Editorial

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex

The crystal structure of the bacterial catalase from M. lysodeikticus has been refined at 0.88 Å using the gene-derived sequence, revealing the active site with unprecedented accuracy. In addition, the structures of the ferryl intermediate of the catalase (compound II) at 1.96 Å resolution and the catalase complex with NADPH at 1.83 Å resolution have been determined.

The impact of Glu→Ala and Glu→Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 Å resolution

Studies of a number of Glu→Ala single and multiple mutants of RhoGDI show that such mutations may be generally useful to enhance protein crystallizability. One of the mutants yielded data to 1.2 Å resolution, showing that surface mutants can be used to dramatically improve the resolution of X-ray data.

Structures of Plasmodium falciparum triosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state

Structures of triosephosphate isomerase (TIM) from the malarial parasite P. falciparum (Pf) complexed to the substrate analogues 3-phosphoglycerate and glycerol-3-phosphate have been determined at 2.4 Å resolution. The catalytic loop of TIM adopts a novel `loop-open' conformation in these complexes. These structures provide insight into the design of inhibitors specific for the malarial enzyme.

Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 Å in complex with the inhibitors rs367 and rs370

Two 1.8 Å resolution crystal structures of the Ser205 mutant plasmepsin II from P. falciparum in complex with two Phe–Leu core inhibitors that incorporate tetrahedral transition-state mimetic hydroxypropylamine are described.

Refinement of the arginine kinase transition-state analogue complex at 1.2 Å resolution: mechanistic insights

The transition-state complex of this 42 kDa homologue of creatine kinase has been refined at 1.2 Å resolution. It indicates that precise positioning of substrates and restriction of the active-site motion are important components in catalysis.

Structure of a circularly permuted phosphoglycerate kinase

The crystallographic structure of a circularly permuted form of yeast PGK has been determined to a resolution of 2.3 Å. The overall fold of the protein is very similar to that of the wild-type protein, directly demonstrating that the continuity of a folding unit is not relevant to the folding process of the whole protein.

An investigation of magnetic field effects on the dissolution of lysozyme crystal and related phenomena

The diffusivity of lysozyme molecules was deduced to decrease under a magnetic field, based on the discovery of magnetic damping of the dissolution process using a Mach–Zehnder interferometer. In the same experiment, a redistribution of the concentration before crystal growth was also found.

Structure of human carbonmonoxyhemoglobin at 2.16 Å: a snapshot of the allosteric transition

A new structure of carbonmonoxyhemoglobin solved at 2.16 Å is reported. The new structure, obtained using a lower pH, shows significant strain at the α1β2 (α2β1) interface, suggests initiation of the R to T allosteric transition.

Structure of mutant human carbonmon­oxy­hemoglobin C (βE6K) at 2.0 Å resolution

The first high-resolution crystal structure for liganded hemoglobin C, a mutant hemoglobin that forms crystals in red blood cells of individuals with CC and SC diseases, was obtained from a COHbC crystal grown in concentrated potassium phosphate buffer. The dynamic structure of the βEK6 side chain could potentially support a number of specific polar interactions that may contribute to enhanced nucleation kinetics for HbC relative to HbA.

Automatic modeling of protein backbones in electron-density maps via prediction of C^α coordinates

A new computational procedure called CAPRA is described that predicts coordinates of C^α atoms in density maps and outputs chains of C^α atoms representing the backbone of the protein.

Structure determination of a cocaine hydrolytic antibody from a pseudomerohedrally twinned crystal

The structure of a cocaine hydrolytic antibody has been determined from a pseudomerohedrally twinned crystal. The lattice is primitive monoclinic with higher apparent primitive orthorhombic symmetry.

Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin

Glycerol displaces water molecules bound to thaumatin.

Multiple rotation function

A simultaneous analysis of several rotation functions allows the model orientation to be found in situations when the standard search fails. An automated procedure has been developed to apply such an analysis routinely.

The influence of detergents on the solubility of membrane proteins

The dependence of protein solubility on ionic strength was measured for the bacterial reaction center in different detergents and amphiphiles. The detergent and amphiphile combinations that yielded the highest solubility of the protein are correlated with those that yield protein crystals.

Statistical density modification with non-crystallographic symmetry

Statistical density modification can make use of NCS in a crystal and can include estimates of the deviations from perfect NCS.

Convergent-beam method in macromolecular crystallography

The convergent-beam method of data collection for macromolecular crystals is described.

S-SAD, Se-SAD and S/Se-SIRAS using Cu Kα radiation: why wait for synchrotron time?

The structure of E. coli argininosuccinate synthetase (EAS) has been determined using S-SAD, Se-SAD and S/Se-SIRAS data measured with Cu Kα radiation.

