3-Carb­oxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenome­thionines

The structure determination of 3-carboxy-cis,cis-muconate lactonizing enzyme from N. crassa by MAD at 3.0 Å is described and some of the difficulties in the structure determination and the methods used to address them are discussed. This represents one of the largest selenium substructures (80 Se atoms) solved.

Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility

A new structure of concanavalin A, in a dimeric crystal form, has been refined using effective model-bias removal methods. The structure provides an opportunity to examine model accuracy and coordinate precision in high- or atomic resolution protein structures.

The structure of substrate-free microbial ribonuclease binase and of its complexes with 3′GMP and sulfate ions

The structure of binase, a member of the guanyl-specific microbial ribonuclease family of proteins, has been solved as a free enzyme at 1.65 Å resolution. This structure is compared with the binase complexes with 3′GMP and sulfate ions determined with data extending to 2.0 Å resolution.

Thaumatin crystallization aboard the International Space Station using liquid–liquid diffusion in the Enhanced Gaseous Nitrogen Dewar (EGN)

The first biological crystal-growth experiment on the International Space Station used the Enhanced Gaseous Nitrogen Dewar and produced thaumatin crystals diffracting to 1.28 Å, which is comparable to previous space-grown thaumatin crystals and better than the best ground-control crystal (1.47 Å).

Simulated-annealing real-space refinement as a tool in model building

Real-space simulated-annealing refinement is implemented within an interactive molecular graphics package. This accelerates the rate-limiting step of model building and improves the starting point and final quality of subsequent conventional refinement.

Conformations of amino acids in proteins

Ramachandran plots for all 20 amino acids were produced from 1042 protein subunits from the PDB, separately for those in SHEET, HELIX and Random coil. The classical Ramachandran plot needs to be revised in every detail. Most amino acids have two distinct conformations in the β-sheet region – one more frequent when the amino acids are really parts of SHEET and the other more typical for those occurring in Random coil. Amino acids in parallel and antiparallel β-strands have nearly the same conformations.

The mechanism of iron uptake by transferrins: the X-ray structures of the 18 kDa NII domain fragment of duck ovotransferrin and its nitrilotri­acetate complex

The crystal structures of the 18 kDa NII-domain fragment of duck ovotransferrin and its complex with nitrilotriacetate are reported at resolutions of 1.95 and 1.90 Å, respectively. The implication of these structures with respect to the mechanism of iron binding by the transferrins is discussed.

Detection and characterization of merohedral twinning in two protein crystals: bacteriorhodopsin and p67^phox

A combination of various approaches was used to determine precise twinning ratios. The importance of second-, third-, and fourth-order moments is discussed.

Rearrangement of Cruickshank's formulae for the diffraction-component precision index

Formulae for the diffraction-component precision index are rearranged for easy calculation and to show how precision varies with such quantities as resolution and completeness of observation.

Comparison of different crystal forms of 3-de­hydroquinase from Salmonella typhi and its implication for the enzyme activity

Crystal structures of two new crystal forms of the type I 3-dehydroquinate dehydratase (DHQase) have been determined and analysed.

FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments

FIP is a French CRG beamline at the European Synchrotron Radiation Facility (ESRF) dedicated exclusively to crystallography of biological macromolecules, with a special emphasis on automated multiwavelength anomalous diffraction data collection in the 0.7–1.81 Å wavelength range.

Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties

The three-dimensional structure of a human light-chain dimer (Sea) is reported to 1.94 Å resolution. This structure is likely to facilitate our understanding of why some seemingly harmless light chains display a propensity to aggregate as pathological amyloid fibrils.

The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging

The C₄-tetrameric enzyme crystallized with 20 protomers in the asymmetric unit. The atomic cstructure was solved using one heavy-atom derivative at 6 Å resolution and the molecular envelope of a related enzyme.

Crystallization and preliminary X-ray analysis of the full-size cubic core of pig 2-oxoglutarate de­hydrogenase complex

The full-length (untruncated) protein dihydrolipoamide succinyltransferase, E2, of OGDC from pig heart, has been crystallized in space group I432, with unit-cell parameter a = 189.9 Å.

