Biological Crystallography

 

Acta Cryst. (2004). D60, 1347-1354  [ doi:10.1107/S0907444904011370 ]

The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48

F. Ruiz, I. Hazemann, A. Mitschler, A. Joachimiak, T. Schneider, M. Karplus and A. Podjarny

Synopsis: The aldose reductase-IDD552 complex confirms the possibility of direct proton donation from the active-site residue Tyr48.

PDB references: 1t41 and 1t40

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1355-1363  [ doi:10.1107/S0907444904011679 ]

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

A. W. Schüttelkopf and D. M. F. van Aalten

Synopsis: The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1364-1373  [ doi:10.1107/S090744490401176X ]

A neutron crystallographic analysis of a rubredoxin mutant at 1.6  Å resolution

T. Chatake, K. Kurihara, I. Tanaka, I. Tsyba, R. Bau, F. E. Jenney, M. W. W. Adams and N. Niimura

Synopsis: A single-crystal neutron diffraction study has been carried out at 1.6  Å resolution on a mutant rubredoxin from the hyperthermophilic archeon P. furiosus.

PDB references: 1iu5 and 1iu6

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1374-1380  [ doi:10.1107/S0907444904012004 ]

The three-dimensional structure of catalase from Enterococcus faecalis

K. O. Håkansson, M. Brugna and L. Tasse

Synopsis: The structure of E. faecalis haem catalase was determined by molecular replacement and refined to 2.3  Å resolution using synchrotron data.

PDB reference: 1si8

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1381-1387  [ doi:10.1107/S0907444904012065 ]

Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers

T.-P. Ko, H.-M. Chu, C.-Y. Chen, C.-C. Chou and A.H.-J. Wang

Synopsis: The crystal structures of two Sac7d-DNA decamer complexes were determined in two different unit cells. The DNA decamers are more bent than the octamer, and they form triple base pairs in the lattice contact regions.

PDB references: 1wd0 and 1wd1

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1388-1395  [ doi:10.1107/S0907444904012971 ]

The role of substrate-binding groups in the mechanism of aspartate--semialdehyde dehydrogenase

J. Blanco, R. A. Moore, C. R. Faehnle, D. M. Coe and R. E. Viola

Synopsis: Structures of active-site mutants have definitively established the identity and roles of the substrate-binding groups in aspartate--semialdehyde dehydrogenase.

PDB references: 1ps8, 1q2x, 1oza, 1pr3 and 1pu2

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1396-1403  [ doi:10.1107/S0907444904012983 ]

Structure, crystal packing and molecular dynamics of the calponin-homology domain of Schizosaccharomyces pombe Rng2

C.-H. Wang, M. K. Balasubramanian and T. Dokland

Synopsis: The structure of the CH domain of Rng2 is described at 2.21  Å resolution. Two features that are new to CH domains are revealed: a carboxyl-terminal tail that wraps around the putative actin-binding site ABS1 and ABS2 from dystrophin, and two loop conformations between Tyr92 and Arg99. This may have useful implications in determining the actin-binding orientation from single CH domains.

PDB references: 1p2x and 1p5s

Online 21 July 2004

    

Acta Cryst. (2004). D60, 1404-1412  [ doi:10.1107/S090744490401354X ]

Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl--D-galactose

K. N. Rao, C. G. Suresh, U. V. Katre, S. M. Gaikwad and M. I. Khan

Synopsis: Two crystal structures of a jacalin-related lectin from A. hirsuta, which is specific for galactose, in complex with methyl--D-galactose are reported. The lectin crystallized in two orthorhombic forms and one hexagonal form under similar conditions. The structure was solved using the molecular-replacement method using the jacalin structure as a search model and the two orthorhombic forms were refined using data to 2.5 and 3.0  Å resolution, respectively.

PDB references: 1toq and 1tp8

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1413-1416  [ doi:10.1107/S0907444904013678 ]

Spectacular improvement of X-ray diffraction through fast desiccation of protein crystals

C. Abergel

Synopsis: A simple and fast desiccation procedure was successfully applied to three cases of poorly diffracting protein crystals leading to a dramatic improvement in their diffraction. This could become a last-resort protocol to be systematically applied to non-diffracting crystals.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1417-1424  [ doi:10.1107/S0907444904013861 ]

Calf spleen purine-nucleoside phosphorylase: crystal structure of the binary complex with a potent multisubstrate analogue inhibitor

M. Luic, G. Koellner, T. Yokomatsu, S. Shibuya and A. Bzowska

Synopsis: Crystal structure of binary complex of calf spleen purine-nucleoside phosphorylase with a potent multisubstrate analogue inhibitor 9-(5,5-difluoro-5-phosphonopentyl)guanine has been refined to 2.2  Å resolution. The present structure may be used in the rational, structure-based design of new PNP inhibitors with potential medical applications.

