Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure

The rigid and the flexible regions of the peanut lectin molecule have been delineated and the invariant water molecules in its hydration shell identified using the structures of the lectin crystals containing ligand-bound and ligand-free subunits, grown under different environmental conditions. The molecule is sturdy and the combining site is essentially preformed.

The influence of positional errors on the Debye effects

A relation between a Gaussian perturbation of the atomic positional parameters and the average squared structure-factor amplitude for the estimation of the quality of an atomic model and corresponding phases is presented.

On the interpretation and use of 〈|E|²〉(d*) profiles

A structural interpretation of 〈|E|²〉(d*) curves is presented and their use for improved parameter estimation in scaling is discussed.

A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase

Spallation neutron diffraction data have been measured to better than 2.0 Å resolution on the metalloenzyme D-xylose isomerase at the Protein Crystallography Station beamline at Los Alamos Neutron Science Center. This represents one of the largest proteins and unit cells (∼10⁶ ų) to be studied to this resolution by neutron diffraction.

Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu Kα diffraction data only

The previously unknown structure of a 64-residue fungal protein, denoted the bubble protein, was solved in a highly automated fashion using the anomalous scattering from eight S atoms in data collected on in-house equipment.

The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus

The crystal structure of the V8 protease from S. aureus is reported. From modeling studies, the residues of the enzyme involved in determining its unique specificity for acidic amino-acid residues are predicted.

On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps

Conventional macromolecular refinement performed at a resolution near 0.6 Å allows regular bond-electron peaks to be observed in difference maps for individual bonds in well ordered molecular domains. These peaks are not visible in the maps if the refinement is performed at a resolution close to 0.9 Å.

The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI

As part of an ongoing effort, the usefulness of Lys→Arg surface mutations in the globular domain of human RhoGDI is studied.

Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin–ligand interaction

The crystal structure of the meso-tetrasulphonatophenylporphyrin (H₂TPPS)-jacalin complex, determined at 1.8 Å resolution, exhibits binding of the pluripotent porphyrin molecule exploiting the plasticity of the carbohydrate binding site.

Structure of the core region of the soybean β-conglycinin α′ subunit

The crystal structure of the core region of the soybean β-conglycinin α′ subunit has been determined at 2.3 Å resolution. The structural factors accounting for the difference in thermal stability between the subunits of β-conglycinin are discussed.

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum

The single Fe atom in the Fe(S-Cys)₄ site of C. pasteurianum rubredoxin was exchanged in turn for Cd, Hg, Co, Ni and Ga and the structures of these derivatives were refined.

Structure of circularly permuted DsbA_Q100T99: preserved global fold and local structural adjustments

The X-ray structure of a circularly permuted variant of thiol-disulfide oxidoreductase, cpDsbA_Q100T99, is reported in which the natural termini are joined by the pentapeptide linker GGGTG, leading to a continuous thioredoxin domain, and new termini that have been introduced in the helical domain by breaking the peptide bond Thr99-Gln100.

Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureus

The S component of the Panton–Valentine leucocidin from S. aureus has been crystallized. A complete native data set to 2.1 Å resolution has been collected.

Purification, crystallization and preliminary X-ray diffraction of a proteolytic fragment of PDK1 containing the pleckstrin homology domain

The construct design by limited proteolysis, subsequent cloning, purification and crystallization of the PH domain of human PDK1 is reported, along with a Patterson map of a gold-derivatized crystal.

Crystallization and preliminary crystallographic analysis of rat mono­amine oxidase A complexed with clorgyline

The crystallization of rat monoamine oxidase A and general considerations for the crystallization of membrane proteins are presented.

Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue

The helicase fragment of Vasa was crystallized in complex with poly(U) RNA and a non-hydrolyzable analogue of ATP. The crystal diffracted to 2.2 Å resolution.

Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia

Preliminary crystallographic analysis of the gene-regulatory protein C.AhdI from the bacterial restriction-modification system A. hydrophilia has been undertaken. Native and selenomethionine-derivative data were collected to resolutions of 2.2 and 1.7 Å, respectively.

