Volume 68(Pt 4); April 1, 2012
Editorial
Manfred S. Weiss, Howard Einspahr, Ted Baker, Zbigniew Dauter
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 365. Published online 2012 March 31. doi: 10.1107/S1744309112011852
Scientific Comment
Bernhard Rupp
The structure factors deposited with PDB entry 3k78 show properties inconsistent with experimentally observed diffraction data, and without uncertainty represent calculated structure factors. The refinement of the 3k78 model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019).
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 366–376. Published online 2012 March 31. doi: 10.1107/S1744309112008421
Nadja Zaborsky, Marietta Brunner, Michael Wallner, Martin Himly, Tanja Karl, Robert Schwarzenbacher, Fatima Ferreira, Gernot Achatz
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 377. Published online 2012 March 31. doi: 10.1107/S1744309112008433
Structural Communications
Structure of the third catalytic domain of the protein disulfide isomerase ERp46
Irina E. Gulerez, Guennadi Kozlov, Angelika Rosenauer, Kalle Gehring
The structure of the third catalytic domain of the human protein disulfide isomerase ERp46 has been determined to 2.0 Å resolution.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 378–381. Published online 2012 March 27. doi: 10.1107/S1744309112005866
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Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin
D. C. Bensen, S. Rodriguez, J. Nix, M. L. Cunningham, L. W. Tari
The crystal structure of MurA from the marine Gram-negative bacterium Vibrio fischeri in complex with UNAG and the drug fosfomycin has been solved to a resolution of 1.93 Å.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 382–385. Published online 2012 March 27. doi: 10.1107/S1744309112006720
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Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2
Dongqing Pan, Yoshiyuki Matsuura
The crystal structures of the C-terminal domain of S. cerevisiae Avo1 and of its human orthologue Sin1 have been determined. The structures show that the C-termini of the two proteins have the PH-domain fold with a putative binding site for phosphoinositides.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 386–392. Published online 2012 March 27. doi: 10.1107/S1744309112007178
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Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
Pradeep Kumar Mandal, Sarkarai Venkadesh, Namasivayam Gautham
The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)2 as an A-DNA duplex and its interaction with a manganese ion are described.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 393–399. Published online 2012 March 27. doi: 10.1107/S174430911200869X
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Structure of the His269Arg mutant of the rat aldose reductase-like protein AKR1B14 complexed with NADPH
Krithika Sundaram, Satoshi Endo, Toshiyuki Matsunaga, Nobutada Tanaka, Akira Hara, Ossama El-Kabbani
The 1.87 Å resolution crystal structure of the His269Arg mutant of rat aldose reductase-like protein (AKR1B14) complexed with NADPH is described.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 400–403. Published online 2012 March 27. doi: 10.1107/S1744309112008810
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High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors
Xavier Fradera, Bert Kazemier, Emma Carswell, Andrew Cooke, Arthur Oubrie, William Hamilton, Maureen Dempster, Stephan Krapp, Susanna Nagel, Anja Jestel
Two structures of factor XIa in complex with small synthetic inhibitors are reported. These are the first structures of factor XIa complexed to small non-basic inhibitors.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 404–408. Published online 2012 March 27. doi: 10.1107/S1744309112009037
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Structure of AKR1C3 with 3-phenoxybenzoic acid bound
Victoria J. Jackson, Yuliana Yosaatmadja, Jack U. Flanagan, Christopher J. Squire
The structure of the nonsteroidal anti-inflammatory drug analogue 3-phenoxybenzoic acid bound to aldo–keto reductase 1C3 (AKR1C3) is presented as a lead for the discovery and development of novel agents for inhibiting AKR1C3, an anticancer target.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 409–413. Published online 2012 March 27. doi: 10.1107/S1744309112009049
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Structure of Escherichia coli aspartate α-decarboxylase Asn72Ala: probing the role of Asn72 in pyruvoyl cofactor formation
Michael E. Webb, Carina M. C. Lobley, Fatima Soliman, Mairi L. Kilkenny, Alison G. Smith, Tom L. Blundell, Chris Abell
The crystal structure of E. coli aspartate α-decarboxylase Asn72Ala reveals the structure of the previously unresolved C-terminus.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 414–417. Published online 2012 March 28. doi: 10.1107/S1744309112009487
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Structural analysis of Pneumocystis carinii dihydrofolate reductase complexed with NADPH and 2,4-diamino-6-[2-(5-carboxypent-1-yn-1-yl)-5-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine
Vivian Cody, Jim Pace, Elizabeth Stewart
Structural data for the ternary complex of P. carinii DHFR with NADPH and the potent inhibitor PY1014 reveal conformational changes that help to explain the weaker potency and selectivity of the pyrido[2,3-d]pyrimidine scaffold compared with the homologous pyrimidine series of antifolates.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 418–423. Published online 2012 March 28. doi: 10.1107/S1744309112008688
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Crystallization Communications