Parallel cloning, expression, purification and crystallization of human proteins for structural genomics

Insights are gained into high-throughput target selection, cloning, expression and crystallization of human genomic proteins. For example, there was a marked difference seen bewteen the ease of expression of proteins of molecular weight (MW) < 25 kDa (93% success), compared with proteins > 25 kDa MW, which were less easy to express (61% success).

A medium-throughput crystallization approach

In the context of a medium-scale structural genomics program, a crystallization approach was based on a two-step procedure: a large screening step employing robotics, followed by manual or automated optimization of the crystallization conditions. A nanodrop dispensing robot (50–200 nl) proved to be useful for obtaining diffracting crystals while using small amounts of protein. In 10 months, 25 proteins were subjectred to crystallization, 13 yielded crystals among which ten led to usuable data sets and five to structures.

Autotracing of Escherichia coli acetate CoA-transferase α-subunit structure using 3.4 Å MAD and 1.9 Å native data

This study demonstrates that phases obtained at low resolution (>3.0 Å) from crystals of SeMet-labeled protein can be successfully used for automated structure determination.

Purification, crystallization and preliminary X-ray analysis of the disintegrin contortrostatin from Agkistrodon contortrix contortrix snake venom

Contortrostatin, a small homodimeric protein (64 residues per chain) from southern copperhead snake venom, has been crystallized successfully. Crystals of the title compound, which is a member of the disintegrin family of proteins, diffract up to a maximum resolution of 1.7 Å.

Crystallization of an α-amylase, AmyA, from the thermophilic halophile Halothermothrix orenii

The first crystallographic study of an α-amylase from an organism that is both thermophilic and halophilic, at 1.89 Å resolution.

Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80

The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been obtained, for which diffraction data extend to 2.3 Å resolution.

The production, purification and crystallization of a soluble heterodimeric form of a highly selected T-cell receptor in its unliganded and liganded state

This report details the production, purification, crystallization and preliminary diffraction analysis of a T-cell receptor.

Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding domain of flocculin, a cell-adhesion molecule from Saccharomyces carlsbergensis

The recombinant carbohydrate-binding domain of the cell-surface lectin flocculin from brewer's yeast has been identified, purified and crystallized.

Crystallization and preliminary X-ray analysis of the ytxM gene product from Bacillus subtilis

The B. subtilis ytxM gene product has been crystallized and a MAD data set has been collected to 2.0 Å resolution.

Crystallization and preliminary X-ray analysis of the tumor metastasis factor p37

P37, an outer-membrane bacterial protein from Mycoplasma hyorhinis whose presence on the surface of many tumor cells correlates highly with increased neoplastic invasivity and metastasis, has been overexpressed in Escherichia coli, purified by affinity chromatography and crystallized.

Crystallization and preliminary X-ray crystallographic analysis of aceto­hydroxy acid isomeroreductase from Pseudomonas aeruginosa

Acetohydroxy acid isomeroreductase from P. aeruginosa was crystallized. X-ray data have been collected to 2.0 Å resolution using synchrotron radiation (P2₁3, a = b = c = 184.38 Å).

Crystallization and preliminary X-ray analysis of the trehalose/maltose ABC transporter MalFGK₂ from Thermococcus litoralis

The crystallization and preliminary characterization of the MalFGK₂ transport complex from T. litoralis is presented.

Overexpression, purification, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa L-arginine deiminase

Overexpression, purification and crystallization of P. aeruginosa L-arginine deiminase allowed collection of a complete MAD data set to 3.2 Å resolution.

Co-crystallization of Staphylococcus aureus peptide de­formylase (PDF) with potent inhibitors

Diffraction-quality Se-met crystals of S. aureus PDF were prepared that belong to space group C222₁ with unit-ell parameters of a = 94.1 b = 121.9 c = 47.6 Å. Crystals were also prepared with three PDF inhibitors: thiorphan, actinonin and PNU-172550.

Crystallization and preliminary X-ray diffraction studies of NusG, a protein shared by the transcription and translation machines

N-utilization factor G (NusG) from A. aeolicus has been overexpressed, purified and crystallized. The crystals diffract to 2.45 Å resolution.

Cloning, expression, purification and preliminary X-ray crystallographic studies of 2-methylisocitrate lyase from Salmonella typhimurium

2-Methylisocitrate lyase from S. typhimurium IFO 12529 has been cloned, overexpressed and crystallized. The crystal belongs to space group P2₁2₁2₁, with unit-cell parameters a = 63.600, b = 100.670, c = 204.745 Å. A complete data set to 2.5 Å resolution has been collected.

Crystallization and preliminary X-ray structure analysis of isocitrate de­hydrogenase from two hyperthermophiles, Aeropyrum pernix and Thermotoga maritima

Extremely thermostable isocitrate dehydrogenases from A. pernix and T. maritima were crystallized and X-ray diffraction data were collected to 2.6 and 2.8 Å, respectively. The crystallization and preliminary crystallographic analysis are described for both enzymes.

