Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 68, Part 4 (April 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration]Cover illustration: Pleckstrin homology domain of Saccharomyces cerevisiae Avo1 (Pan & Matsuura, p. 386).

editorial


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2012). F68, 365  [ doi:10.1107/S1744309112011852 ]

Another case of fraud in structural biology

M. S. Weiss, H. Einspahr, E. N. Baker and Z. Dauter

Synopsis: Editorial.

Online 31 March 2012


scientific comment


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [RE]  [Open access]

Acta Cryst. (2012). F68, 366-376  [ doi:10.1107/S1744309112008421 ]

Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen

B. Rupp

Synopsis: 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).

Online 31 March 2012


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2012). F68, 377  [ doi:10.1107/S1744309112008433 ]

Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen

N. Zaborsky, M. Brunner, M. Wallner, M. Himly, T. Karl, R. Schwarzenbacher, F. Ferreira and G. Achatz

Synopsis: A response to the article by Rupp (2012), Acta Cryst. F68, 366-376.

Online 31 March 2012


structural communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 378-381  [ doi:10.1107/S1744309112005866 ]

Structure of the third catalytic domain of the protein disulfide isomerase ERp46

I. E. Gulerez, G. Kozlov, A. Rosenauer and K. Gehring

Synopsis: The structure of the third catalytic domain of the human protein disulfide isomerase ERp46 has been determined to 2.0 ┼ resolution.

PDB reference: 3uvt

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2012). F68, 382-385  [ doi:10.1107/S1744309112006720 ]

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 and L. W. Tari

Synopsis: 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 ┼.

PDB reference: 3vcy

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 386-392  [ doi:10.1107/S1744309112007178 ]

Structures of the pleckstrin homology domain of Saccharomyces cerevisiae Avo1 and its human orthologue Sin1, an essential subunit of TOR complex 2

D. Pan and Y. Matsuura

Synopsis: 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.

PDB references: 3ulb, 3ulc and 3voq

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 393-399  [ doi:10.1107/S174430911200869X ]

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

P. K. Mandal, S. Venkadesh and N. Gautham

Synopsis: The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)2 as an A-DNA duplex and its interaction with a manganese ion are described.

PDB reference: 3v9d

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 400-403  [ doi:10.1107/S1744309112008810 ]

Structure of the His269Arg mutant of the rat aldose reductase-like protein AKR1B14 complexed with NADPH

K. Sundaram, S. Endo, T. Matsunaga, N. Tanaka, A. Hara and O. El-Kabbani

Synopsis: The 1.87 ┼ resolution crystal structure of the His269Arg mutant of rat aldose reductase-like protein (AKR1B14) complexed with NADPH is described.

PDB reference: 3qkz

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 404-408  [ doi:10.1107/S1744309112009037 ]

High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors

X. Fradera, B. Kazemier, E. Carswell, A. Cooke, A. Oubrie, W. Hamilton, M. Dempster, S. Krapp, S. Nagel and A. Jestel

Synopsis: 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.

PDB references: 3sor and 3sos

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 409-413  [ doi:10.1107/S1744309112009049 ]

Structure of AKR1C3 with 3-phenoxybenzoic acid bound

V. J. Jackson, Y. Yosaatmadja, J. U. Flanagan and C. J. Squire

Synopsis: 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.

PDB reference: 3uwe

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 414-417  [ doi:10.1107/S1744309112009487 ]

Structure of Escherichia coli aspartate [alpha]-decarboxylase Asn72Ala: probing the role of Asn72 in pyruvoyl cofactor formation

M. E. Webb, C. M. C. Lobley, F. Soliman, M. L. Kilkenny, A. G. Smith, T. L. Blundell and C. Abell

Synopsis: The crystal structure of E. coli aspartate [alpha]-decarboxylase Asn72Ala reveals the structure of the previously unresolved C-terminus.

PDB reference: 3tm7

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 418-423  [ doi:10.1107/S1744309112008688 ]

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

V. Cody, J. Pace and E. Stewart

Synopsis: 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.

PDB reference: 3td8

Online 28 March 2012


crystallization communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 424-427  [ doi:10.1107/S1744309112004046 ]

Purification, crystallization and preliminary crystallographic studies of a PacL homologue from Listeria monocytogenes

K. L. Hein, P. Nissen and J. P. Morth

Synopsis: A PacL homologue from L. monocytogenes has been purified and crystallized. The crystals diffracted to 3.2 ┼ resolution.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 428-431  [ doi:10.1107/S1744309112004940 ]

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. GarcÝa-Ruiz, T. Krell and E. Pineda-Molina

Synopsis: The crystallization of the ligand-binding domain of the methyl-accepting chemotaxis protein chemoreceptor McpS (McpS-LBD) is reported.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 432-435  [ doi:10.1107/S1744309112005295 ]

Preparation, crystallization and preliminary X-ray diffraction studies of the glycosylated form of human interleukin-23

T. Shirouzono, M. Chirifu, C. Nakamura, Y. Yamagata and S. Ikemizu

Synopsis: 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.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 436-439  [ doi:10.1107/S1744309112005532 ]

Crystallization and preliminary crystallographic characterization of the N-terminal Kunitz domain of boophilin

T. B. Cereija, A. C. Figueiredo, D. de Sanctis, A. S. Tanaka and P. J. B. Pereira

Synopsis: 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 ┼ resolution at a synchrotron source.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 440-442  [ doi:10.1107/S1744309112005829 ]

