A drunken search in crystallization space

The PDB is looked at to find data to answer the question `How well do our current screens cover crystallization space?' and to try to find answers to the more general question about the most efficient strategy to employ in a crystallization campaign.

The structure of lactoferrin-binding protein B from Neisseria meningitidis suggests roles in iron acquisition and neutralization of host defences

The crystal structure of the N-terminal domain of lactoferrin-binding protein B (LbpB) from N. meningitidis is reported. Docking of the structure with lactoferrin suggests roles for LbpB in both host iron acquisition and neutralization of the toxic effects of the lactoferricin peptide.

Structure of a short-chain de­hydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii

The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified.

Human carbonic anhydrase II–cyanate inhibitor complex: putting the debate to rest

A controversy has existed in the literature between crystallographic and spectroscopic data on the binding mode of cyanate to carbonic anhydrase II (CA II). To settle this ambiguity, the X-ray crystal structures of the complexes of wild-type and V207I variant CA II with cyanate were redetermined to 1.7 and 1.5 Å resolution, respectively. The data clearly support that cyanate binds directly to the catalytic zinc and not as an outer sphere ligand mimicking the binding of CO₂.

Structure of an Aspergillus fumigatus old yellow enzyme (EasA) involved in ergot alkaloid biosynthesis

The structure of the A. fumigatus old yellow enzyme EasA was determined to 1.8 Å resolution. This enzyme catalyzes the reduction of chanoclavine-I aldehyde to dihydrochanoclavine aldehyde and works in conjunction with festuclavine synthase at the branchpoint for ergot alkaloid pathways.

Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate de­hydrogenase holoenzyme reveals a novel surface

The crystal structure of group B streptococcus glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution.

Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure

The structure of homoserine O-acetyltransferase (HTA) from the human pathogen Staphylococcus aureus has been determined. Despite a similar overall fold and active site architecture to other α/β-hydrolases, this more compact HTA structure has a more narrow access to the active site than can confer important specificity differences.

Expression, purification and preliminary crystallographic analysis of the cryptic polo-box domain of Caenorhabditis elegans ZYG-1

The cryptic polo-box (CPB) domain of the polo-like kinase ZYG-1 from C. elegans was cloned, overexpressed, purified and crystallized. Anomalous X-ray diffraction data were collected to 2.54 Å resolution.

Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes

IL-18 and its two receptors, IL-18Rα and IL-18Rβ, were purified for crystallization and biochemical analysis. IL-18 was crystallized in free, IL-18Rα-bound and IL-18Rα/IL-18Rβ-bound states and complete X-ray data sets suitable for further structural analysis were obtained from each crystal.

Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element

Crystals of the Pax9 paired domain bound to a DC5 enhancer DNA element that diffract anisotropically to 3.0 Å resolution are reported.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa

The integral membrane lysine permease from P. aeruginosa was cloned and overexpressed in E. coli as a GFP-fusion protein. Crystals of the tag-less transporter diffracted to 7.5 Å resolution.

Expression, crystallization and preliminary X-ray crystallographic analysis of cysta­thionine β-lyase from Acinetobacter baumannii OXA-23

Cystathionine β-lyase from multidrug-resistant A. baumannii OXA-23 (AbCBL), an enzyme involved in the methionine-metabolism pathway and a novel antibacterial drug target, was cloned, expressed, purified and crystallized. Preliminary X-ray crystallography was performed to analyse the AbCBL crystal.

Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from Mycobacterium smegmatis

The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from M. smegmatis are described..

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of fructose-1,6-bis­phosphate aldolase from Escherichia coli

FBPA I from E. coli was expressed, purified and crystallized. The crystals diffracted to 2.0 Å resolution and belonged to space group C2.

Crystallization of the Ets1–Runx1–CBFβ–DNA complex formed on the TCRα gene enhancer

The Ets1–Runx1–CBFβ–DNA complex, a higher-order TF–DNA complex formed on the T-cell receptor α gene enhancer, was crystallized.

