Structure of a complex of the potent and specific inhibitor BW284C51 with Torpedo californica acetylcholinesterase

The X-ray structure of the complex of BW284C51 with T. californica acetylcholinesterase was determined at 2.85 Å resolution and compared with the structures of complexes of the same enzyme with two other active-site gorge-spanning inhibitors, viz decamethonium and E2020.

Substructure solution with SHELXD

The application of the SHELXD program to the location of heavy-atom sites from MAD or SAD data is illustrated with the help of examples.

Physical estimation of triplet phases from two new proteins

Triplet phases have been obtained for three new proteins from three-beam diffraction. A brief discussion of strategies for the collection of triplet phases and their application in macromolecular crystallography is given.

Comparison of the refined crystal structures of wild-type (1.34 Å) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 Å) at 100 K

The structure at 100 K (synchrotron radiation) of the S35C mutant of D. vulgaris flavodoxin at 1.44 Å resolution has been compared with the refined wild-type (wt) structure at 1.34 Å resolution. A different orientation of the Cys35 thiol group with respect to the Ser35 hydroxyl has been found.

Secondary structures at polypeptide-chain termini and their features

An analysis of length and residue distributions, interactions and location in the overall tertiary structure of α-helices and β-strands at polypeptide-chain termini is presented and discussed in the context of protein folding and design.

Structural analysis of the two horseradish peroxidase catalytic residue variants H42E and R38S/H42E: implications for the catalytic cycle

The crystal structures of two mutants of horseradish peroxidase C (HRPC) with substitutions of the key catalytic residues Arg83 and His42 have been determined to 2.5 Å (H42E HRPC) and 2.0 Å (R38S/H42E HRPC) resolution.

Design of specific peptide inhibitors of phospholipase A₂: structure of a complex formed between Russell's viper phospholipase A₂ and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS)

The structure of the complex formed between Russell's viper phospholipase A₂ and a designed peptide LAIYS has been determined at 2.0 Å resolution. The peptide binds to phospholipase A₂ specifically and fills the hydrophobic channel completely.

On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation

A fast method for fitting model electron densities into EM reconstructions is presented. This new procedure was inspired by a rigid-body refinement method used in macromolecular X-ray crystallography.

Purification, crystallization and preliminary X-ray analysis of the BRCT domains of human 53BP1 bound to the p53 tumour suppressor

To investigate how the BRCT domains of 53BP1 protein bind to p53, the 53BP1 BRCT region in complex with the DNA-binding domain of p53 was overexpressed, purified and crystallized. The crystals of the complex belong to the space group P2₁2₁2₁ and diffraction data have been collected to 2.6 Å resolution.

Crystallization and preliminary X-ray characterization of archaeal group II chaperonin α-subunit from Thermococcus strain KS-1

The mutant α-subunit of group II chaperonin from Thermococcus strain KS-1 was crystallized. Diffraction data were collected to 2.4 Å with a synchrotron-radiation source.

Purification, crystallization and preliminary X-ray diffraction analysis of a novel mannose-binding lectin from Gastrodia elata with antifungal properties

A plant antifungal protein, Gastrodia antifungal protein (GAFP-1) has been purified from terminal corms of the orchid G. elata and crystallized in space group P2₁2₁2 and with unit-cell parameters a = 61.087, b = 91.488, c = 81.132 Å. A set of diffraction data to resolution 2 Å has been collected with an overall R_merge of 0.097 and a completeness of 99.8%, which will help to solve the first structure of a monomeric monocot mannose-binding lectin.

Preliminary crystallographic study of an acidic phospholipase A₂ from Ophiophagus hannah (king cobra)

A non-toxic acidic phospholipase A₂ from the venom of O. hannah (king cobra) has been crystallized and X-ray data have been collected and reduced to 2.1 Å resolution. Analysis by molecular replacement showed there to be six enzyme molecules per asymmetric unit.

Crystallization and preliminary crystallographic studies of a novel antifungal protein with five di­sulfide bridges from Eucommia ulmoides Oliver

A novel antifungal protein with five disulfide bridges from E. ulmoides Oliver has been crystallized. X-ray diffraction data at 1.0 Å have been collected and used to obtain phase information directly by an ab initio method.

Crystallization and preliminary X-ray diffraction analysis of recombinant hydrolase domain of 10-formyltetra­hydrofolate de­hydrogenase

10-Formyltetrahydrofolate dehydrogenase is important for the regulation of intracellular folate pools, for de novo purine biosynthesis and for the removal of formate in the form of CO₂. Crystals of the amino-terminal hydrolase domain of this enzyme that diffract to 2.3 Å resolution have been obtained.

Crystallization and preliminary crystallographic characterization of the extracellular Ig-like domain of human natural killer cell activating receptor NKp44

NKp44, a natural killer cell activating receptor, is composed of an extracellular region (168 amino acids), a membrane-spanning segment (25 amino acids) and a cytoplasmic domain (63 amino acids). The extracellular region Ig-like domain, held to be involved in target-cell recognition/binding, has been crystallized in a form suitable for structural investigation.

