Another case of fraud in structural biology

Editorial.

Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen

The structure factors deposited with PDB entry 3k78 show properties inconsistent with experimentally observed diffraction data, and without uncertainty represent calculated structure factors. The refinement of the 3k78 model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019).

Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen

A response to the article by Rupp (2012), Acta Cryst. F68, 366–376.

Structure of the third catalytic domain of the protein di­sulfide isomerase ERp46

The structure of the third catalytic domain of the human protein disulfide isomerase ERp46 has been determined to 2.0 Å resolution.

Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin

The crystal structure of MurA from the marine Gram-negative bacterium Vibrio fischeri in complex with UNAG and the drug fosfomycin has been solved to a resolution of 1.93 Å.

Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2

The crystal structures of the C-terminal domain of S. cerevisiae Avo1 and of its human orthologue Sin1 have been determined. The structures show that the C-termini of the two proteins have the PH-domain fold with a putative binding site for phosphoinositides.

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)₂ as an A-DNA duplex

The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)₂ as an A-DNA duplex and its interaction with a manganese ion are described.

Structure of the His269Arg mutant of the rat aldose reductase-like protein AKR1B14 complexed with NADPH

The 1.87 Å resolution crystal structure of the His269Arg mutant of rat aldose reductase-like protein (AKR1B14) complexed with NADPH is described.

High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors

Two structures of factor XIa in complex with small synthetic inhibitors are reported. These are the first structures of factor XIa complexed to small non-basic inhibitors.

Structure of AKR1C3 with 3-phenoxybenzoic acid bound

The structure of the nonsteroidal anti-inflammatory drug analogue 3-phenoxybenzoic acid bound to aldo–keto reductase 1C3 (AKR1C3) is presented as a lead for the discovery and development of novel agents for inhibiting AKR1C3, an anticancer target.

Structure of Escherichia coli aspartate α-de­carboxylase Asn72Ala: probing the role of Asn72 in pyruvoyl cofactor formation

The crystal structure of E. coli aspartate α-decarboxylase Asn72Ala reveals the structure of the previously unresolved C-terminus.

Structural analysis of Pneumocystis carinii di­hydrofolate reductase complexed with NADPH and 2,4-di­amino-6-[2-(5-carboxypent-1-yn-1-yl)-5-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine

Structural data for the ternary complex of P. carinii DHFR with NADPH and the potent inhibitor PY1014 reveal conformational changes that help to explain the weaker potency and selectivity of the pyrido[2,3-d]pyrimidine scaffold compared with the homologous pyrimidine series of antifolates.

Purification, crystallization and preliminary crystallographic studies of a PacL homologue from Listeria monocytogenes

A PacL homologue from L. monocytogenes has been purified and crystallized. The crystals diffracted to 3.2 Å resolution.

Crystallization and crystallographic analysis of the ligand-binding domain of the Pseudomonas putida chemoreceptor McpS in complex with malate and succinate

The crystallization of the ligand-binding domain of the methyl-accepting chemotaxis protein chemoreceptor McpS (McpS-LBD) is reported.

Preparation, crystallization and preliminary X-ray diffraction studies of the glycosylated form of human interleukin-23

Interleukin-23 (IL-23), a member of the IL-12 family, is a heterodimeric cytokine composed of p19 and p40 subunits. Human p19 and p40 subunits were cloned and coexpressed in N-acetylglucosaminyltransferase I-negative 293S cells. The glycosylated human IL-23 was purified and crystallized by the hanging-drop vapour-diffusion method.

Crystallization and preliminary crystallographic characterization of the N-terminal Kunitz domain of boophilin

The N-terminal Kunitz domain of boophilin, a specific thrombin inhibitor, was crystallized. The orthorhombic crystals had an unusually low solvent content and diffracted to beyond 0.87 Å resolution at a synchrotron source.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii

Pyridoxal biosynthesis lyase PdxS from P. horikoshii has been overexpressed and crystallized. X-ray diffraction data have been collected to 2.61 Å resolution.

