Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data

PeakProbe facilitates the automated modelling of ordered solvent in macromolecular crystal structures by analysing features of the electron density and chemical environment surrounding a given coordinate. The extracted data are transformed to a resolution-independent score space and likely solvent models are predicted based on the frequency distributions observed in a large-scale sample of the PDB.

Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change

Pili, polymers of the major pilin, in Gram-positive bacteria are flexible rod proteins associated with the bacterial cell surface that play important roles in initial adhesion to host tissues and colonization. Crystal structures of major pilins from Clostridium perfringens strains have been determined, which were considered to be in an equilibrium state between an elongated and a bent structure through dynamic conformational change.

Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative de­carboxylation reaction

Structural and enzymological explorations of α-hydroxyacid oxidases uncover new flavin mononucleotide-mediated reactions and intermediates.

A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity

A new haloacid dehalogenase (HAD) phosphatase originating from Thermococcus thioreducens was expressed, purified and crystallized, and its structure was refined to 1.75 Å resolution. Structural studies confirmed the presence of the canonical HAD phosphatase fold with the HAD signature motifs and of Mg²⁺ ion in the active site. The results of computational docking and enzymatic assays identified possible substrates of the enzyme.

Sequence assignment for low-resolution modelling of protein crystal structures

Recent advances in automated protein model building using ARP/wARP are presented. The new methods include machine-learning-enhanced sequence assignment and loop building using a fragment database.

Location-specific qu­antification of protein-bound metal ions by X-ray anomalous dispersion: Q-XAD

A method is described for the quantification of the relative amounts of different metal ions in the binding sites of metalloproteins using X-ray anomalous dispersion.

Structure determination of the CAMP factor of Streptococcus agalactiae with the aid of an MBP tag and insights into membrane-surface attachment

The CAMP factor of group B streptococcus, a pore-forming toxin, was crystallized with an MBP tag. Structural and functional analysis suggests that the basic patch formed by helices 6 and 7 within the C-terminal domain is critical for its activity.