Purification, crystallization and preliminary crystallographic studies of a PacL homologue from Listeria monocytogenes
Kim Langmach Hein, Poul Nissen, Jens Preben Morth
A PacL homologue from L. monocytogenes has been purified and crystallized. The crystals diffracted to 3.2 Å resolution.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 424–427. Published online 2012 March 27. doi: 10.1107/S1744309112004046
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Crystallization and crystallographic analysis of the ligand-binding domain of the Pseudomonas putida chemoreceptor McpS in complex with malate and succinate
J. A. Gavira, J. Lacal, J. L. Ramos, J. M. García-Ruiz, T. Krell, E. Pineda-Molina
The crystallization of the ligand-binding domain of the methyl-accepting chemotaxis protein chemoreceptor McpS (McpS-LBD) is reported.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 428–431. Published online 2012 March 27. doi: 10.1107/S1744309112004940
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Preparation, crystallization and preliminary X-ray diffraction studies of the glycosylated form of human interleukin-23
Takumi Shirouzono, Mami Chirifu, Chiharu Nakamura, Yuriko Yamagata, Shinji Ikemizu
Interleukin-23 (IL-23), a member of the IL-12 family, is a heterodimeric cytokine composed of p19 and p40 subunits. Human p19 and p40 subunits were cloned and coexpressed in N-acetylglucosaminyltransferase I-negative 293S cells. The glycosylated human IL-23 was purified and crystallized by the hanging-drop vapour-diffusion method.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 432–435. Published online 2012 March 27. doi: 10.1107/S1744309112005295
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Crystallization and preliminary crystallographic characterization of the N-terminal Kunitz domain of boophilin
Tatiana B. Cereija, Ana C. Figueiredo, Daniele de Sanctis, Aparecida S. Tanaka, Pedro José Barbosa Pereira
The N-terminal Kunitz domain of boophilin, a specific thrombin inhibitor, was crystallized. The orthorhombic crystals had an unusually low solvent content and diffracted to beyond 0.87 Å resolution at a synchrotron source.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 436–439. Published online 2012 March 27. doi: 10.1107/S1744309112005532
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Overexpression, crystallization and preliminary X-ray crystallographic analysis of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
Ji Young Yoon, Chan Ryang Park, Hyung Ho Lee, Se Won Suh
Pyridoxal biosynthesis lyase PdxS from P. horikoshii has been overexpressed and crystallized. X-ray diffraction data have been collected to 2.61 Å resolution.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 440–442. Published online 2012 March 27. doi: 10.1107/S1744309112005829
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Crystal optimization and preliminary diffraction data analysis of the SCAN domain of Zfp206
Yu Liang, Siew Hua Choo, Michael Rossbach, Nithya Baburajendran, Paaventhan Palasingam, Prasanna R Kolatkar
Crystals of the SCAN domain of Zfp206 are tetragonal, belonging to space group I422 with unit-cell parameters a = 67.57, c = 87.54 Å and one molecule in the asymmetric unit, and diffract to 1.85 Å resolution.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 443–447. Published online 2012 March 27. doi: 10.1107/S1744309112006070
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Crystallization and preliminary X-ray diffraction analysis of a novel wild-type blue fluorescent protein from Vibrio vulnificus CKM-1
Chin-Feng Liu, Chao-Hung Kao, Yen-Chao Su, Yeh Chen
The wild type BFPvv has been crystallized for the first time in order to obtain its tertiary structure and to further understand how chromophore formation occurs via a different oxygen-independent mechanism.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 448–450. Published online 2012 March 27. doi: 10.1107/S1744309112006355
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Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis
Andrzej Łyskowski, Kerstin Steiner, Ivan Hajnal, Georg Steinkellner, Helmut Schwab, Karl Gruber
Recombinant AciX9_0562 from Acidobacterium sp. MP5ACTX9 containing sequence motifs characteristic of the RmlC-type cupins superfamily and containing Pfam motif PF07883 has been successfully cloned, expressed and purified, and crystallized in a number of conditions from the Morpheus protein crystallization screen.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 451–454. Published online 2012 March 28. doi: 10.1107/S1744309112006550
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Towards the crystal structure elucidation of eukaryotic UDP-galactopyranose mutase
Karin E. van Straaten, Francoise H. Routier, David A. R. Sanders
UDP-galactopyranose mutase from A. fumigatus was crystallized and structure solution is in progress.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 455–459. Published online 2012 March 28. doi: 10.1107/S1744309112006914
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Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark β2-microglobulin
Shuangshuang Lu, Shugang Yao, Rong Chen, Nianzhi Zhang, Jianmin Chen, Feng Gao, Chun Xia
A crystal of nurse shark β2-microglobulin diffracted to 2.3 Å resolution and belonged to space group P3221, with unit-cell parameters a = b = 88.230, c = 67.146 Å and two molecules per asymmetric unit. The Matthews coefficient V
M was calculated to be about 3.28 Å3 Da−1, corresponding to 62.5% solvent content.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 460–463. Published online 2012 March 28. doi: 10.1107/S1744309112006811