Crystal optimization and preliminary diffraction data analysis of the SCAN domain of Zfp206

Crystals of the SCAN domain of Zfp206 are tetragonal, belonging to space group I422 with unit-cell parameters a = 67.57, c = 87.54 Å and one molecule in the asymmetric unit, and diffract to 1.85 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of a novel wild-type blue fluorescent protein from Vibrio vulnificus CKM-1

The wild type BFPvv has been crystallized for the first time in order to obtain its tertiary structure and to further understand how chromophore formation occurs via a different oxygen-independent mechanism.

Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis

Recombinant AciX9_0562 from Acidobacterium sp. MP5ACTX9 containing sequence motifs characteristic of the RmlC-type cupins superfamily and containing Pfam motif PF07883 has been successfully cloned, expressed and purified, and crystallized in a number of conditions from the Morpheus protein crystallization screen.

Towards the crystal structure elucidation of eukaryotic UDP-galacto­pyranose mutase

UDP-galactopyranose mutase from A. fumigatus was crystallized and structure solution is in progress.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark β₂-microglobulin

A crystal of nurse shark β₂-microglobulin diffracted to 2.3 Å resolution and belonged to space group P3₂21, with unit-cell parameters a = b = 88.230, c = 67.146 Å and two molecules per asymmetric unit. The Matthews coefficient V_M was calculated to be about 3.28 ų Da⁻¹, corresponding to 62.5% solvent content.

Crystallization and preliminary X-ray analysis of stationary phase survival protein E (SurE) from Xylella fastidiosa in two crystal forms

The crystallization and preliminary analysis of two crystal forms of survival protein E from X. fastidiosa are reported.

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2

The luminal domain of human endoplasmic reticulum aminopeptidase 2 has been expressed, purified and crystallized. The crystals belonged to the orthorhombic space group P2₁2₁2 and diffracted anisotropically to 3.3 Å resolution in the best direction on an in-house source.

Purification, crystallization and preliminary X-ray analysis of the aminoglycoside-6′-acetyltransferase AAC(6′)-Im

AAC(6′)-Im is an N-acetyltransferase enzyme responsible for aminoglycoside resistance in E. faecium and E. coli isolates. Crystals of the kanamycin complex of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken.

Crystallization and preliminary crystallographic analysis of the complex between tri­iodothyronine and the bb′ fragment of rat protein di­sulfide isomerase

Protein disulfide isomerase (PDI) is known to bind to the thyroid hormone triiodothyronine (T3). Here, the expression, crystallization and preliminary X-ray studies of the b and b′ domains of rat PDI in ligand-free and T3-complexed states are reported.

Crystallization and preliminary X-ray diffraction studies of the abscisic acid receptor PYL3 and its complex with pyrabactin

Crystals of the abscisic acid receptor PYL3 and of the PYL3–pyrabactin complex were obtained and optimized in order to obtain high-quality diffraction data. Diffraction data sets were collected and processed to 2.5 and 1.83 Å resolution, respectively.

Cocrystallization and preliminary crystallographic analysis of an inactive MaoC-like hydratase mutant with the substrate crotonyl-CoA

An inactive MaoC-like hydratase mutant from P. capsici was obtained and purified, and the purified mutant was cocrystallized in the presence of the substrate crotonyl-CoA.

In praise of impurity: 30S ribosomal S15 protein-assisted crystallization of turnip yellow mosaic virus proteinase

Diffraction-quality crystals of the turnip yellow mosaic virus proteinase/ubiquitin hydrolase could only be obtained from a protein preparation that was heavily contaminated with E. coli 30S ribosomal S15 protein. Crystal packing reveals the basis of this observation.

Purification, crystallization and preliminary X-ray analysis of OsAREB8 from rice, a member of the AREB/ABF family of bZIP transcription factors, in complex with its cognate DNA

OsAREB8 from rice (O. sativa), a member of the AREB/ABF family of bZIP transcription factors, was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. A crystal of OsAREB8 in complex with its cognate DNA diffracted X-rays to 3.65 Å resolution.

Fast high-pressure freezing of protein crystals in their mother liquor

Protein crystals were vitrified using high-pressure freezing in their mother liquor at 210 MPa and 77 K without cryoprotectants or oil coating. The method was successfully applied to photosystem II, which is representative of a membrane protein with a large unit cell and weak crystal contacts.