
Comparison of fasciculin 1 and 2, potent acetylcholine inhibitors from green mamba snake venom, show unusual flexibility in one of the loops.
PDB reference: 1fsc
The refined X-ray structure of this signal-transduction protein is presented along with a discussion of structural implications for function and a comparison with other proteins.
PDB reference: 2pii
Bulgecin, a bacterial metabolite, binds in the same way to the g-type lysozyme from the Australian black swan as to the c-type lysozyme from the rainbow trout and the C-terminal domain of a soluble lytic transglycosylase from E. coli.
PDB reference: 1lsp
Structure of a complex between bulgecin, a bacterial metabolite, and lysozyme from the rainbow trout
The crystal structure of a complex between lysozyme from the rainbow trout and bulgecin shows that the NAG moiety is bound in site C and the proline residue is seen in site D.
An internal reprieve tolerance mechanism had been postulated through the studies of flexible-loop-deleted IPMDH.
PDB reference: 1idm
A real-space procedure has been used in the refinement of the canine parvovirus structure. The method is particularly fast and convenient when only a small fraction of the crystallographic asymmetic unit needs to be refined, as is the case when there is high non-crystallographic redundancy.
The concanavalin A complex with this sugar is a classical tetamer of protein subunits of total MW 100 kDa. The correct space group was finally established as I213 by MIR. Calculations performed initially in the related, but incorrect, space group I23, and by molecular replacement, proved to be instructive.
Crystals of apocrustacyanin C1 grown under microgravity on the IML-2 NASA space shuttle mission are compared with earth-grown crystals in ground controls and in the laboratory.
The structure of tetragonal crystal form of RNaseB complexed with d(pA)4 has been solved. The structure shows the binding of nucleic acid at the active site and suggests the mode of binding for an extende polynucleotide chain.
PDB reference: 1fvp
As compared to the previously reported structures, the main differences concern the conformation of the N-terminal residues and the packing in the unit cell.
PDB reference: 1pvb
The low-pH form of monoclinic hen egg-white lysozyme has been refined at 1.8 Å resolution. Polymorphous crystal forms of hen egg-white lysozyme display lattice contacts at the variable regions.
PDB reference: 5lym
Xenopus laevis Cu,Zn superoxide dismutase (isoenzyme b) was determined at 1.49 Å resolution and refined to an R factor of 0.104. The higher thermal stability of the bb X. laevis SOD dimer with respect to the aa hormodimer can be explained by structural analysis which reveals a number of conserved water-molecule sites in the two subunits and in homologous SOD models.
PDB reference: 1xso
short communications
Crystals of a bacterial glutathione 5-transferase from Proteus mirabilis have been grown and they have been characterized by collecting X-ray data to 2.7 Å resoution
Recombinant transaldolase from Eschericha coli has been crystallized. The crystals are orthorhombic space group P212121 with cell dimensions a = 68.9, b = 91.3 and c = 130.5 Å and diffract to 2 Å resolution.
DMSO reductase from Rhodobacter capsulatus has been crystallized in two forms suitable for structural analysis. This is the simplest model to study this class of Mo-pterin enzyme.
β phenylethylamine oxidase. a copper amine oxidase from Arthrobacter globoformis has been crystallized in two monoclinic forms and an orthorhombic form
A new crystal form of cytochrome c' from Rhodobacter capsulatus was obtained with unit-cell dimensions a = 47.82, b = 72.59, c = 34.22 Å. the space group being P212121
Haemorrhagin I from the snake venom of Agkistrodon acutus been crystallized. Its space group is P41212 or P43212 with dimensions a = b = 63.61 and c = 95.69 Å
Crystallization of a 14-3-3 protein and characterization of crystals obtained
Crystals of an FKBPl2/13 chimeric protein complexed to the immunosuppressive agent FK506 grew as twinned crystals in space group P1. Data were collected with synchrotron radiation at CHESS molecular-replacement solution reveals the structural basis for twinning.
Crystals diffracting to 2.7 Å resolution of E. coli aspartyl-tRNA synthetase and of its non-efficient complex with the cognate tRNA from yeast have been obtained.
Crystals of 7-α-hydroxysteroid dehydrogenase from E. coli belong to one of the enantiomorphic space groups P41212 or P43212 with cell dimensions a = b = 81.66 and c = 214.6 Å and diffract to at least 2.3 Å resolution.
The iron-dependent alcohol dehydrogenase from Zymomonas mobilis has been crystallized in a form suitable for X-ray, analysis. The Fe atom has been substituted by cobalt.
Crystals diffracting to high resolution have been obtained of 3-carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa. Cryo-cooling and cross-linking with glutaraldehyde extend the life time of the crystals in the X-ray beam.
Microsomal triglyceride transfer protein from bovine liver has been crystallized in space group P212122 (a = 88.7. b = 100.9, c = 201.1 Å) using polyethylene glycol as a precipitant at pH 7.0
Recombinant T4 deoxynucleotide kinase has been crystallized in space group C2 with two molecules in the asymmetric unit. Diffraction data to 2.0 Å resolution have been collected.
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A report is given of the meeting entitled Integrated procedures for recording and validating results of 3-D structural studies of biological macromolecules held in York, April 1995.
