Expanding the model: anisotropic displacement parameters in protein structure refinement

The distribution of atomic anisotropy is proposed as a validation tool for protein structures refined with individual anisotropic displacement parameters U^ij. This distribution is examined for all such protein models currently in the Protein Data Bank.

Atomic resolution structure of biotin-free Tyr43Phe streptavidin: what is in the binding site?

Atomic resolution refinement of the Y43F mutant of streptavidin shows 2-methyl-2,4-pentanediol molecules in the biotin binding site.

The three-dimensional structures of two isoforms of nucleoside diphos­phate kinase from bovine retina

The crystal structures of two isoforms of nucleoside diphosphate kinase from bovine retina with nucleoside in the active site are reported to 2.4 Å resolution.

An A-DNA structure with two independent duplexes in the asymmetric unit

The crystal structure contains two A-DNA decamer duplexes of d(G₄CGC₄) in the asymmetric unit. The structural differences between the two molecules appear to originate from an inherent propensity of the sequence for varied intermolecular interactions and malleability.

Three-dimensional structure of β-momorcharin at 2.55 Å resolution

The secondary and tertiary structure of β-momorcharin is similar to other single-chained ribosome-inactivating proteins (RIPs). The oligosaccharide is linked to the protein through an N-glycosidic bond, stretches from the molecular surface far from the active site and interacts with the protein through hydrogen bonds, most of them being intermolecular interactions with the protein atoms in an adjacent unit cell.

Structure of mare apolactoferrin: the N and C lobes are in the closed form

The structure of mare apolactoferrin shows that both N and C lobes adopt closed conformations. Thus, the structure of mare apolactoferrin is different from the structures of human apolactoferrin and duck apoovotransferrin.

1.7 Å structure of the stabilized REI_v mutant T39K. Application of local NCS restraints

SHELX refinement strategies at medium resolution are illustrated for an immunoglobulin fragment. The effect of local NCS restraints, anisotropic scaling and anisoropic refinement has been tested, and standard uncertainties calculated.

Taking MAD to the extreme: ultrafast protein structure determination

A multiwavelength anomalous diffraction experiment has been completed in 45 min using synchrotron radiation from the Structural Biology Center's 19ID undulator beamline at the Advanced Photon Source.

σ²_R, a reciprocal-space measure of the quality of macromolecular electron-density maps

A reciprocal-space measure of the quality of macromolecular crystallographic phases based on the variance of the local roughness of the map is presented.

Detection and treatment of twinning: an improvement and new results

An improvement for a statistical test aimed at detecting twinning and a new method to determine the level of twinning, as well as a new parametrization for twinning, are proposed.

Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex

New low-salt crystallization conditions have been obtained for T7 RNA polymerase and have been used to produce crystals of the native enzyme, a chimeric T7/T3 RNA polymerase and native T7 RNA polymerase containing an N-terminal histidine tag.

Purification, characterization, crystallization and preliminary X-ray diffraction of acuthrombin-B, a thrombin-like enzyme from Agkistrodon acutus venom

The crystals of acuthrombin-B, a thrombin-like enzyme consisting of two non-identical polypeptide chains (14.4 and 16 kDa) from A. acutus venom, bleong to space group P2₁ with a resolution limit near 2 Å and unit-cell parameters a = 34.97, b = 53.58, c = 67.88 Å, β = 98.89°, and contain one molecule per asymmetric unit.

Crystallization and preliminary X-ray diffraction analysis of a biologically active fragment of CD55

Crystals have been grown of a virus-binding construct of CD55 which diffract X-rays to at least 1.65 Å.

Purification, crystallization and preliminary X-ray analysis of Drosophila melanogaster ferrochelatase

Ferrochelatase of D. melanogaster has been purified and crystallized with an intact [2Fe–25] cluster. The crystals diffract to 3.0 Å resolution with a space group of I422.

Crystallization and preliminary X-ray studies of the basic lectin from the seeds of Artocarpus hirsuta

Preliminary X-ray characterization of the two orthorhombic and one hexagonal crystal forms of a basic lectin from A. hirsuta is reported.

Crystallization and preliminary X-ray analysis of the formiminotransferase domain from the bifunctional enzyme formiminotransferase–cyclodeaminase

The formiminotransferase domain of formiminotransferase cyclodeaminase, a bifunctional channeling enzyme involved in folate metabolism, has been crystallized in space group P2₁2₁2₁. Native diffraction data and data for a mercurial derivative have been collected to 2.8 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of cytochrome P450_sca-2 from Streptomyces carbophilus involved in production of pravastatin sodium, a tissue-selective inhibitor of HMG-CoA reductase

Cytochrome P450_sca-2 from S. carbophilus has been crystallized using ammonium sulfate as precipitant. The crystals diffract to 2.2 Å resolution.