Purification, characterization and preliminary crystallographic studies of a PR-10 protein from Pachyrrhizus erosus seeds

A new PR-10 family protein SPE16 with ribonuclease activity was purified from the seeds of P. erosus as a constitutive protein and has been crystallized.

Crystallization and preliminary X-ray diffraction analysis of FKBP52 N-terminal domain

The N-terminal (amino acids 1–140) domain of human FKBP52 has been crystallized. The crystals belong to space group P2₁ with unit-cell parameters a = 27.8, b = 58.4, c = 70.9 Å, β = 98.3° and diffract to 2.4 Å resolution limit.

Expression, crystallization and preliminary X-ray studies of the recombinant PTB domain of human dok-5 protein

The PTB domain of human dok-5 protein has been crystallized as well as a selenomethionmine-substituted protein for MAD phasing determination. The crystals belong to space group P3₂21 (a = b = 75.9, c = 108.0 Å) and diffract up to 2.3 Å resolution using synchrotron radiation.

Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038

Naphthalene dioxygenase from Rhodococcus has been crystallized in space group P2₁2₁2₁. The crystals diffract to 2.3 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of a thermostable D-hydantoinase from the mesophilic Bacillus sp. AR9

A thermostable D-hydantoinase from mesophilic Bacillus sp. AR9 was crystallized and diffracted to 2.3 Å resolution having unit-cell parameters a = b = 129.55, c = 102.8 Å, α = β = 90, γ = 120°.

Crystallization of Pichia pastoris lysyl oxidase

The lysyl oxidase isolated from the yeast P. pastoris has been crystallized and synchrotron data have been recorded to a resolution of 1.65 Å.

Preliminary crystallographic studies of the creatinine amido­hydrolase from Pseudomonas putida

Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from P. putida has been overexpressed in E. coli and crystallized by the hanging-drop method.

Crystallization and preliminary X-ray crystallographic studies on the class II cholesterol oxidase from Burkholderia cepacia containing bound flavin

Crystals of B. cepacia cholesterol oxidase, a 3β-hydroxysteroid oxidase containing covalently bound FAD, were obtained by the hanging-drop method using polyethylene glycol as a precipitant. The crystals diffract to beyond 2.0 Å and belong to space group P3₁21, with approximate unit-cell parameters a = b = 119.6, c = 101.1 Å and one subunit in the asymmetric unit.

Crystallization and preliminary X-ray analysis of the catalase–peroxidase KatG from Burkholderia pseudomallei

Crystals of the catalase–peroxidase from B. pseudomallei diffract to beyond 1.8 Å.

Expression, purification, crystallization and preliminary X-ray diffraction studies of human cathepsin F complexed with an irreversible vinyl sulfone inhibitor

A human papain-family cysteine protease has been expressed in P. pastoris, purified by conventional chromatography and crystallized.

Expression, purification, crystallization and preliminary characterization of an HHED aldolase homologue from Escherichia coli K12

An ORF from the E. coli K12 genome with 56% sequence identity to 2,4-dihydroxy-hept-2-ene-1,7-dioic acid (HHED) aldolase has been cloned, expressed and purified. Crystals obtained from the purified recombinant enzyme, belonging to space group C222₁, diffracted to a resolution of 1.78 Å.

Co-crystallization of the human nuclear cap-binding complex with a m⁷GpppG cap analogue using protein engineering

A long solvent-exposed coiled coil in the large subunit (CBP80) of the heterodimeric nuclear cap-binding complex (CBC) has been truncated to permit crystallization of CBC with the cap analogue m⁷GpppG in two crystal forms diffracting to 2.15 and 2.3 Å resolution.

The 2.2 Å resolution structure of thermolysin (TLN) crystallized in the presence of potassium thio­cyanate

The structure of the thermolysin (TLN) crystallized in the presence of SCN⁻ suggests explanations for the solubility increase of TLN and for the inhibitory effect of high SCN⁻ concentrations on the TLN activity.

Structure of the Humicola insolens cellobio­hydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-β-cellobioside, at 1.9 Å

The complex of the H. insolens cellobiohydrolase Cel6A in complex with a thiooligosaccharide substrate analogue has been determined at 1.9 Å resolution.

When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

Crystallization analyasis of twinned diffraction data of d(ApTpApTpApT) in a hexagonal packing.

Structure of Escherichia coli pyruvate formate-lyase with pyruvate

The structure of inactive pyruvate formate-lyase in complex with a natural substrate, pyruvate, has been solved at 2.7 Å resolution.

Rapid automatic NCS identification using heavy-atom substructures

A rapid algorithm for identifying NCS in heavy-atom sites is described.

FOX two-dimensional X-ray focusing optic

New developments in protein-crystallization platforms and barcoding for cryogenic storage