Crystallization and preliminary diffraction studies of the ectodomain of the envelope glycoprotein D from herpes simplex virus 1 alone and in complex with the ectodomain of the human receptor HveA

The crystallization of the complex between glycoprotein D (gD) from HSV-1 and the receptor HveA is decribed as well as the preparation of a selenomethionine-substituted gD in insect cells.

Purification, N-terminal sequencing, crystallization and preliminary X-ray diffraction analysis of atratoxin, a new short-chain α-neurotoxin from the venom of Naja naja atra

Single crystals of atratoxin have been grown from drops containing the necessary Cu²⁺ ions by the conventional hanging-drop vapour-diffusion method.

Characterization and crystallization of a novel haemoglobinase from pathogenic Escherichia coli

A novel haemoglobinase from pathogenic E. coli has been crystallized. The crystals diffract to 2.5 Å resolution.

Cloning, high-level expression, purification and crystallization of peptide de­formylase from Leptospira interrogans

Peptide deformylase from the pathogenic bacterium L. interrogans was identified. The enzyme was overexpressed in E. coli in high yield. The purified enzyme was crystallized and X-ray diffraction data were collected to 3 Å resolution.

Crystallization and preliminary X-ray analysis of human carbonic anhydrase III

Carbonic anhydrases catalyze the interconversion of carbon dioxide to bicarbonate. Human carbonic anhydrase isozyme III with a C-terminal hexahistidine tag was overexpressed in E. coli, purified and crystallized.

Crystallization and preliminary X-ray analysis of the hydroperoxidase I C-terminal domain from Escherichia coli

The C-terminal domain of catalase-peroxidase HPI (hydroperoxidase I) from E. coli has been crystallized.

Crystallization of the functional domain of human thrombopoietin using an antigen-binding fragment derived from neutralizing monoclonal antibody

The functional domain of human thrombopoietin was crystallized using a Fab fragment digested from its neutralizing antibody. Preliminary X-ray analysis suggests that each Fab fragment provides a suitable interface for crystallization.

Purification, crystallization and preliminary X-ray diffraction analysis of yeast regulatory particle non-ATPase subunit 6 (Nas6p)

The regulatory particle non-ATPase subunit, Nas6p, from S. cerevisiae has been crystallized by the hanging-drop method. A complete diffraction data set using synchrotron radiation was collected to 2.6 Å resolution.

Crystallization and preliminary X-ray crystallographic analysis of aspartate 1-de­carboxylase from Helicobacter pylori

Aspartate 1-decarboxylase (PanD) from H. pylori has been overexpressed and crystallized (space group I422; unit-cell parameters a = b = 81.83, c = 93.78 Å). Diffraction data have been collected to 1.55 Å using synchrotron X-rays.

Crystallization and preliminary X-ray crystallographic analysis of UDP-N-acetylglucosamine acyltransferase from Helicobacter pylori

UDP-N-acetylglucosamine acyltransferase (LpxA) from H. pylori has been overexpressed and crystallized (space group P6₃22; unit-cell parameters a = b = 90.69, c = 148.20 Å, α = β = 90, γ = 120°). Diffraction data have been collected to 2.1 Å using synchrotron X-rays.

Towards the crystal structure of glycerol de­hydrogenase from Thermotoga maritima

The NAD⁺-dependent glycerol dehydrogenase from the extremely thermophilic bacterium T. maritima has been crystallized in the presence of glycerol by the hanging-drop vapour-diffusion method using 2-methyl-2,4-pentanediol (MPD) as the precipitating agent.

Crystallization and preliminary X-ray analysis of recombinant histone HPhA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Crystals of recombinant hyperthermophilic archael histone HPhA were obtained by the hanging-drop vapour-diffusion method. Diffraction data have been collected to 2.3 Å.

Metal–ligand geometry relevant to proteins and in proteins: sodium and potassium

For sodium and potassium, geometry around the metal ion found in high-resolution protein structures in the Protein Data Bank is compared with that in appropriate small-molecule complexes in the Cambridge Structural Database. Target distances for refinement or for validation are proposed.

Spoilt for choice: protein target selection in a time of plenty

Exploiting genomic sequence databases for structural genomics target selection.

Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6 Å resolution against experimental MAD phases. Addendum

An addendum to Coste et al. [Acta Cryst. (2002) D58, 431–440].