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Crystallization and preliminary X-ray analysis of stationary phase survival protein E (SurE) from Xylella fastidiosa in two crystal forms
Marcelo Augusto dos Reis, Antonio Marcos Saraiva, Marcelo Leite dos Santos, Anete Pereira de Souza, Ricardo Aparicio
The crystallization and preliminary analysis of two crystal forms of survival protein E from X. fastidiosa are reported.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 464–467. Published online 2012 March 28. doi: 10.1107/S1744309112007129
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Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2
David B. Ascher, Galina Polekhina, Michael W. Parker
The luminal domain of human endoplasmic reticulum aminopeptidase 2 has been expressed, purified and crystallized. The crystals belonged to the orthorhombic space group P21212 and diffracted anisotropically to 3.3 Å resolution in the best direction on an in-house source.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 468–471. Published online 2012 March 28. doi: 10.1107/S1744309112006963
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Purification, crystallization and preliminary X-ray analysis of the aminoglycoside-6′-acetyltransferase AAC(6′)-Im
Marta Toth, Sergei B. Vakulenko, Clyde A. Smith
AAC(6′)-Im is an N-acetyltransferase enzyme responsible for aminoglycoside resistance in E. faecium and E. coli isolates. Crystals of the kanamycin complex of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 472–475. Published online 2012 March 28. doi: 10.1107/S1744309112007117
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Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb′ fragment of rat protein disulfide isomerase
Shoko Hashimoto, Len Ito, Masaki Okumura, Tomohisa Shibano, Marina Nawata, Takashi Kumasaka, Hiroshi Yamaguchi, Susumu Imaoka
Protein disulfide isomerase (PDI) is known to bind to the thyroid hormone triiodothyronine (T3). Here, the expression, crystallization and preliminary X-ray studies of the b and b′ domains of rat PDI in ligand-free and T3-complexed states are reported.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 476–478. Published online 2012 March 28. doi: 10.1107/S1744309112007439
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Crystallization and preliminary X-ray diffraction studies of the abscisic acid receptor PYL3 and its complex with pyrabactin
Xingliang Zhang, Wei Wu, Zhongzhou Chen
Crystals of the abscisic acid receptor PYL3 and of the PYL3–pyrabactin complex were obtained and optimized in order to obtain high-quality diffraction data. Diffraction data sets were collected and processed to 2.5 and 1.83 Å resolution, respectively.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 479–482. Published online 2012 March 28. doi: 10.1107/S1744309112007506
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Cocrystallization and preliminary crystallographic analysis of an inactive MaoC-like hydratase mutant with the substrate crotonyl-CoA
Huizheng Wang, Jie Zhu, Weiwei Song, Xiuguo Zhang
An inactive MaoC-like hydratase mutant from P. capsici was obtained and purified, and the purified mutant was cocrystallized in the presence of the substrate crotonyl-CoA.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 483–485. Published online 2012 March 28. doi: 10.1107/S1744309112007671
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In praise of impurity: 30S ribosomal S15 protein-assisted crystallization of turnip yellow mosaic virus proteinase
Charlotte Robin, Lionel Beaurepaire, Mélanie Chenon, Isabelle Jupin, Stéphane Bressanelli
Diffraction-quality crystals of the turnip yellow mosaic virus proteinase/ubiquitin hydrolase could only be obtained from a protein preparation that was heavily contaminated with E. coli 30S ribosomal S15 protein. Crystal packing reveals the basis of this observation.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 486–490. Published online 2012 March 28. doi: 10.1107/S1744309112008445
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Purification, crystallization and preliminary X-ray analysis of OsAREB8 from rice, a member of the AREB/ABF family of bZIP transcription factors, in complex with its cognate DNA
Ken-ichi Miyazono, Tsubasa Koura, Keiko Kubota, Takuya Yoshida, Yasunari Fujita, Kazuko Yamaguchi-Shinozaki, Masaru Tanokura
OsAREB8 from rice (O. sativa), a member of the AREB/ABF family of bZIP transcription factors, was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. A crystal of OsAREB8 in complex with its cognate DNA diffracted X-rays to 3.65 Å resolution.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 491–494. Published online 2012 March 28. doi: 10.1107/S1744309112009384
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Laboratory Communications
Fast high-pressure freezing of protein crystals in their mother liquor
Anja Burkhardt, Martin Warmer, Saravanan Panneerselvam, Armin Wagner, Athina Zouni, Carina Glöckner, Rudolph Reimer, Heinrich Hohenberg, Alke Meents
Protein crystals were vitrified using high-pressure freezing in their mother liquor at 210 MPa and 77 K without cryoprotectants or oil coating. The method was successfully applied to photosystem II, which is representative of a membrane protein with a large unit cell and weak crystal contacts.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 April 1; 68(Pt 4): 495–500. Published online 2012 March 31. doi: 10.1107/S1744309112009670
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Articles from Acta Crystallographica Section F: Structural Biology and Crystallization Communications are provided here courtesy of International Union of Crystallography