Expression, purification and crystallization of an extended-spectrum β-lactamase from Klebsiella oxytoca

An extended-spectrum β-lactamase, OXY-1a, from K. oxytoca has been crystallized in two crystal forms which diffracted to different resolutions. The orthorhombic crystal diffracted to at least 1.9 Å and is thus suitable for high-resolution structural studies.

Crystallization of YloQ, a GTPase of unknown function essential for Bacillus subtilis viability

YloQ, a putative GTPase essential for the viability of B. subtilis, has been purified and crystallized. A complete diffraction data set to 2.5 Å spacing has been collected using synchrotron radiation.

Crystallization and preliminary X-ray diffraction analysis of a dihaem cytochrome c peroxidase from Paracoccus denitrificans

Two different crystal forms have been obtained of the fully oxidized form of the dihaem cytochrome c peroxidase from P. denitrificans. One of them diffracts X-rays beyond 2.3 Å resolution and is suitable for structure determination.

Expression, crystallization and preliminary X-ray studies of the recombinant PTB domain of mouse dok1 protein

The PTB domain of mouse dok1 has been purified and crystallized. A selenomethionmine-substituted protein that diffracts to 2.5 Å resolution has been used to collect a full three-wavelength MAD data set.

Crystallization and preliminary X-ray diffraction analysis of an oxidized state of Ohr from Xylella fastidiosa

Recombinant Ohr was expressed in E. coli as a His₆-tagged fusion protein, purified by nickel-affinity chromatography and crystallized using PEG 4000 as precipitant after treatment with t-butyl hydroperoxide. Crystals belong to space group P6₅22, with unit-cell parameters a = b = 87.66, c = 160.28 Å, and diffract X-rays to a resolution of 1.8 Å.

Crystallization and preliminary crystallographic analysis of a novel orange fluorescent protein from the Cnidaria tube anemone Cerianthus sp.

A novel orange fluorescent protein from the Cnidaria tube anemone Cerianthus sp. was crystallized in space group R3, with hexagonal unit-cell parameters a = b = 216.947, c = 51.839 Å. A set of complete diffraction data was collected to 2.0 Å.

Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium

A crystal of mature xylanase B from C. stercorarium has been prepared and the X-ray diffraction data have been collected to 1.80 Å resolution.

Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fu­cosyltransferase NodZ

Native crystals of recombinant fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus) diffract X-rays to 2.85 Å resolution at 100 K. The crystals are hexagonal, space group P6₁22 or P6₅22, with unit-cell parameters a = 125.5, c = 95.6 Å, and contain one protein molecule in the asymmetric unit.

Crystallization and preliminary X-ray analysis of the human-specific toxin intermedilysin

Crystals of the human-specific toxin intermedilysin from S. intermedius have been obtained by manipulating the dialysis conditions prior to crystallization.

Expression, purification and crystallization of human 3′-phosphoadenosine-5′-phospho­sulfate synthetase 1

Recombinant purified full-length human PAPS synthetase 1 migrates as a dimer in solution. Monoclinic crystal diffraction intensities have been measured to 1.75 Å resolution using synchrotron radiation.

Crystallization and preliminary crystallographic analysis of Mycoplasma arthritidis-derived mitogen complexed with peptide/MHC class II antigen

The crystallization and preliminary crystallographic analysis of M. arthritidis-derived mitogen complexed with peptide/MHC class II antigen is described.

Expression, purification, crystallization and preliminary crystallographic analysis of osmotically inducible protein C

The osmotically inducible protein C from T. thermophilus was overexpressed, purified and crystallized. Data were collected at five wavelengths for MAD phasing and the unit-cell contents were analyzed.

