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Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 69, Part 2 (February 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Structure of an amidohydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL (Girish et al., p. 103).

editorial


 

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Acta Cryst. (2013). F69, 83  [ doi:10.1107/S1744309113001486 ]

Expectation bias and information content

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

Synopsis: Editorial.

Online 19 January 2013


structural communications


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Acta Cryst. (2013). F69, 84-89  [ doi:10.1107/S1744309112050270 ]

Structure of ALD1, a plant-specific homologue of the universal diaminopimelate aminotransferase enzyme of lysine biosynthesis

V. Sobolev, M. Edelman, O. Dym, T. Unger, S. Albeck, M. Kirma and G. Galili

Synopsis: The structure of AtALD1 from the flowering plant Arabidopsis thaliana was solved at a resolution of 2.3 Å. The structural analysis supports previous biochemical evidence for differential expression and distinct functions of AtALD1 and AtDAP-AT.

PDB reference: 4fl0

Online 26 January 2013


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Acta Cryst. (2013). F69, 90-93  [ doi:10.1107/S1744309112050750 ]

Structure of a low-melting-temperature anti-cholera toxin: llama VHH domain

P. M. Legler, D. Zabetakis, G. P. Anderson, A. Lam, W. G. J. Hol and E. R. Goldman

Synopsis: The X-ray crystal structure of a camelid VHH domain with a melting temperature of 319.9 ± 1.6 K, which is among the lowest reported for a VHH domain, is reported at 2.1 Å resolution.

PDB reference: 4idl

Online 26 January 2013


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Acta Cryst. (2013). F69, 94-102  [ doi:10.1107/S1744309113000286 ]

The structure of the FnI-EGF-like tandem domain of coagulation factor XII solved using SIRAS

D. X. Beringer and L. M. J. Kroon-Batenburg

Synopsis: The structure of the FnI-EGF-like tandem domain was solved to 1.6 Å using data sets of native and holmium chloride bound protein. Putative biological roles of this tandem domain are discussed based on the structure.

PDB references: 4bdx and 4bdw

Online 26 January 2013


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Acta Cryst. (2013). F69, 103-108  [ doi:10.1107/S1744309112049822 ]

Structure of an amidohydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL

T. S. Girish, V. B, M. Colaco, S. Misquith and B. Gopal

Synopsis: The crystal structure of the S. aureus amidohydrolase SACOL0085 reveals that a conserved cysteine residue at the active site serves as a bidentate ligand coordinating two Mn2+ ions.

PDB reference: 4ewt

Online 30 January 2013


crystallization communications


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Acta Cryst. (2013). F69, 109-114  [ doi:10.1107/S1744309112048622 ]

Crystallization and preliminary X-ray diffraction analysis of YhbJ from Escherichia coli, a key protein involved in the GlmYZ sRNA regulatory cascade

M. Resch, Y. Göpel, B. Görke and R. Ficner

Synopsis: The homotrimeric protein YhbJ from E. coli has been homologously expressed, purified and crystallized in two distinct crystal forms. The crystals diffracted to 3.26 and 3.44 Å resolution.

Online 30 January 2013


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Acta Cryst. (2013). F69, 115-117  [ doi:10.1107/S1744309112049020 ]

Overexpression, crystallization and preliminary X-ray crystallographic analysis of [beta]-N-acetylglucosaminidase from Thermotoga maritima encoded by the Tm0809 gene

H. H. Lee and S. T. Jung

Synopsis: [beta]-N-Acetylglucosaminidase from T. maritima has been overexpressed and crystallized. X-ray diffraction data have been collected to 3.80 Å resolution.

Online 30 January 2013


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Acta Cryst. (2013). F69, 118-121  [ doi:10.1107/S1744309112050208 ]

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8

S. K. Chaudhary, J. Jeyakanthan and K. Sekar

Synopsis: Thymidylate kinase from T. thermophilus HB8 has been cloned, expressed, purified and crystallized.

Online 30 January 2013


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Acta Cryst. (2013). F69, 122-125  [ doi:10.1107/S1744309112050300 ]

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the chicken MHC class I molecule BF2*1501

B. Sun, X. Li, Z. Wang and C. Xia

Synopsis: X-ray diffraction data were collected to 2.6 Å resolution from a crystal of the chicken MHC class I molecule BF2*1501. The crystal belonged to space group P3121, with unit-cell parameters a = 125.1, b = 125.1, c = 80.9 Å, and contained two molecules in the asymmetric unit. The Matthews coefficient and solvent content were calculated to be 2.08 Å3 Da-1 and 40.78%, respectively.

Online 30 January 2013


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Acta Cryst. (2013). F69, 126-129  [ doi:10.1107/S174430911205083X ]

Purification, crystallization and preliminary crystallographic studies of haemoglobin from mongoose (Helogale parvula) in two different crystal forms induced by pH variation

M. Mohamed Abubakkar, K. Saraboji and M. N. Ponnuswamy

Synopsis: Preliminary crystallographic study of low-oxygen affinity haemoglobin from mongoose; the first structural study of haemoglobin from a member of the Herpestidae family.

