On the propagation of errors

The policy of the Protein Data Bank that the first deposition of a small-molecule ligand, even with erroneous atom numbering, sets a precedent over accepted nomenclature rules is disputed.

Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium

In this study, the crystal structure of CueP, a periplasmic copper-binding protein from Salmonella enterica, has been determined, revealing a V-shaped dimeric structure.

Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phyllo­quinone biosynthesis

The crystal structures of two 1,4-dihydroxy-2-naphthoyl-CoA thioesterases of plant and cyanobacterial origin that are involved in the biosynthesis of phylloquinone are presented. The divergent structures of these two functionally similar enzymes indicate convergent evolution.

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein

The structure of the Tse3–Tsi3 complex associated with the bacterial type VI secretion system of P. aeruginosa has been solved and refined at 1.9 Å resolution. The structural basis of the recognition of the muramidase effector and its inactivation by its cognate immunity protein is revealed.

A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel

The diamagnetic levitation technique can aid in obtaining high-quality protein crystals. Comparison of the results obtained using three containerless conditions indicated that the diamagnetic levitation technique exhibited the greatest improvement in crystal quality, followed by that using agarose gel.

Structure of the JmjC-domain-containing protein JMJD5

The crystal structure of JMJD5^176-C revealed that three residues with large side chains located at the entrance to the substrate-binding pocket abolish the histone demethylase activity of this fragment of JMJD5. The structural similarity of JMJD5 to FIH suggested that human JMJD5 might function as a protein hydroxylase.

On effective and optical resolutions of diffraction data sets

The notion of `resolution' is discussed and a formal definition applicable to various diffraction data sets, both complete and incomplete and both isotropic and anisotropic, is suggested.

Structural basis for the antibody neutralization of Herpes simplex virus

The gD–E317-Fab complex crystal revealed the conformational epitope of human mAb E317 on HSV gD, providing a molecular basis for understanding the viral neutralization mechanism.

A functional and structural study of the major metalloprotease secreted by the pathogenic fungus Aspergillus fumigatus

The secreted success of cone-moulded weapons: unveiling the structural and functional details of the major collagenolytic and elastinolytic zinc-dependent proteinase from Aspergillus fumigatus.

Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus

The crystal structure of the antitumoral and cell-penetrating polypeptide crotamine from C. durissus terrificus venom is reported.

Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes

The first crystal structure of a proteorhodopsin shows a hexametric ring of protein in which the conserved photoactive-site histidine forms a hydrogen bond to the Schiff base proton acceptor from the same molecule and also to a tryptophan residue of a neighboring protomer. The structure and mutant studies reveal novel aspects of the ion translocation mechanism and cooperative behavior between protomers involving the inter-molecular His-Trp pair.

Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like di­sulfide oxidases

The gene product of M. tuberculosis Rv2969c is shown to be a disulfide oxidase enzyme that has a canonical DsbA-like fold with novel structural and functional characteristics.

The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N₁₁-A sequence motif by LysR-type transcriptional regulators

The first structures of DNA–protein complexes that include the DNA-binding domain from a LysR-type transcriptional regulator (LTTR) are described here and are used to explain the high degree of conservation in a DNA-sequence motif recognized by LTTRs (T-N₁₁-A). Sequence-specific recognition depends primarily on direct protein–nucleotide base contacts.

High-resolution structure of an atypical α-phosphoglucomutase related to eukaryotic phosphomannomutases

The structure of α-phosphoglucomutase from L. lactis reveals overall structure similarity to eukaryotic phosphomannomutases, but with differences at the active site.

High-resolution structure of a papaya plant-defence barwin-like protein solved by in-house sulfur-SAD phasing

The first crystal structure of a barwin-like protein is determined at high resolution by single-wavelength anomalous diffraction phasing using the six intrinsic sulfur atoms present in the protein.

The structure of a glycoside hydrolase family 81 endo-β-1,3-glucanase

The crystal structure of the endo-β-1,3-glucanase from Rhizomucor miehei (RmLam81A) was determined in two crystal forms at 2.3 and 2.0 Å resolution, respectively. The structure of RmLam81A is greatly different from all endo-β-1,3-glucanase structures available.

Improving experimental phases for strong reflections prior to density modification

A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases.

Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states

A combination of small-angle X-ray scattering and atomic force microscopy reveals that the trimeric two-domain protein gephyrin adopts a multitude of compact and extended conformations, with a preference for compact states. This behaviour is caused by the long and primarily unstructured linker region, which also interacts with the structured domains located at either end of gephyrin. Potential functional implications of the structural data are discussed.

Structure of fully liganded Hb ζ₂β₂^s trapped in a tense conformation

The crystallographic analysis of fully liganded Hb ζ₂β₂^s trapped in a tense conformation is reported.

Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography

Combined small-angle X-ray scattering (SAXS) and crystallographic data were used to probe the two-step catalytic mechanism of the acyl acid–amido synthetase GH3.12. On-line size-exclusion chromatography directly upstream of the X-ray beam improved the sample homogeneity and allowed the determination of changes in the protein conformation in solution. X-ray models were fitted to the SAXS data to unambiguously determine the protein conformation in the presence of different ligands.

Structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain involved in the targeting of tail-anchored membrane proteins to the endoplasmic reticulum

The structure of the complex between the N-terminal dimerization domain of Sgt2 and the ubiquitin-like domain of Get5 was determined in order to understand the interaction between Sgt2 and Get5 and to reveal how this complex is essential for the function of TA-protein delivery under stress conditions.

Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator.

Structure of a bifunctional alcohol de­hydrogenase involved in bio­ethanol generation in Geobacillus thermoglucosidasius

The crystal structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from G. thermoglucosidasius has been determined to 2.5 Å resolution. Docking of this with a homology model of the aldehyde dehydrogenase domain, for which no structure has been determined, has enabled the construction of a model of the complete ADHE and a putative mechanism of formation of the large multimeric `spirosomes' that have been reported for ADHE from this and other organisms.

Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase

The intriguing crystal organization of the domain-swapped dimer of a human pancreatic ribonuclease variant indicates that the protein can form fibrils in solution. They were observed and characterized by atomic force microscopy. The importance of domain swapping in inducing native-like fibril formation is highlighted.

Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 β-D-mannosidase

The structures of rice Os7BGlu26 β-D-mannosidase, of its product complex with β-D-mannose and of Os7BGlu26 computationally docked with 4-nitrophenyl β-D-mannoside suggest that the D-­mannose pyranose ring makes a conformational transition from ^OS₂ skew boat to B_2,5 boat to ¹S₅ skew boat during the deglycosylation of the enzyme in hydrolysis. These structures led to the hypothesis that the residues interacting with the catalytic acid/base play a role in determining β-D-mannosidase activity, which was supported by site-directed mutagenesis and kinetic analysis.

Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone

Three crystal structures of the prolyl-tRNA synthetase domain of human glutamyl-prolyl-tRNA synthetase, two of which were complexed with small molecules, were determined by Zn-SAD phasing combined with molecular replacement. The structures revealed that conformational changes occur in the active site upon small-molecule binding.

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53.

The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography

The first neutron protein structure refined against 1.75 Å resolution data collected on the new IMAGINE instrument at HFIR (ORNL) is reported.

Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain

Different orientations of similar low-molecular-weight fragments in the acetylated lysine-recognition pocket of the BRD4 N-terminal bromodomain are reported.