Crystallization and preliminary X-ray crystallographic studies of CrArsM, an arsenic(III) S-adenosylme­thionine methyltransferase from Chlamydomonas reinhardtii

The crystallization and preliminary crystallographic analysis of CrArsM, an arsenic(III) S-adenosylmethionine methyltransferase from C. reinhardtii, is described.

Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands

Crystallization experiments of the BRPF1 bromodomain in complex with its H4K12ac and H2AK5ac histone ligands yielded crystals that are suitable for high-resolution X-ray diffraction analysis. These structures will be solved in order to elucidate the molecular mechanism of histone recognition.

Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal α/β-hydrolase from Candidatus Nitrososphaera gargensis

The chemolithoautotrophic nitrifying thaumarchaeon Ca. Nitrososphaera gargensis with unusual metabolic pathways was enriched by cultivation over six years. A novel α/β-hydrolase was identified, isolated and crystallized for further functional analysis.

Crystallization and preliminary X-ray diffraction analysis of Lin1840, a putative β-glucosidase from Listeria innocua

Lin1840 from L. innocua has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to a resolution of 1.8 Å.

Expression, crystallization and preliminary X-ray analysis of McbB, a multifunctional enzyme involved in β-carboline skeleton biosynthesis

McbB, a multifunctional enzyme responsible for catalysing Pictet–Spengler cyclization, decarboxylation and oxidation reactions in the biosynthesis of β-carboline, was expressed and crystallized. The crystals belonged to the monoclinic space group P2₁, with unit-cell parameters a = 66.06, b = 85.48, c = 106.19 Å, α = 90.00, β = 106.77, γ = 90.00°.

Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase

A crystal was obtained of the complex between reduced terminal oxygenase and oxidized ferredoxin components of carbazole 1,9a-dioxygenase. The crystal belonged to space group P2₁ and diffracted to 2.25 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of the cis-isoprenyl diphosphate synthase superfamily

Cyclolavandulyl diphosphate synthase, which catalyzes both the condensation of two molecules of C₅ dimethylallyl diphosphate and the subsequent cyclization, has been crystallized and X-ray diffraction data have been collected and analyzed.

Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain

The CIDE domain of Drep2 was purified and crystallized in space group P2₁2₁2₁, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37 Å. The crystals diffracted to a resolution of 2.3 Å.

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom

The SMase D from L. gaucho venom was expressed, purified, crystallized and diffraction data were collected to 2.6 Å resolution.

Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase from Bacillus thuringiensis

The first crystal structure for an intracellular poly(3-hydroxybutyrate) depolymerase at 1.42 Å resolution was determined by molecular replacement using a search model with 24% sequence identity.

Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thio­sulfate de­hydrogenase TsdA, an unusual acidophilic c-type cytochrome

The thiosulfate dehydrogenase TsdA from A. vinosum was recombinantly expressed, purified and crystallized. The crystals belonged to space group C2, with unit-cell parameters a = 79.2, b = 69.9, c = 57.9 Å, β = 129.3°, and diffracted to a resolution of 1.98 Å.

Crystallization and preliminary X-ray diffraction analysis of full-length spr1814, a response regulator of Streptococcus pneumoniae, in complex with a phosphoryl analogue

A crystal of the full-length response regulator spr1814 of S. pneumoniae in complex with a phosphoryl analogue was obtained and diffraction data were collected to 1.9 Å resolution.

Crystallization and preliminary X-ray diffraction studies of the C-terminal domain of Chlamydia trachomatis CdsD

The C-terminal domain of C. trachomatis CdsD was purified and crystallized. The preliminary X-ray diffraction studies are presented.

Enhancing ubiquitin crystallization through surface-entropy reduction

All seven possible single-site lysine-to-serine mutations of ubiquitin were tested for crystallization behavior and were found to yield crystallization `hit rates' varying by two orders of magnitude. High-resolution structures of three mutants revealed that mutations can exert both promoting and permissive effects on crystallization.

Felix Frolow (1947–2014)

Obituary for Felix Frolow.