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Volume 65(Pt 12);  2009 December 1

RIKEN-UK structural genomics

Svetlana V. Antonyuk, Richard W. Strange, Mark J. Ellis, Yoshitaka Bessho, Seiki Kuramitsu, Akeo Shinkai, Shigeyuki Yokoyama, S. Samar Hasnain

The structure of a protein involved in the molybdopterin and molybdenum co-factor biosynthesis pathways of Sulfolobus tokodaii has been solved to a resolution of 1.9 Å.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1200–1203. Published online 2009 November 27. doi: 10.1107/S1744309109043772
PMCID:
PMC2802863
Svetlana V. Antonyuk, Mark J. Ellis, Richard W. Strange, Yoshitaka Bessho, Seiki Kuramitsu, Akeo Shinkai, Shigeyuki Yokoyama, S. Samar Hasnain

The structure of the stationary phase survival protein SurE protein from the hyperthermophile Aquifex aeolicus has been solved to 1.5 Å resolution. The divalent-metal-ion-dependent phosphatase active-site pocket is occupied by sulfate ions from the crystallization medium.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1204–1208. Published online 2009 November 27. doi: 10.1107/S1744309109043814
PMCID:
PMC2802864
Svetlana V. Antonyuk, Richard W. Strange, Mark J. Ellis, Yoshitaka Bessho, Seiki Kuramitsu, Yumiko Inoue, Shigeyuki Yokoyama, S. Samar Hasnain

The structure of d-lactate dehydrogenase from Aquifex aeolicus has been determined with each subunit of the homodimer in a ‘closed’ conformation and with the NAD+ cofactor and lactate (or pyruvate) bound at the inter-domain active-site cleft.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1209–1213. Published online 2009 November 27. doi: 10.1107/S1744309109044935
PMCID:
PMC2802865
Richard W. Strange, Svetlana V. Antonyuk, Mark J. Ellis, Yoshitaka Bessho, Seiki Kuramitsu, Shigeyuki Yokoyama, S. Samar Hasnain

The structure of ribose-5-phosphate isomerase from Methanocaldococcus jannaschii has been solved to 1.78 Å resolution, with the active site occupied by two molecules of propylene glycol mimicking the binding of a known arabinose-5-phosphate inhibitor.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1214–1217. Published online 2009 November 27. doi: 10.1107/S1744309109044923
PMCID:
PMC2802866
Richard W. Strange, Svetlana V. Antonyuk, Mark J. Ellis, Yoshitaka Bessho, Seiki Kuramitsu, Akeo Shinkai, Shigeyuki Yokoyama, S. Samar Hasnain

The structure of a putative β-phosphoglucomutase from Thermotoga maritima belonging to the haloacid dehalogenase (HAD) hydrolase family has been determined to 1.74 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1218–1221. Published online 2009 November 27. doi: 10.1107/S1744309109046302
PMCID:
PMC2802867
Balasundaram Padmanabhan, Richard W. Strange, Svetlana V. Antonyuk, Mark J. Ellis, S. Samar Hasnain, Hitoshi Iino, Yoshihiro Agari, Yoshitaka Bessho, Shigeyuki Yokoyama

The crystal structure of dihydrodipicolinate synthase from the (S)-lysine synthesis pathway of Methanocaldococcus jannaschii has been solved to 2.2 Å resolution, revealing a functional homotetramer.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1222–1226. Published online 2009 November 27. doi: 10.1107/S174430910904651X
PMCID:
PMC2802868
Ali D. Malay, Yoshitaka Bessho, Mark J. Ellis, Svetlana V. Antonyuk, Richard W. Strange, S. Samar Hasnain, Akeo Shinkai, Balasundaram Padmanabhan, Shigeyuki Yokoyama

The structure of glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanocaldococcus jannaschii was determined to 1.81 Å resolution with the NADP+ cofactor at the nucleotide binding site.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1227–1233. Published online 2009 November 27. doi: 10.1107/S1744309109047046
PMCID:
PMC2802869
Balasundaram Padmanabhan, Yoshitaka Bessho, Akio Ebihara, Svetlana V. Antonyuk, Mark J. Ellis, Richard W. Strange, Seiki Kuramitsu, Nobuhisa Watanabe, S. Samar Hasnain, Shigeyuki Yokoyama

The putative 4-amino-4-deoxychorismate lyase (TTHA0621) from T. thermophilus HB8 was cloned, overexpressed, purified and crystallized. Its crystal structure was determined by a combination of SAD and molecular-replacement methods and was refined to 1.93 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1234–1239. Published online 2009 November 27. doi: 10.1107/S1744309109050052
PMCID:
PMC2802870