PDB reference: 1v48

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1425-1428  [ doi:10.1107/S0907444904012041 ]

The production and purification of the human T-cell receptors, the CD3 and CD3 heterodimers: complex formation and crystallization with OKT3, a therapeutic monoclonal antibody

M. A. Dunstone, L. Kjer-Nielsen, L. Kostenko, A. W. Purcell, A. G. Brooks, J. Rossjohn and J. McCluskey

Synopsis: This report details the production, purification, crystallization and preliminary diffraction analysis of CD3 and CD3 complexed with OKT3.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1429-1431  [ doi:10.1107/S0907444904012120 ]

Expression, crystallization and crystallographic analysis of DegS, a stress sensor of the bacterial periplasm

M. Grininger, R. B. G. Ravelli, U. Heider and K. Zeth

Synopsis: The membrane-bound DegS protease from E. coli has been crystallized in a free and a substrate-bound form. The structure has been solved by molecular replacement and the solution was verified by radiation-induced phasing (RIP).

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1432-1434  [ doi:10.1107/S0907444904012247 ]

Facile crystallization of Escherichia coli ketol-acid reductoisomerase

J. A. McCourt, R. Tyagi, L. W. Guddat, V. Biou and R. G. Duggleby

Synopsis: E. coli ketol-acid reductoisomerase has been crystallized under a wide range of conditions and in several crystal forms. Most of the crystals diffract poorly but we have collected several data sets at better than 3.2  Å resolution.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1435-1437  [ doi:10.1107/S0907444904012533 ]

Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis

H. Dubourg, C. Stines-Chaumeil, C. Didierjean, F. Talfournier, S. Rahuel-Clermont, G. Branlant and A. Aubry

Synopsis: Methylmalonate-semialdehyde dehydrogenase which is a singular member of the aldehyde dehydrogenase family was overexpressed and crystallized. Crystals diffract to 2.5  Å and belong to the orthorhombic space group P2₁2₁2₁.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1438-1440  [ doi:10.1107/S0907444904012521 ]

Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens

C. Dong, A. Kotzsch, M. Dorward, K.-H. van Pée and J. H. Naismith

Synopsis: Crystallization of PrnA (tryptophan 7-halogenase), an enzyme that regioselectively chlorinates tryptophan, cocrystallized with tryptophan and FAD is reported.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1441-1444  [ doi:10.1107/S0907444904012661 ]

Crystallization and preliminary crystallographic studies of the mitochondrial F₁-ATPase from the yeast Saccharomyces cerevisiae

D. M. Mueller, N. Puri, V. Kabaleeswaran, C. Terry, A. G. W. Leslie and J. E. Walker

Synopsis: Crystallization of the yeast S. cerevisiae mitochondrial F₁-ATPase with improvements leading to diffraction from 3.3 to 2.8  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1445-1446  [ doi:10.1107/S0907444904012557 ]

Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus

K. Nagata, S. Tsutsui, W. C. Lee, K. Ito, M. Kamo, Y. Inoue and M. Tanokura

Synopsis: The crystallization and preliminary X-ray analysis of carboxypeptidase 1 from T. thermophilus have been conducted.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1447-1449  [ doi:10.1107/S0907444904012727 ]

Crystallization and preliminary X-ray crystallographic study of UDP-glucose pyrophosphorylase (UGPase) from Helicobacter pylori

H. Kim, C. A. Wu, D. Y. Kim, Y.-H. Han, S. C. Ha, C.-S. Kim, S. W. Suh and K. K. Kim

Synopsis: UDP-glucose pyrophosphorylase from H. pylori has been overexpressed, purified and crystallized. The crystals were analyzed by X-ray crystallography to a resolution of 2.9  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1450-1452  [ doi:10.1107/S0907444904012910 ]

Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3

N. K. Lokanath, C. Kuroishi, N. Okazaki and N. Kunishima

Synopsis: The glycine-cleavage system component T-protein from P. horikoshii OT3 was overexpressed and purified. Orthorhombic crystals were obtained and native data were collected to 1.5  Å resolution using synchrotron radiation.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1453-1455  [ doi:10.1107/S0907444904013204 ]

Crystallization and initial X-ray analysis of phenoxazinone synthase from Streptomyces antibioticus

