Expectation bias and information content

Editorial.

Structure of ALD1, a plant-specific homologue of the universal di­aminopimelate aminotransferase enzyme of lysine biosynthesis

The structure of AtALD1 from the flowering plant Arabidopsis thaliana was solved at a resolution of 2.3 Å. The structural analysis supports previous biochemical evidence for differential expression and distinct functions of AtALD1 and AtDAP-AT.

Structure of a low-melting-temperature anti-cholera toxin: llama V_HH domain

The X-ray crystal structure of a camelid V_HH domain with a melting temperature of 319.9 ± 1.6 K, which is among the lowest reported for a V_HH domain, is reported at 2.1 Å resolution.

The structure of the FnI-EGF-like tandem domain of coagulation factor XII solved using SIRAS

The structure of the FnI-EGF-like tandem domain was solved to 1.6 Å using data sets of native and holmium chloride bound protein. Putative biological roles of this tandem domain are discussed based on the structure.

Structure of an amido­hydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL

The crystal structure of the S. aureus amidohydrolase SACOL0085 reveals that a conserved cysteine residue at the active site serves as a bidentate ligand coordinating two Mn²⁺ ions.

Crystallization and preliminary X-ray diffraction analysis of YhbJ from Escherichia coli, a key protein involved in the GlmYZ sRNA regulatory cascade

The homotrimeric protein YhbJ from E. coli has been homologously expressed, purified and crystallized in two distinct crystal forms. The crystals diffracted to 3.26 and 3.44 Å resolution.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of β-N-acetylglucosaminidase from Thermotoga maritima encoded by the Tm0809 gene

β-N-Acetylglucosaminidase from T. maritima has been overexpressed and crystallized. X-ray diffraction data have been collected to 3.80 Å resolution.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8

Thymidylate kinase from T. thermophilus HB8 has been cloned, expressed, purified and crystallized.

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the chicken MHC class I molecule BF2*1501

X-ray diffraction data were collected to 2.6 Å resolution from a crystal of the chicken MHC class I molecule BF2*1501. The crystal belonged to space group P3₁21, with unit-cell parameters a = 125.1, b = 125.1, c = 80.9 Å, and contained two molecules in the asymmetric unit. The Matthews coefficient and solvent content were calculated to be 2.08 ų Da⁻¹ and 40.78%, respectively.

Purification, crystallization and preliminary crystallographic studies of haemoglobin from mongoose (Helogale parvula) in two different crystal forms induced by pH variation

Preliminary crystallographic study of low-oxygen affinity haemoglobin from mongoose; the first structural study of haemoglobin from a member of the Herpestidae family.

Crystallization and preliminary crystallographic analysis of two eukaryotic fructosyl peptide oxidases

Fructosyl peptide oxidases from Coniochaeta sp. and E. terrenum were crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 and 1.6 Å resolution, respectively.

Crystallization and preliminary X-ray analysis of L-serine 3-de­hydrogenase complexed with NADP⁺ from the hyperthermophilic archaeon Pyrobaculum calidifontis

An NAD(P)⁺-dependent L-serine 3-dehydrogenase from a hyperthermophilic archaeon was successfully isolated and crystallized.

Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris

Major endoglucanase was purified from the extracellular extract of X. campestris pv. campestris and crystals of the catalytic domain were obtained. X-ray diffraction data were collected to 2.7 Å resolution.

Crystallization of a self-assembled three-dimensional DNA nanostructure

In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described.

Crystallization and preliminary X-ray crystallographic analysis of sterol transcription factor Upc2 from Saccharomyces cerevisiae

In this study, the C-terminal regulatory domain of Upc2 from Saccharomyces cerevisiae was purified and crystallized by the vapour-diffusion method.

The expression, purification and crystallization of a ubiquitin-conjugating enzyme E2 from Agrocybe aegerita underscore the impact of His-tag location on recombinant protein properties

The purification and crystallization of UbcA1, a novel ubiquitin-conjugating enzyme identified from the medicinal mushroom A. aegerita, are described.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana

AHP2 from A. thaliana was cloned, expressed, purified and crystallized.

Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus

The expression, purification, characterization and crystallization of GK2848, a carbonic anhydrase from G. kaustophilus, are described. The crystals diffracted to a resolution of 2.70 Å.

Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles

Novel hepatitis B virus-like particles of recombinant dimeric core–GFP fusion protein were expressed, purified and crystallized. The crystals diffracted to 2.15 Å resolution and belonged to space group F432, with unit-cell parameters a = b = c = 219.7 Å.

Crystallization and preliminary X-ray crystallographic analysis of the functional form of BinB binary toxin from Bacillus sphaericus

The BinB subunit of mosquito-larvicidal binary toxin from B. sphaericus has been crystallized. The crystal could diffract to a resolution of 1.75 Å and belongs to space group P6₂22.

Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase

Backtracked bacterial RNA polymerase (RNAP) complexes were reconstituted by assembling Thermus thermophilus RNAP with nucleic acid scaffolds. The complexes were crystallized, and their X-ray diffraction data were collected and analyzed.

Crystallization and preliminary structure determination of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501

This paper reports the successful purification, crystallization and preliminary structure solution of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501.

Crystallization and preliminary X-ray characterization of an NAD(P)-dependent butanol de­hydrogenase A from Geobacillus thermodenitrificans NG80-2

ADH2, an NAD(P)-dependent butanol dehydrogenase A, is part of the terminal oxidation pathway in the long-chain alkane-degrading G. thermodenitrificans NG80-2. The expression, purification, crystallization and preliminary crystallographic analysis of ADH2 are reported.

Crystallization of the acyl-CoA thioesterase TesB from Yersinia pestis

The expression, purification, crystallization and diffraction of the acyl-CoA thioesterase TesB from Y. pestis are reported. X-ray crystallographic diffraction data to 2.0 Å resolution were collected at the Australian Synchrotron.

Overproduction, purification, crystallization and preliminary X-ray characterization of the C-terminal family 65 carbohydrate-binding module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens

The C-terminal carbohydrate-binding module (CBM65B) of family 5 glycoside hydrolase endoglucanase 5A (Cel5A) of E. cellulosolvens has been co-crystallized with cellohexaose and xyloglucan heptasaccharide and various data collected to 1.42–3.5 Å resolution.

Visualizing ligand molecules in twilight electron density

A software script is presented for facilitating the analysis and visual inspection of ligand molecules in the context of the electron-density maps calculated from experimental data associated with protein structures determined by X-ray crystallography.

Some practical guidelines for UV imaging in the protein crystallization laboratory

The use of UV imaging as a means of locating protein crystals is a fairly new tool, however not suitable for all protein crystallization trials. Practical examples of the strengths and some of the pitfalls of the technology are presented.

Optimization of protein buffer cocktails using Thermofluor

The Thermofluor assay constitutes a quick and easy-to-perform high-throughput method with which it is possible to identify protein-stabilizing buffer compositions or small-molecule additives.