Structural Communications

Hugh P. Morgan, Martin A. Wear, Iain McNae, Maurice P. Gallagher, Malcolm D. Walkinshaw

The crystal structure of cold-shock protein E from S. typhimurium (StCspE) has been determined at 1.1 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1240–1245. Published online 2009 November 27. doi: 10.1107/S1744309109033788
PMCID:
PMC2802871
Jean-Marie Bourhis, Caroline Vignaud, Nicolas Pietrancosta, Françoise Guéritte, Daniel Guénard, Florence Lederer, Ylva Lindqvist

The crystal structure of human glycolate oxidase in complex with an inhibitor is described. A comparison with complexes with other inhibitors and with structures of homologous enzymes is given.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1246–1253. Published online 2009 November 27. doi: 10.1107/S1744309109041670
PMCID:
PMC2802872
Monica Fiorentini, Ann Kallehauge Nielsen, Ole Kristensen, Jette S. Kastrup, Michael Gajhede

This article describes the trimeric structure of the first PDZ domain of human PSD-93 at 2 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1254–1257. Published online 2009 November 27. doi: 10.1107/S1744309109043267
PMCID:
PMC2802873
Petr Kolenko, Tereza Skálová, Ondřej Vaněk, Andrea Štěpánková, Jarmila Dušková, Jindřich Hašek, Karel Bezouška, Jan Dohnálek

The structure of the extracellular domain of human CD69 was crystallized using a novel polymer precipitant: di[poly(ethylene glycol)] adipate. The structure was refined at 1.37 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1258–1260. Published online 2009 November 27. doi: 10.1107/S1744309109043152
PMCID:
PMC2802874

Crystallization Communications

Vinod B. Agarkar, Nigar D. Babayeva, Angie Rizzino, Tahir H. Tahirov

The cloning, expression, purification and crystallization of the mouse Elf3 C-terminal DNA-binding domain in complex with mouse type II TGF-β receptor promoter DNA are reported. The crystals were characterized and an X-ray diffraction data set was collected to a resolution of 2.2 Å.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1261–1263. Published online 2009 November 27. doi: 10.1107/S1744309109038007
PMCID:
PMC2802875
Noella Silva-Martin, Joseph D. Schauer, Chae Gyu Park, Juan A. Hermoso

The carbohydrate-recognition domain of the SIGN-R1 receptor from M. musculus has been crystallized by the hanging-drop vapour-diffusion method. A native data set has been collected to 1.87 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1264–1266. Published online 2009 November 27. doi: 10.1107/S1744309109041992
PMCID:
PMC2802876
Yuichiro Kezuka, Takashi Itagaki, Rie Satoh, Reiko Teshima, Takamasa Nonaka

A 16 kDa buckwheat protein (BWp16) is a major allergen responsible for immediate hypersensitivity reactions including anaphylaxis. An immunologically active mutant of BWp16 was prepared and a three-wavelength MAD data set was collected from a crystal of selenomethionine-labelled mutant protein.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1267–1270. Published online 2009 November 27. doi: 10.1107/S1744309109043127
PMCID:
PMC2802877
Hyun-Ju Lee, Kosuke Nishi, Jung-Mi Song, Jeong-Sun Kim

The crystallization of an HsdM subunit, a component of the methyltransferase of a putative type I restriction enzyme, from V. vulnificus YJ016 and the collection of diffraction data to 1.86 Å resolution are reported.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1271–1273. Published online 2009 November 27. doi: 10.1107/S1744309109043115
PMCID:
PMC2802878
Takuya Ishida, Zui Fujimoto, Hitomi Ichinose, Kiyohiko Igarashi, Satoshi Kaneko, Masahiro Samejima

Selenomethionyl exo-β-1,3-galactanase from P. chrysosporium K-3 produced in Pichia pastoris was crystallized. The crystals diffracted to a resolution of 1.8 Å and belonged to space group P21.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1274–1276. Published online 2009 November 27. doi: 10.1107/S1744309109043395
PMCID:
PMC2802879
E. V. Baranova, S. Beelen, N. B. Gusev, S. V. Strelkov

A procedure for obtaining diffraction-quality crystals of the α-crystallin domain from human small heat-shock protein 27 with the help of limited proteolysis and rational surface mutagenesis is described.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1277–1281. Published online 2009 November 27. doi: 10.1107/S1744309109044571
PMCID:
PMC2802880
Akito Kawai, Shigesada Higuchi, Masaru Tsunoda, Kazuo T. Nakamura, Shuichi Miyamoto

