Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity

Five crystal structures of three diphtheria toxin repressor (DtxR) variants in the two trigonal space groups P3₁21, and P3₂21 have been determined. The three variants exhibit decreased repressor activity and the structures are compared with the wild-type DtxR structures.

Caged and clustered structures of endothelin inhibitor BQ123, cyclo(-D-Trp-D-Asp⁻-Pro-D-Val-Leu-)Na⁺, forming five and six coordination bonds between sodium ions and peptides

BQ123 is a cyclic pentapeptide and a potent endothelin-1 inhibitor. The crystal structure of the BQ123 sodium salt was determined as the first example of an endothelin inhibitor.

NADP⁺ and NAD⁺ binding to the dual coenzyme specific enzyme Leuconostoc mesenteroides glucose 6-phosphate de­hydrogenase: different interdomain hinge angles are seen in different binary and ternary complexes

NADP⁺ is important in biosynthesis while NAD⁺ is involved in catabolism; glucose-6-phosphate dehydrogenase from L. mesenteroides is rare in its functional dual specificity for coenzyme. Structures of coenzyme complexes show different interdomain hinge angles and a less complementary fit of NAD⁺ than of NADP⁺ to the coenzyme site.

Ultrahigh-resolution structure of a BPTI mutant

Anisotropic refinement of the structure of a BPTI mutant at 0.86 Å resolution without restraining the main-chain geometry confirms that the peptide group can show significant deviations from strict planarity and that the N—C^α—C angle has a wide spread. In addition to previously noted features, the structure reveals a high proportion of alternate-conformation residues, correlation of disorder on the intermolecular scale and the positions of many H atoms (including those in water molecules) and their involvement in C—H⋯O and N—H⋯π interactions.

Structure of Escherichia coli fragment TR₂C from calmodulin to 1.7 Å resolution

The comparison of the crystal structure of fragment TR₂C with intact calmodulin and with the NMR structure of TR₂C is presented.

Structure of cytochrome c₇ from Desulfuromonas acetoxidans at 1.9 Å resolution

The crystal structure of the smallest representative of the c₃ superfamily, cytochrome c₇, is reported. The haem arrangement is compared with that of the homologous c₃ cytochromes and the importance of highly conserved residues is discussed.

Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI

The crystallization properties of multiple site-directed mutants were explored, and structures were determined for four of the resulting crystals. Surface mutations are located at crystal lattice contacts, and a rationale is proposed to improve the crystallization of other proteins.

On the routine use of soft X-rays in macromolecular crystallography

The results of diffraction experiments using soft X-rays of wavelength λ = 2.6 Å prove that such experiments can be carried out in a routine fashion without making time-consuming changes to the synchrotron beamline setup.

X-LIGAND: an application for the automated addition of flexible ligands into electron density

X-LIGAND is an application designed to allow the automated placement of large flexible ligands into electron density using Monte Carlo real-space torsion-angle refinement.

Expression, crystallization and preliminary characterization of methylmalonyl coenzyme A epimerase from Propionibacterium shermanii

Methylmalonyl coenzyme A epimerase (MMCE) is essential for interconversions between propionyl-CoA and succinyl-CoA. Crystals suitable for X-ray analysis have been obtained for recombinant MMCE from P. shermanii, for both native and selenomethionyl forms.

Crystallization and preliminary X-ray analysis of cardiotoxic phospholipase A₂ from Ophiophagus hannah (king cobra)

The venom phospholipase A₂ with a `pancreatic loop' exhibits cardiotoxicity, myotoxicity and anti-platelet activity. Crystals of the enzyme have been obtained and X-ray data have been collected to a resolution of 2.6 Å.

Crystallization and preliminary crystallographic analysis of mannitol de­hydrogenase (MtDH) from the common mushroom Agaricus bis­porus

Crystallization and preliminary analysis of the enzyme mannitol dehydrogenase (MtDH) from the common mushroom A. bisporus.

Crystallographic characterization of the PDZ1 domain of the human Na⁺/H⁺ exchanger regulatory factor

The PDZ1 domain of the human Na⁺/H⁺ exchanger regulatory factor has been expressed in E. coli, purified and crystallized. The crystals diffract to 1.5 Å resolution and belong to the space group P3₁21 or P3₂21.

Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43

A novel alkaline serine protease (KP-43) which belongs to a new class of the subtilisin superfamily was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant.

