June 2004 issue
Cover illustration: Hexameric assembly of E. coli MoaB viewed along the threefold crystallographic symmetry axis (p. 1068).
The anisotropic mosaicity of protein crystals was investigated using high-resolution X-ray diffraction rocking-curve measurements. Statistical data analysis was used to quantitatively evaluate whether a homogeneous magnetic field of 2.4 T applied during crystal growth can lead to improved crystal quality in the example of the tetragonal form of hen egg-white lysozyme.
The crystal structure of A. irakense pectate lyase (PelA) has been determined at a resolution of 2.65 Å. The overall structure of PelA does not adopt the characteristic parallel β-helix fold displayed by pathogenic pectate lyases; instead, it displays a predominantly α-helical structure with irregular coils and short β-strands.
Photoactive yellow protein was solved at high resolution under a variety of conditions in order to investigate the unusually short hydrogen bonds to its coumaric acid chromophore.
A novel benzoic acid inhibitor of influenza virus neuraminidase induces a previously unobserved conformational change in the side chain of the crucial active-site residue Glu275.
It is shown that in the presence of severe site-specific radiation damage the use of unmerged data and a parametrization that implements dose-dependent occupancies for the anomalous scatterers can give significant improvements in SAD/MAD and/or heavy-atom phases. Such an option is now implemented in the program SHARP; results on a brominated RNA molecule are presented.
The crystal quality of three kinds of biomolecules have been assessed by a `relative Wilson plot' method and a rational method has been developed for estimating crystal quality.
An orthorhombic actin crystal was converted into a partially hemihedrally twinned tetragonal crystal by condensation induced by flash-freezing. The structure, with two actin molecules in the crystallographic asymmetric unit, was determined by molecular-replacement methods.
The crystal structure of Mn–Mn ConA grown by the gel-acupuncture method at pH 8 contains 25 molecules of glycerol, the majority of them at conserved positions. A relation exists between the crystal contacts and the space group, the contact Asp58–Ser62 being a universal feature of ConA crystals.
This paper presents an efficient quaternion-based algorithm for analyzing peaks from a cross-rotation function to identify model orientations consistent with proper non-crystallographic symmetry (NCS), and to generate NCS-consistent orientations missing from the list of cross-rotation peaks.
The crystal structure of E. coli MoaB protein and a detailed comparison with the homologues MogA, Cnx1 G-domain and gephyrin are reported.
A simple screening test for optimized stabilization and conditions for an ABC-ATPase was established that preserves activity, avoids precipitation and provided material suitable for crystallization and X-ray analysis for all of the functional states of the catalytic cycles of the HlyB-NBD.
An analysis of radiation-damage-induced structural and intensity changes is presented on the model protein thaumatin.
The crystal structure of PH1161 protein, a transcriptional activator B. subtilis TenA homologue from P. horikoshii, was analyzed at 2.15 Å resolution.
structural genomics papers
This paper reports the crystal structure of the product of the YdeN gene.
The purification and crystallization of two cysteine-rich secretory protein (CRISP) family members, natrin and stecrisp from N. atra and T. stejnegeri venoms, allowed the collection of two complete data sets to 2.1 and 1.6 Å resolution, respectively.
L. laeta SMase I, a 32 kDa sphingomyelinase present in L. laeta venom, has been crystallized and diffraction data have been collected to 1.8 Å resolution.
The DNA-binding domain of BldD from S. coelicolor has been crystallized. The crystals diffract to 1.8 Å resolution and belong to space group C2.
Nogalonic acid methyl ester cyclase, a polyketide cyclase in the biosynthetic pathway of the antibiotic nogalamycin, has been crystallized. The crystals obtained in the presence of the substrate are orthorhombic, space group I222, with unit-cell parameters a = 69.1, b = 72.0, c = 65.4 Å and diffract to 1.35 Å resolution.
A novel plant defensin protein, SPE10, was isolated and characterized from P. erosus seeds. Preliminary crystallographic studies have been performed.