A PCNA2−PCNA3 complex which has recently been identified from S. tokodaii strain 7 was overexpressed, purified and crystallized in two crystal forms.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1282–1284. Published online 2009 November 27. doi: 10.1107/S1744309109044479
PMCID:
PMC2802881
Beatriz Herguedas, Marta Martínez-Júlvez, Susana Frago, Milagros Medina, Juan A. Hermoso

Native and selenomethionine-labelled FAD synthetase from C. ammoniagenes have been crystallized by the hanging-drop vapour-diffusion method. A MAD data set for SeMet-labelled FAD synthetase was collected to 2.42 Å resolution, while data sets were collected to 1.95 Å resolution for the native crystals.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1285–1288. Published online 2009 November 27. doi: 10.1107/S1744309109044789
PMCID:
PMC2802882
Qiao-Ming Hou, Xiang Liu, Erik Brostromer, Lan-Fen Li, Xiao-Dong Su

Purine nucleoside phosphorylase (PNP), which is a pivotal enzyme in the nucleotide-salvage pathway, has been expressed in Escherichia coli strain BL21 (DE3) in a soluble form at a high level. After purification of the PNP enzyme, the protein was crystallized using the sitting-drop vapour-diffusion technique.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1289–1291. Published online 2009 November 27. doi: 10.1107/S1744309109045059
PMCID:
PMC2802883
Tatsuki Ebisawa, Akihiro Yamamura, Yasuhiro Kameda, Kou Hayakawa, Koji Nagata, Masaru Tanokura

A monomeric mutant of Azami-Green from G. fascicularis was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal belonged to space group P1 and diffracted X-rays to 2.20 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1292–1295. Published online 2009 November 27. doi: 10.1107/S1744309109045382
PMCID:
PMC2802884
Peder E. Cedervall, Alan B. Hooper, Carrie M. Wilmot

A new crystal form of N. europaea hydroxylamine oxidoreductase (space group P21212) diffracted to 2.25 Å resolution at a third-generation synchrotron X-ray source.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1296–1298. Published online 2009 November 27. doi: 10.1107/S1744309109046119
PMCID:
PMC2802885
Saeyoung Lee, Jonas Yun Lee, Sung Chul Ha, Jina Jung, Dong Hae Shin, Kyoung Heon Kim, In-Geol Choi

Neoagarobiose hydrolase from the marine bacterium Saccharophagus degradans 2-40 was overexpressed in Escherichia coli and crystallized in the monoclinic space group C2, with unit-cell parameters a = 129.83, b = 76.81, c = 90.11 Å, β = 101.86°.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1299–1301. Published online 2009 November 27. doi: 10.1107/S174430910904603X
PMCID:
PMC2802886
Kodai Hara, Toshiyuki Shimizu, Satoru Unzai, Satoko Akashi, Mamoru Sato, Hiroshi Hashimoto

The crystallization and initial X-ray diffraction of REV7 in complex with REV3 is reported.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1302–1305. Published online 2009 November 27. doi: 10.1107/S1744309109046181
PMCID:
PMC2802887
Daisuke Nakayama, Youssef Ben Ammar, Soichi Takeda

The crystallization and preliminary X-ray crystallographic analysis of blood coagulation factor V-activating proteinase are reported. The best crystal diffracted to 1.9 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1306–1308. Published online 2009 November 27. doi: 10.1107/S1744309109046697
PMCID:
PMC2802888
Ana Rita Seabra, Helena Carvalho, Pedro José Barbosa Pereira

The enzyme glutamine synthetase from M. truncatula has been expressed, purified and crystallized. The crystals belonged to the monoclinic space group P21 and diffracted to 2.35 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1309–1312. Published online 2009 November 27. doi: 10.1107/S1744309109047381
PMCID:
PMC2802889
Archana Chauhan, Zeyaul Islam, Rakesh Kumar Jain, Subramanian Karthikeyan

Purification and preliminary X-ray crystallographic analysis of maleylacetate reductase encoded by the pnpD gene is reported.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1313–1316. Published online 2009 November 27. doi: 10.1107/S1744309109047319
PMCID:
PMC2802890
Ronny C. Hughes, Stephen J. Tomanicek, Joseph D. Ng, Leighton Coates

The overexpression, purification and crystallization of endonuclease IV from T. maritima are reported. The crystals belonged to the hexagonal space group P61 and diffracted to 2.36 Å resolution.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 December 1; 65(Pt 12): 1317–1319. Published online 2009 November 27. doi: 10.1107/S1744309109047393
PMCID:
PMC2802891

Articles from Acta Crystallographica Section F: Structural Biology and Crystallization Communications are provided here courtesy of International Union of Crystallography