Expression, purification, crystallization and preliminary characterization of uridine 5′-di­phospho-N-acetylmuramoyl L-alanyl-D-glutamate:lysine ligase (MurE) from Streptococcus pneumoniae 110K/70

An open reading frame from S. pneumoniae 110K/70, a penicillin-sensitive strain, has been cloned, expressed and purified. Crystals obtained from the purified recombinant enzyme have been obtained in two different forms, which may represent different liganded states, diffracting to 2.7 and 1.5 Å, respectively.

Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum

Sylvaticin, a protein of the elicitin family, has been crystallized by the vapour-diffusion method and diffracts to 2.1 Å resolution.

Crystallization and preliminary X-ray crystallographic analysis of a ytfG gene product from Escherichia coli

The E. coli ytfG gene product, with NAD(P)H:quinone oxidoreductase activity, has been crystallized by the hanging-drop vapour-diffusion method at 296 K.

Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF

The ribosome recycling factor from M. tuberculosis has been crystallized and the crystals have been characterized.

Purification, crystallization and preliminary X-ray diffraction analysis of the catalytic domain of adenylyl cyclase Rv1625c from Mycobacterium tuberculosis

A mutant of the catalytic domain of mycobacterial adenylyl cyclase Rv1625c has been overexpressed, purified and crystallized. X-ray diffraction data were collected to 3.4 Å resolution.

Crystallization and preliminary X-ray crystallographic studies on recombinant rat choline acetyltransferase

Using purified, recombinant rat choline acetyltransferase crystals that diffract X-rays to 1.55 Å resolution were generated.

Crystals of the ribonucleotide reductase R2 protein from Chlamydia trachomatis obtained by heavy-atom co-crystallization

The R2 protein of ribonucleotide reductase from C. trachomatis has been crystallized. Co-crystallization with lead was necessary to obtain crystals.

Crystallization and preliminary X-ray crystallographic analysis of the RecR protein from Deinococcus radiodurans, a member of the RecFOR DNA-repair pathway

RecR from D. radiodurans has been crystallized (space group C222₁; unit-cell parameters a = 106.96, b = 122.25, c = 156.01 Å). Diffraction data have been collected to 2.90 Å using Cu Kα X-rays.

Crystallization and preliminary X-ray crystallographic analyses of CMY-1 and CMY-10, plasmidic class C β-lactamases with extended substrate spectrum

CMY-1 and CMY-10, the plasmid-encoded class C β-lactamases with extended substrate spectrum, were purified and crystallized.

Crystallization and preliminary X-ray analysis of an acetone carboxylase from Xanthobacter autotrophicus strain Py2

The unique carboxylating enzyme acetone carboxylase from X. autotropicus strain Py2 has been crystallized in the native state and 3.2 Å resolution data have been collected.

Crystallization of 4-hydroxybenzoyl-CoA reductase and the structure of its electron donor ferredoxin

4-Hydroxybenzoyl-CoA reductase from Thauera aromatica and its electron donor ferredoxin were anaerobically crystallized. The structure of the ferredoxin was solved at 2.9 Å resolution.

Structural analysis of neprilysin with various specific and potent inhibitors

The crystal structures of the soluble extracellular domain of human neutral endopeptidase (residues 52–749) complexed with various potent and competitive inhibitors are described.

Refinement of Haemophilus influenzae di­aminopimelic acid epimerase (DapF) at 1.75 Å resolution suggests a mechanism for stereocontrol during catalysis

The crystal structure of diaminopimelate epimerase has been refined to 1.75 Å, highlighting differences from the previously determined structure and enabling mechanistic deductions and comparisons with the functionally related amino-acid racemases to be made.

Structure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1

p75/AIRM1, also known as Siglec-7, is a sialoadhesin expressed on natural killer cells that is able to inhibit their cytolytic activity. The X-ray crystal structure of the extracellular IgV-like domain, thought to be involved in target-cell recognition, has been determined at higher resolution (1.45 Å) and in a different space group to the previously reported Siglec-7 structure.

Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure. Erratum

An erratum to the paper by Sunami et al. (2004), Acta Cryst. D60, 90–96.