Two peroxisomal acyl-CoA oxidase enzymes from A. thaliana have been expressed in E. coli and one of them was crystallized in a selenomethionine-substituted form. Diffraction data from both enzymes have been collected at synchrotron sources.
The cloning, overexpression and crystallization of PhzA, an enzyme involved in the final steps of phenazine-1-carboxylic acid biosynthesis, were undertaken. Details of data collection from both native and seleno-L-methionine-labelled crystals are described.
GyrA14, a fragment of GyrA, was crystallized in its free state and as a complex with the toxin CcdB.
Acylphosphatase from a hyperthermophilic archaea, P. horikoshii OT3, has been crystallized and X-ray diffraction data have been collected to 1.72 Å resolution.
The S. coelicolor actIII ORF5 gene has been isolated and cloned into a His-tagged vector to overexpress an active NADPH-dependent ketoreductase used in type II polyketide synthesis. Protein crystals obtained in the presence of NADP+ diffract to 2.5 Å.
A novel haemolytic lectin from the parasitic mushroom L. sulphureus has been crystallized by the hanging-drop vapour-diffusion method. Native data have been collected to 2.7 Å resolution.
The expression, purification, crystallization and preliminary X-ray analysis of a novel human DNA glycosylase are presented.
CylR2 was expressed with a C-terminal six-histidine tag and purified to homogeneity with a cobalt-affinity column followed by size-exclusion chromatography. Both native and SeMet proteins were produced and crystallized.
The thermostable endo-1,5-α-L-arabinanase ABN-TS from B. thermodenitrificans TS-3 was crystallized. A complete diffraction data set was collected to 1.9 Å resolution using synchrotron radiation.
Crystallization of B. subtilis guanine deaminase, a key enzyme in nucleotide metabolism which catalyzes the hydrolytic deamination of guanine to xanthine.
γ-Filamin is a multidomain protein present in the myofibrillar Z-disc, where it cross-links the actin filaments. Recombinant repeat 23 of γ-filamin was crystallized and a SAD data set was collected to 2.05 Å resolution.
Crystals of the motor domain of the human centromere-associated protein E (CENP-E) have been obtained by high-throughput crystallization screening using an automated TECAN crystallization robot. The best-diffracting crystals belong to space group P21, with unit-cell parameters a = 49.35, b = 83.70, c = 94.16 Å, β = 103.05°, and diffract to better than 2.1 Å.
Crystals of the fusion core of both Nipah and Hendra viruses were obtained; the crystals diffract X-rays to 2.0–2.1 Å.
Tetragonal and orthorhombic crystals of EcoO109I and its complex with DNA were obtained and diffraction data were collected to 2.4 and 1.9 Å resolution, respectively.
α-Isopropylmalate synthase from M. tuberculosis (Rv3710), which catalyses the first committed step of leucine biosynthesis, has been expressed, purified and crystallized in a form suitable for high-resolution X-ray structural analysis.
This study describes the crystallization and preliminary X-ray analysis of a heterodimer containing the ligand-binding domains of the retinoid X receptor α and of the retinoic acid receptor β in complex with 9-cis-retinoic acid and a fragment of the transcriptional coactivator TRAP220. The complex crystallizes in space group P3121 and diffracts to 2.9 Å resolution.
The crystal structure of the plant-type asparaginase from E. coli, EcAIII, has been solved by molecular replacement and refined to a resolution of 1.65 Å. Sodium ion-binding sites have been identified that were not observed in other related enzymes. The structure of EcAIII helps to explain some of the differences between the substrate specificities of plant-type asparaginases and glycosylasparaginases.
The crystal structure of a novel acylphosphatase (AcpDro2) has been solved at 1.5 Å resolution in order to improve knowledge of the enzyme catalytic cycle as well as of the molecular basis of protein folding, misfolding and aggregation.
The ArsC triple mutant C10SC15AC82S has a structure that is very similar to that of the reduced form of wild-type ArsC, with a folded redox helix and a buried catalytic Cys89. In the adduct form, the TNB molecule is buried in a hydrophobic pocket and the disulfide bridge between TNB and Cys89 is sterically inaccessible to thioredoxin.