A. W. Smith, A. Camara-Artigas, C. Olea, W. A. Francisco and J. P. Allen

Synopsis: Phenoxazinone synthase was crystallized using the sitting-drop vapour-diffusion method. Crystals were formed under two separate conditions, with crystals from each condition assigned to a different space group. Diffraction data from the two different crystals forms were measured to resolution limits of 3.35 and 2.30  Å and processed in space groups R32 and P1, respectively.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1456-1460  [ doi:10.1107/S0907444904013289 ]

Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms

A. Nagpal, M. P. Valley, P. F. Fitzpatrick and A. M. Orville

Synopsis: The active oxidized form of nitroalkane oxidase, an FAD-dependent enzyme isolated from Fusarium oxysporum, has been crystallized in three space groups. A multiwavelength data set from Se-Met enriched enzyme is suitable for determining the structure.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1461-1463  [ doi:10.1107/S0907444904013320 ]

Crystallization and preliminary crystallographic analysis of a thermostable family 52 -D-xylosidase from Geobacillus stearothermophilus T-6

M. Czjzek, T. Bravman, B. Henrissat and Y. Shoham

Synopsis: This study describes the first crystallization and preliminary X-ray analysis of a family 52 glycoside hydrolase, the -D-xylosidase from G. stearothermophilus T-6. Purified native enzyme was crystallized and belongs to space group P1. The native crystal diffracted X-rays to a resolution of 2.0  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1464-1466  [ doi:10.1107/S0907444904013484 ]

Crystallization and preliminary X-ray crystallographic studies on a Kunitz-type potato serine protease inhibitor

E. A. J. Thomassen, L. Pouvreau, H. Gruppen and J. P. Abrahams

Synopsis: A dimeric double-headed Kunitz-type potato serine protease inhibitor isolated from potato tubers was crystallized. Preliminary X-ray data were collected to 1.8  Å. The crystals are monoclinic, space group P2₁, with unit-cell parameters a = 54.82, b = 93.92, c = 55.44  Å, = 100.7°.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1467-1469  [ doi:10.1107/S0907444904013496 ]

Crystallization and preliminary X-ray analysis of the outer membrane pyoverdine receptor FpvA from Pseudomonas aeruginosa

D. Cobessi, H. Célia, N. Folschweiller, M. Heymann, I. Schalk, M. Abdallah and F. Pattus

Synopsis: The crystallization and X-ray data analysis of crystals of the outer membrane pyoverdine receptor FpvA from P. aeruginosa are described. Crystals of the in vivo FpvA-pyoverdine complex and the selenomethionine-labelled protein were obtained in the presence of C₈E₅ detergent. Both crystal forms belong to space group C2.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1470-1472  [ doi:10.1107/S0907444904013411 ]

Preparation and preliminary X-ray analysis of the catalytic module of -1,3-xylanase from the marine bacterium Vibrio sp. AX-4

K. Sakaguchi, M. Kiyohara, N. Watanabe, K. Yamaguchi, M. Ito, T. Kawamura and I. Tanaka

Synopsis: The catalytic module of -1,3-xylanase from Vibrio sp. AX-4 has been crystallized and X-ray diffraction data have been collected to 1.44  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1473-1475  [ doi:10.1107/S0907444904013587 ]

Complex assembly, crystallization and preliminary X-ray crystallographic studies of MHC H-2K^d complexed with an HBV-core nonapeptide

M. Zhou, Y. Xu, Z. Lou, D. K. Cole, X. Li, Y. Liu, P. Tien, Z. Rao and G. F. Gao

Synopsis: Crystals of MHC H-2K^d complexed with an HBV immunodominant nonapeptide were produced that diffracted X-rays to 2.06  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1476-1480  [ doi:10.1107/S0907444904013241 ]

Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form

G. Golan, D. O. Zharkov, A. S. Fernandes, E. Zaika, J. H. Kycia, Z. Wawrzak, A. P. Grollman and G. Shoham

Synopsis: The DNA-repair enzyme endonuclease VIII (Nei) from E. coli has been crystallized in its DNA-free form. The new I222 crystals enabled a full X-ray diffraction data measurement for wild-type Nei at 2.6  Å resolution, for the Nei-E2A mutant at 2.25  Å resolution and for the Nei-R252A mutant at 2.05  Å resolution.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1481-1483  [ doi:10.1107/S0907444904014052 ]

Crystallization and preliminary X-ray diffraction analysis of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum

M. K. Swan, T. Hansen, P. Schönheit and C. Davies

Synopsis: Crystals of an enzyme from the crenarchaeon P. aerophilum that catalyzes both phosphoglucose isomerase and phosphomannose isomerase activities have been obtained. They belong to space group P2₁ and diffract to at least 1.6  Å resolution.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1484-1486  [ doi:10.1107/S0907444904014222 ]