Overexpression, crystallization and preliminary X-ray crystallographic analysis of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii

J. Y. Yoon, C. R. Park, H. H. Lee and S. W. Suh

Synopsis: Pyridoxal biosynthesis lyase PdxS from P. horikoshii has been overexpressed and crystallized. X-ray diffraction data have been collected to 2.61 ┼ resolution.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 443-447  [ doi:10.1107/S1744309112006070 ]

Crystal optimization and preliminary diffraction data analysis of the SCAN domain of Zfp206

Y. Liang, S. H. Choo, M. Rossbach, N. Baburajendran, P. Palasingam and P. R. Kolatkar

Synopsis: Crystals of the SCAN domain of Zfp206 are tetragonal, belonging to space group I422 with unit-cell parameters a = 67.57, c = 87.54 ┼ and one molecule in the asymmetric unit, and diffract to 1.85 ┼ resolution.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 448-450  [ doi:10.1107/S1744309112006355 ]

Crystallization and preliminary X-ray diffraction analysis of a novel wild-type blue fluorescent protein from Vibrio vulnificus CKM-1

C.-F. Liu, C.-H. Kao, Y.-C. Su and Y. Chen

Synopsis: 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.

Online 27 March 2012


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2012). F68, 451-454  [ doi:10.1107/S1744309112006550 ]

Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis

A. Lyskowski, K. Steiner, I. Hajnal, G. Steinkellner, H. Schwab and K. Gruber

Synopsis: 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.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 455-459  [ doi:10.1107/S1744309112006914 ]

Towards the crystal structure elucidation of eukaryotic UDP-galactopyranose mutase

K. E. van Straaten, F. H. Routier and D. A. R. Sanders

Synopsis: UDP-galactopyranose mutase from A. fumigatus was crystallized and structure solution is in progress.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 460-463  [ doi:10.1107/S1744309112006811 ]

Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark [beta]2-microglobulin

S. Lu, S. Yao, R. Chen, N. Zhang, J. Chen, F. Gao and C. Xia

Synopsis: A crystal of nurse shark [beta]2-microglobulin diffracted to 2.3 ┼ resolution and belonged to space group P3221, with unit-cell parameters a = b = 88.230, c = 67.146 ┼ and two molecules per asymmetric unit. The Matthews coefficient VM was calculated to be about 3.28 ┼3 Da-1, corresponding to 62.5% solvent content.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 464-467  [ doi:10.1107/S1744309112007129 ]

Crystallization and preliminary X-ray analysis of stationary phase survival protein E (SurE) from Xylella fastidiosa in two crystal forms

M. A. dos Reis, A. M. Saraiva, M. L. dos Santos, A. P. de Souza and R. Aparicio

Synopsis: The crystallization and preliminary analysis of two crystal forms of survival protein E from X. fastidiosa are reported.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 468-471  [ doi:10.1107/S1744309112006963 ]

Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2

D. B. Ascher, G. Polekhina and M. W. Parker

Synopsis: 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 ┼ resolution in the best direction on an in-house source.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 472-475  [ doi:10.1107/S1744309112007117 ]

Purification, crystallization and preliminary X-ray analysis of the aminoglycoside-6'-acetyltransferase AAC(6')-Im

M. Toth, S. B. Vakulenko and C. A. Smith

Synopsis: 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.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 476-478  [ doi:10.1107/S1744309112007439 ]

Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb' fragment of rat protein disulfide isomerase

S. Hashimoto, L. Ito, M. Okumura, T. Shibano, M. Nawata, T. Kumasaka, H. Yamaguchi and S. Imaoka

Synopsis: 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.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2012). F68, 479-482  [ doi:10.1107/S1744309112007506 ]

Crystallization and preliminary X-ray diffraction studies of the abscisic acid receptor PYL3 and its complex with pyrabactin

X. Zhang, W. Wu and Z. Chen

Synopsis: 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 ┼ resolution, respectively.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 483-485  [ doi:10.1107/S1744309112007671 ]

Cocrystallization and preliminary crystallographic analysis of an inactive MaoC-like hydratase mutant with the substrate crotonyl-CoA

H. Wang, J. Zhu, W. Song and X. Zhang

Synopsis: 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.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 486-490  [ doi:10.1107/S1744309112008445 ]

In praise of impurity: 30S ribosomal S15 protein-assisted crystallization of turnip yellow mosaic virus proteinase

C. Robin, L. Beaurepaire, M. Chenon, I. Jupin and S. Bressanelli

Synopsis: 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.

Online 28 March 2012


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 491-494  [ doi:10.1107/S1744309112009384 ]

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

K. Miyazono, T. Koura, K. Kubota, T. Yoshida, Y. Fujita, K. Yamaguchi-Shinozaki and M. Tanokura

Synopsis: 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 ┼ resolution.

Online 28 March 2012


laboratory communications


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2012). F68, 495-500  [ doi:10.1107/S1744309112009670 ]

Fast high-pressure freezing of protein crystals in their mother liquor

A. Burkhardt, M. Warmer, S. Panneerselvam, A. Wagner, A. Zouni, C. Gl÷ckner, R. Reimer, H. Hohenberg and A. Meents

Synopsis: 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.

PDB references: 4a7d and 4a7e

Online 31 March 2012