Crystallization and preliminary X-ray crystallographic studies of wild-type human ornithine transcarbamylase and two naturally occurring mutants at position 277

Human ornithine transcarbamylase and two mutants (R277Q and R277W) have been crystallized in the space group I23 or/and P4₃32. The structures for both crystal forms have been solved by molecular replacement.

Crystallization and preliminary X-ray analysis of the complex of the ∊-subunit and the central domain of the γ-subunit from the Escherichia coli ATP synthase

A complex of the ∊-subunit and the central domain of the γ-subunit from the ATP synthase of E. coli has been purified and crystallized and preliminary X-ray analysis has been carried out.

Crystallization and preliminary X-ray analysis of Drosophila gluta­thione S-transferase-2

The D. melanogaster σ-class GST has been expressed, purified and crystallized. The crystals diffract to at least 1.75 Å resolution using synchrotron radiation.

Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli RbsD, a component of the ribose-transport system with unknown biochemical function

RbsD was overexpressed in E. coli and crystallized using the hanging-drop vapour-diffusion method at 296 K. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 285.9, b = 92.3, c = 93.3 Å, β = 105.0°.

Overexpression, purification, crystallization and data collection of 3-methylaspartase from Clostridium tetanomorphum

3-Methylaspartase catalyses the deamination of 3-methylaspartic acid in the metabolism of (2S)-glutamic acid in C. tetanomorphum. The crystallization and preliminary structural characterization of 3-methylaspartase are reported.

Crystallization and preliminary X-ray crystallographic analysis of FlhD/FlhC complex from Escherichia coli

The purification and crystallization of FlhD/FlhC complex from E. coli are reported. The preliminary X-ray crystallographic analysis of FlhD/FlhC complex is discussed.

Purification, crystallization and preliminary X-ray analysis of two crystal forms of ribonuclease Sa3

The most important property of microbial ribonuclease Sa3 is the relatively high cytotoxic activity. Diffraction data have been collected to 2.0 Å for the P3₁21 form and to 1.7 Å for the P4₁2₁2 form.

Purification, crystallization and preliminary X-ray investigation of the complex of human vitamin D binding protein and rabbit muscle actin

The complex between human vitamin D binding protein and rabbit muscle actin has been purified and crystallized. Crystals diffract to at least 2.4 Å using synchrotron radiation.

Crystallization and preliminary characterization of crystals of the C-terminal half fragment of tropomodulin

The C-terminal half of tropomodulin, the P-end capping protein of the actin filament, has been crystallized. Crystals belong to the trigonal space group and diffract to 1.9 Å on a rotating-anode X-ray source.

Crystallization and preliminary X-ray diffraction studies of the ∊ζ addiction system encoded by Streptococcus pyogenes plasmid pSM19035

The proteins ∊ and ζ crystallized as complexes in four different forms at pH 5.0 and 7.0 using vapour diffusion with PEG 3350 and ethylene glycol as precipitants. The resolution of one of the crystal forms improved from 2.9 to 1.95 Å after soaking at pH 7.0.

Cloning, expression, purification and preliminary X-ray crystallographic studies of yeast Hsp40 Sis1 complexed with Hsp70 Ssa1 C-terminal lid domain

The protein complex of yeast Hsp40 Sis1 and yeast Hsp70 Ssa1 C-terminal domain has been constituted and crystallized. The structure determination is under way.

How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data

X-ray crystallography is a powerful imaging technique, but still requires careful interpretation. The geometry of carbon monoxide binding to myoglobin is revisited.

Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur

The anomalous signal from five S atoms in the antibiotic thiostrepton has been used to solve the structure of a tetragonal crystal form. The coordinates, which were not available from an earlier structure determination, are now placed in the public domain.

Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase

Crystals of the wild type and W43I mutant of the SH3 domain from chicken src tyrosine kinase were obtained. The post-translational modification of the N-terminal His tag was identified and characterized. Deletion of the His tag eliminated heterogeneity and facilitated crystallization.

Effects of different post-crystallization soaking conditions on the diffraction of Mtcp1 crystals

The diffraction of Mtcp1 crystals was examined after post-crystallization soaking for different times in various concentrations of ammonium sulfate and PEG 3400. Freshly grown crystals show disordered low-resolution diffraction, whereas, crystals soaked for one week in 1.5 M ammonium sulfate and 2% PEG 3400 showed ordered high-resolution diffraction.

Protein structure prediction: methods and protocols