Crystallization and preliminary X-ray analysis of cyclophilin from Leishmania donovani

Cyclophilin from the parasite L. donovani has been crystallized, with crystals diffracting up to 3.5 Å resolution. Unambiguous solutions in rotation and translation functions have been obtained with human cyclophilin as the search model.

Human neuroglobin: crystals and preliminary X-ray diffraction analysis

Human neuroglobin (151 amino acids), a haemoglobin involved in the neuronal response to hypoxia or ischaemia, has been expressed, purified and crystallized as a Cys-free mutant protein, with a view to three-dimensional structure determination.

Expression, purification and crystallization of Dpr, a ferritin-like protein from the Gram-positive meningitis-associated bacterium Streptococcus suis

Dpr, a ferritin-like protein from S. suis, was expressed in E. coli, purified and crystallized. Full data were collected to 2.3 Å resolution using synchrotron radiation.

Cloning, purification and crystallization of full-length human annexin 2

Crystallization and preliminary diffraction data analysis for recombinant human annexin 2 to 1.52 Å resolution.

Crystallization of cyclase-associated protein from Dictyostelium discoideum

Cyclase-associated protein (CAP) from D. discoideum, a protein involved in signal transduction, has been crystallized and a complete native data set has been collected at 2.2 Å resolution.

Crystallization and preliminary X-ray diffraction studies on the DNA-binding domain of the transcriptional activator protein PhoB from Escherichia coli

The DNA-binding domain of the transcriptional activator PhoB (PhoBC) has been expressed in E. coli and crystallized in two crystal forms, one of which led to experimental maps at 3.0 Å resolution.

Purification, crystallization and preliminary diffraction studies of AcrB, an inner-membrane multi-drug efflux protein

The multi-drug efflux transporter AcrB from E. coli was purified and crystallized. AcrB crystallizes in space group R32, with unit-cell parameters a = b = 143, c = 513 Å. Crystals diffract to 3.0 Å resolution.

Expression, purification, crystallization and preliminary X-ray analysis of the sexual stage-specific protein Pfg27 from Plasmodium falciparum

To aid studies in understanding gametocytogenesis in P. falciparum, Pfg27 has been expressed and purified yielding ∼5 mg l⁻¹ of purified protein in soluble form. This protein has been crystallized by the hanging-drop vapor diffusion method using PEG 8000 as a precipitant. Native diffraction data were collected under cryogenic conditions, and phase resolution by selenium-methionine aided multiple-wavelength anomalous dispersion technique is in progress.

Preparation of a crystallizable mRNA-binding fragment of Moorella thermo­acetica elongation factor SelB

A C-terminal 30 kDa fragment of the selenocysteine-specific elongation factor SelB from M. thermoacetica has been recloned, expressed in E. coli and crystallized in a suitable form for X-ray analysis. The crystals diffract to 2.7 Å in an in-house X-ray source.

Crystallization and preliminary X-ray crystallographic analysis of peptide de­formylase from Pseudomonas aeruginosa

Peptide deformylase from P. aeruginosa has been crystallized (P2₁2₁2₁; a = 68.75, b = 74.46, c = 77.18 Å). Diffraction data have been collected to 1.85 Å using synchrotron X-rays.

Purification, crystallization and preliminary X-ray diffraction analysis of yeast nucleosome-assembly factor Cia1p

The nucleosome-assembly factor Cia1p from S. cerevisiae has been crystallized by the hanging-drop method. A complete diffraction data set using synchrotron radiation was collected to 2.95 Å resolution.

Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidus

Crystallization of bucain, a three-finger toxin structurally homologous to snake-venom muscarin toxins, from the venom of the Malayan krait B. candidus is presented.

Crystallization, X-ray characterization and selenome­thionine phasing of Mlc1p bound to IQ motifs from myosin V

Mlc1p is a myosin light chain that binds to IQ motifs of a class V myosin (Myo2p) and an IQGAP-like protein (Iqg1p), playing a role in cytokinesis and organelle transport in S. cerevisiae. Complexes of Mlc1p with IQ motifs 2, 3, 4, and 2,3 of Myo2p were crystallized and their structures determined.

The use of construct variation and diffraction data analysis in the crystallization of the TRAF domain of human tumor necrosis factor receptor associated factor 6

Construct variation in conjunction with diffraction data analysis were used in the successful crystallization of the TRAF domain of TRAF6.

Xtrack – a web-based crystallographic notebook

A web-based database-backed crystallographic notebook system is presented.

A crystallographic glimpse of a nucleotide triphosphate (AMPPNP) bound to a protein surface: external and internal AMPPNP molecules in crystalline N-acetyl-L-glutamate kinase

A large volume of electron density in the crystal of Escherichia coli N-acetyl-L-glutamate kinase is interpreted as an external AMPPNP molecule that makes contacts with the enzyme through its γ-imidophosphate. This external nucleotide differs in a number of respects from the internal AMPPNP bound to the active site, and the possibility that the external AMPPNP is waiting to occupy the active center is discussed.