Crystallization and preliminary X-ray analysis of the 6-phospho-α-glucosidase from Bacillus subtilis

Crystals of GlvA, the 6-phospho-α-glucosidase from B. subtilis, have been grown in a form suitable for X-ray diffraction studies.

Dynamic light-scattering and preliminary crystallographic studies of the sensor domain of the haem-based oxygen sensor FixL from Rhizobium meliloti

A novel purification method of the oxygen-sensor domain of R. meliloti FixL, dynamic light-scattering studies of its solution and preliminary crystallographic data are reported.

Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction

Recombinant S. cerevisiae Ypd1p fused with a His₆-tag at its C-terminus has been crystallized. The triclinic crystal contains four monomeric Ypd1p in the asymmetric unit and native data have been collected to 2.3 Å.

Crystallization and preliminary X-ray crystallographic analysis of a periplasmic tetrahaem flavocytochrome c₃ from Shewanella frigidimarina NCIMB400 which has fumarate reductase activity

A periplasmic tetrahaem flavocytochrome c₃ from S. frigidimarina NCIMB400 which possesses fumarate reductase activity has been crystallized. The crystals belong to space group P2₁2₁2₁ with unit-cell parameters a = 72.4, b = 110.1, c = 230.2 Å. Assuming a molecular dimer in the asymmetric unit, the crystals contain 65% solvent and, when cryocooled to 100 K, diffract to at least 3.0 Å resolution. An iron X-ray absorption edge has been measured in preparation for a MAD phasing experiment.

Cubic crystals of phosphopantetheine adenylyltransferase from Escherichia coli

Recombinant phosphopantetheine adenylyltransferase, a key late enzyme in coenzyme A (CoA) biosynthesis from E. coli has been crystallized in complex with various substrates, its inhibitor (CoA) and as the apo form.

Crystallization and preliminary X-ray diffraction studies of piratoxin III, a D-49 phospholipase A₂ from the venom of Bothrops pirajai

Piratoxin III, a D-49 phospholipase A₂ from B. pirajai has been crystallized in the monoclinic space group C2 and its structure has been solved by molecular replacement at 2.7 Å.

Crystallization and preliminary X-ray diffraction analysis of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

Hydrolytic haloalkane dehalogenase from S. paucimobilis UT26 has been crystallized by the vapour-diffusion method using PEG 6000 as a precipitant. Native diffraction data were collected to 1.6 Å resolution under cryogenic conditions.

Purification, crystallization and preliminary X-ray crystallographic studies of S. cerevisiae Hsp40 Sis1

S. cerevisiae Hsp40 Sis1 has been purified and crystallized. The crystals diffract to 2.7 Å and belong to space group P4₁2₁2 or P4₃2₁2.

Preliminary crystallographic studies of a protease-resistant botulinum neurotoxin associated protein Hn-33

Hn-33, a protein in the botulinum neurotoxin type A toxic complex, has been crystallized using vapour-diffusion techniques. The crystals belong to an orthorhombic space group and diffract to a resolution of 2.6 Å.

Purification, crystallization and preliminary crystallographic analysis of a natural complex of phospholipase A₂ from Echis carinatus (saw-scaled viper)

A novel complex of phospholipase A₂ complexed with another venom protein has been isolated and purified from saw-scaled viper (E. carinatus) venom. It was crystallized with 7%(w/v) PEG 4000 and the crystals belonged to monoclinic space group P2₁ with unit-cell parameters a = 74.47, b = 47.87, c = 106.19 Å.

Crystallization and preliminary X-ray studies of metallo­thionein II from rabbit liver

Cadmium-induced metallothionein II from rabbit liver has been crystallized in space group P6₂22 or P6₄22. Unit-cell parameters have been obtained for crystallization from sodium citrate and Tris–HCl buffers.

Crystallization and preliminary X-ray analysis of a complex between the Bowman–Birk trypsin inhibitor from barley and porcine pancreatic trypsin

A 1:2 complex between the Bowman–Birk trypsin inhibitor from barley seeds and porcine pancreatic trypsin has been crystallized. Native X-ray diffraction data have been collected to 2.2 Å.

Use of super-water-repellent fractal surfaces in the crystallization of macromolecules

Fractal surfaces are effective and promising in the crystallization of macromolecules using the sitting-drop vapour-diffusion method.