Deposition of diffraction images to be discussed at the Open Meeting of the Commission on Biological Macromolecules of the IUCr in Osaka

Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin

The crystal structure of the kinase domain of wild-type polo-like kinase 1 (Plk-1) has been determined after identifying suitable domain borders via a parallel cloning and expression approach and upon generation of a selective designed ankyrin-repeat protein (DARPin) which served as a crystallization tool.

Towards a rational approach for heavy-atom derivative screening in protein crystallography

Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue.

Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida

The adaptation of enzymes to low temperatures and seawater salinity has been investigated on a structural level. The crystal structure of V. salmonicida endonuclease I is presented and compared with the corresponding enzyme structures from V. cholerae and V. vulnificus.

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine de­carboxylase from Methanococcus jannaschii

The crystal structures of two arginine decarboxylase mutant proteins provide insights into the mechanisms of pyruvoyl-group formation and the decarboxylation reaction.

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed.

Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2

The crystal structures of the homodimeric diphthine synthases from A. pernix K1 and P. horikoshii OT3 were determined by X-ray diffraction. The present study suggests the biological importance of the asymmetry in the dimeric structure of this enzyme for the effective recognition of a large substrate, EF-2.

A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein

A protein from E. coli was crystallized from an inhomogeneous protein sample and identified as Gab protein by structure determination. The obtained structure is compared with a previously deposited structure of the same protein and potential ligand binding is discussed.

A knowledge-driven approach for crystallographic protein model completion

A novel method that uses the conformational distribution of C^α atoms in known structures is used to build short missing regions (`loops') in protein models. An initial tree of possible loop paths is pruned according to structural and electron-density criteria and the most likely loop conformation(s) are selected and built.

A 7 µm mini-beam improves diffraction data from small or imperfect crystals of macromolecules

An X-ray mini-beam of 8 × 6 µm cross-section was used to collect diffraction data from protein microcrystals with volumes as small as 150–300 µm³. The benefits of the mini-beam for experiments with small crystals and with large inhomogeneous crystals are investigated.

Structure of hepatitis C virus IRES subdomain IIa

The structure of the HCV IRES subdomain IIa has been solved at 2.3 Å resolution in the presence of Mg²⁺ and Sr²⁺. The results provide additional insight into the specific interactions that stabilize the unique conformation.

Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state

The crystal structure of peptidyl-tRNA hydrolase 2 from P. horikoshii OT3 has been determined in two different crystal forms. The present study suggests the practical importance of the dimeric structure for tRNA binding.

Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

Multiple crystal structures are reported of cross-linked actin dimers. Interactions that are conserved across crystal structures suggest detailed interactions that are likely to be present in F-actin filaments.

Structure of acostatin, a dimeric disintegrin from Southern copperhead (Agkistrodon contortrix contortrix), at 1.7 Å resolution

Two acostatin heterodimers interact together to form an αββα tetramer.