Expectation bias and information content

Editorial.

Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system

The crystal structure of the the natural fusion protein EpsAB from V. vulnificus is described.

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

The potential causes of severe misinterpretation of ligand electron density in a surprisingly large number of protein–ligand structure complexes are analyzed. Techniques and tools are presented together with suggestions for good practice aimed at minimizing overinterpretation and mistakes in protein–ligand structure models.

Structure of full-length Toxascaris leonina galectin with two carbohydrate-recognition domains

The full-length crystal structure of Toxascaris leonine galectin (Tl-gal), a galectin-9 homologue protein, was determined at a resolution of 2.0 Å. The NCRD of Tl-gal resembles that of human galectin-7 and its CCRD resembles human galectin-9, but the residues in the interface and loop regions of the NCRD and CCRD are flexible and are related to interaction.

Intensity statistics in the presence of translational noncrystallographic symmetry

The statistical effects of translational noncrystallographic symmetry can be characterized by maximizing parameters describing the noncrystallographic symmetry in a likelihood function, thereby unmasking the competing statistical effects of twinning.

Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima

A 2.15 Å resolution crystal structure of TM0159 with bound IMP and enzyme-kinetic data are presented. This noncanonical nucleoside triphosphatase from T. maritima helps to maintain a correct pool of DNA and RNA precursor molecules.

Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals

The results observed for three different crystal forms of the enzyme PurE are reported and an attempt is made to infer some initial conclusions regarding the role that the solvent, the crystallization agents (mainly salts and polyethylene glycol) and interactions within the protein structures play in determining the changes in the diffraction pattern upon alteration of the external relative humidity of the crystals.

Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis

The structure, reaction mechanism and behaviour of a promiscuous plant nuclease are described. Structure solution was achieved by a combination of MAD and MR on multiple crystal forms.

Evolution of vitamin B₂ biosynthesis: eubacterial RibG and fungal Rib2 deaminases

The crystal structure of B. subtilis RibG complexed with a deaminase product was determined and the yeast Rib2 structure was modelled. Subsequent mutational analysis was carried out to illustrate its distinct substrate specificity. An essential amino-binding hole which is conserved in the RNA/DNA-editing deaminases was also identified.

Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE

The crystal structure of the C-terminal half of human XPB helicase was determined to 1.8 Å resolution. A disease-causing mutation (XP11BE) at the C-terminus produces a less soluble XPB mutant, significantly reducing the cellular level of the TFIIH complex.

Structure of the oncoprotein Rcl bound to three nucleotide analogues

High-resolution crystal structures of the oncoprotein Rcl in complexes with apoptotic nucleotides have been solved by molecular replacement using combined information from NMR, SAXS and fold recognition.

Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron–sulfur cluster-binding domain

The crystal structure of DppD, the nucleotide-binding domain of a dipeptide ABC transporter from T. tengcongensis, bound with an iron–sulfur cluster is reported at 2.89 Å resolution.

Identification of quercitrin as an inhibitor of the p90 S6 ribosomal kinase (RSK): structure of its complex with the N-terminal domain of RSK2 at 1.8 Å resolution

The crystal structure of quercitrin, a naturally occurring flavonol glycoside, has been determined in a complex with the N-terminal kinase domain of murine RSK2. The structure revealed that quercitrin inhibits the RSK2 kinase in the same fashion as another known inhibitor, SL0101.

Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide de­acetylase from Bacillus cereus

The structure of a polysaccharide deacetylase from B. cereus has been determined using an adventurous molecular-replacement procedure.

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data.

Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity

X-ray structures of Rhizobium sp. sucrose isomerase mutants have improved the understanding of the enzyme mechanism and have allowed the factors that govern the hydrolytic activity of this industrially important enzyme to be pinpointed.

Structure determination from a single high-pressure-frozen virus crystal

High-pressure-freezing allowed low-temperature data collection from a single virus crystal for which no standard cryoprotection could be established.