Crystallization and preliminary X-ray diffraction study of the catalytic subunit of archaeal H⁺-transporting ATP synthase from Pyrococcus horikoshii OT3

Y. Maegawa, H. Morita, M. Yao, N. Watanabe and I. Tanaka

Synopsis: Archaeal ATP synthase catalytic subunit A from P. horikoshii OT3 was overexpressed, purified and crystallized. X-ray diffraction data were collected to 2.55  Å resolution.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1487-1489  [ doi:10.1107/S0907444904014295 ]

Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment

T. Uchiyama, A. Kounosu, T. Sato, N. Tanaka, T. Iwasaki and T. Kumasaka

Synopsis: A novel hyperthermophilic archaeal Rieske protein, sulredoxin from S. tokodaii, has been overproduced, purified and crystallized in the oxidized conformation. The cubic crystals diffract to beyond 2.0  Å resolution using synchrotron radiation.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1490-1492  [ doi:10.1107/S0907444904014313 ]

Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate

M. Akita, N. Takeda, K. Hirasawa, H. Sakai, M. Kawamoto, M. Yamamoto, W. D. Grant, Y. Hatada, S. Ito and K. Horikoshi

Synopsis: An alkaline mannanase from a Bacillus sp. was crystallized and the crystals diffracted to 1.65  Å using synchrotron radiation. Phasing was successfully carried out using the molecular-replacement method.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1493-1495  [ doi:10.1107/S0907444904014489 ]

Crystallization and preliminary X-ray diffraction analysis of the lectin from Canavalia gladiata seeds

F. B. M. B. Moreno, P. Delatorre, B. T. Freitas, B. A. M. Rocha, E. P. Souza, F. Facó, F. Canduri, A. L. H. Cardoso, V. N. Freire, J. L. Lima Filho, A. H. Sampaio, J. J. Calvete, W. F. De Azevedo and B. S. Cavada

Synopsis: The seed lectin of C. gladiata was crystallized in orthorhombic space group C222₁. X-ray data were collected at 2.3  Å resolution.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1496-1497  [ doi:10.1107/S090744490401460X ]

Crystallization of the major cytosolic glutathione S-transferase from Onchocerca volvulus

J. Höppner, M. Perbandt, Ch. Betzel, R. D. Walter and E. Liebau

Synopsis: Glutathione S-transferase from the pathogenic human filarial parasite O. volvulus has been crystallized, allowing its X-ray structure determination.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1498-1499  [ doi:10.1107/S0907444904014684 ]

Crystallization and preliminary crystallographic analysis of monodehydroascorbate radical reductase from cucumber

S. Sano, Y.-N. Kang, H. Shigemizu, N. Morishita, H.-J. Yoon, K. Saito, K. Asada and B. Mikami

Synopsis: Monodehydroascorbate (MDA) radical reductase from cucumber has been crystallized and X-ray diffraction data have been collected to 2.4  Å.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1500-1501  [ doi:10.1107/S0907444904014787 ]

Purification, crystallization and preliminary X-ray diffraction study of a recombinant cytokinin oxidase from Zea mays

D. Kopecný, P. Briozzo, N. Joly, N. Houba-Hérin, C. Madzak, C. Pethe and M. Laloue

Synopsis: A 1.95  Å resolution data set was collected from a crystal of a recombinant Z. mays cytokinin oxidase (ZmCKO1). This enzyme degrades cytokinins, hormones that are involved in plant growth and development.

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1502-1505  [ doi:10.1107/S0907444904011680 ]

C3 exoenzyme from Clostridium botulinum: structure of a tetragonal crystal form and a reassessment of NAD-induced flexure

H. R. Evans, D. E. Holloway, J. M. Sutton, J. Ayriss, C. C. Shone and K. R. Acharya

Synopsis: The structure of a tetragonal crystal form of C. botulinum C3 exoenzyme has been determined. NAD-induced main-chain flexure is concentrated in two lobes peripheral to a rigid -stranded core.

PDB reference: 1uzi

Online 21 July 2004

 

Acta Cryst. (2004). D60, 1506-1508  [ doi:10.1107/S0907444904011710 ]

Heavy-atom derivatives in lipidic cubic phases: results on hen egg-white lysozyme tetragonal derivative crystals with Gd-HPDO3A complex

É. Girard, E. Pebay-Peyroula, J. Vicat and R. Kahn

Synopsis: Excellent gadolinium-derivative crystals of hen egg-white lysozyme were obtained by co-crystallizing the protein with 100  mM Gd-HPDO3A using the lipidic cubic phase method known to be effective for crystallizing membrane proteins.

Online 21 July 2004