Online 30 January 2013


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Acta Cryst. (2013). F69, 130-133  [ doi:10.1107/S1744309112051445 ]

Crystallization and preliminary crystallographic analysis of two eukaryotic fructosyl peptide oxidases

A. Ichiyanagi, K. Hirokawa, K. Gomi, T. Nakatsu, H. Kato and N. Kajiyama

Synopsis: Fructosyl peptide oxidases from Coniochaeta sp. and E. terrenum were crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 and 1.6 Å resolution, respectively.

Online 30 January 2013


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Acta Cryst. (2013). F69, 134-136  [ doi:10.1107/S1744309112051391 ]

Crystallization and preliminary X-ray analysis of L-serine 3-dehydrogenase complexed with NADP+ from the hyperthermophilic archaeon Pyrobaculum calidifontis

K. Yoneda, H. Sakuraba, T. Araki, T. Shibata, T. Nikki and T. Ohshima

Synopsis: An NAD(P)+-dependent L-serine 3-dehydrogenase from a hyperthermophilic archaeon was successfully isolated and crystallized.

Online 31 January 2013


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Acta Cryst. (2013). F69, 137-140  [ doi:10.1107/S1744309112051408 ]

Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris

F. R. Rosseto, A. C. Puhl, M. O. Andrade and I. Polikarpov

Synopsis: Major endoglucanase was purified from the extracellular extract of X. campestris pv. campestris and crystals of the catalytic domain were obtained. X-ray diffraction data were collected to 2.7 Å resolution.

Online 31 January 2013


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Acta Cryst. (2013). F69, 141-146  [ doi:10.1107/S1744309112052128 ]

Crystallization of a self-assembled three-dimensional DNA nanostructure

K. N. Rendek, R. Fromme, I. Grotjohann and P. Fromme

Synopsis: In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described.

Online 31 January 2013


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Acta Cryst. (2013). F69, 147-152  [ doi:10.1107/S1744309112051597 ]

Crystallization and preliminary X-ray crystallographic analysis of sterol transcription factor Upc2 from Saccharomyces cerevisiae

S. Ha, J. Tong, H. Yang, H.-S. Youn, S. H. Eom and Y. J. Im

Synopsis: In this study, the C-terminal regulatory domain of Upc2 from Saccharomyces cerevisiae was purified and crystallized by the vapour-diffusion method.

Online 31 January 2013


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Acta Cryst. (2013). F69, 153-157  [ doi:10.1107/S1744309112051755 ]

The expression, purification and crystallization of a ubiquitin-conjugating enzyme E2 from Agrocybe aegerita underscore the impact of His-tag location on recombinant protein properties

D.-F. Li, L. Feng, Y.-J. Hou and W. Liu

Synopsis: The purification and crystallization of UbcA1, a novel ubiquitin-conjugating enzyme identified from the medicinal mushroom A. aegerita, are described.

Online 31 January 2013


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Acta Cryst. (2013). F69, 158-161  [ doi:10.1107/S174430911205186X ]

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana

O. Degtjarik, R. Dopitova, S. Puehringer, E. Nejedla, M. Kuty, M. S. Weiss, J. Hejatko, L. Janda and I. Kuta Smatanova

Synopsis: AHP2 from A. thaliana was cloned, expressed, purified and crystallized.

Online 31 January 2013


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Acta Cryst. (2013). F69, 162-164  [ doi:10.1107/S1744309112051913 ]

Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus

P. Ragunathan, G. Raghunath, S. Kuramitsu, S. Yokoyama, T. Kumarevel and K. Ponnuraj

Synopsis: The expression, purification, characterization and crystallization of GK2848, a carbonic anhydrase from G. kaustophilus, are described. The crystals diffracted to a resolution of 2.70 Å.

Online 31 January 2013


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Acta Cryst. (2013). F69, 165-169  [ doi:10.1107/S1744309112052074 ]

Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles

M. Kikuchi, S. Iwabuchi, T. Kikkou, K. Noguchi, M. Odaka, M. Yohda, M. Kawata, C. Sato and O. Matsumoto

Synopsis: Novel hepatitis B virus-like particles of recombinant dimeric core-GFP fusion protein were expressed, purified and crystallized. The crystals diffracted to 2.15 Å resolution and belonged to space group F432, with unit-cell parameters a = b = c = 219.7 Å.

Online 31 January 2013


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Acta Cryst. (2013). F69, 170-173  [ doi:10.1107/S1744309113000110 ]

Crystallization and preliminary X-ray crystallographic analysis of the functional form of BinB binary toxin from Bacillus sphaericus

K. Srisucharitpanit, M. Yao, S. Chimnaronk, B. Promdonkoy, I. Tanaka and P. Boonserm

Synopsis: The BinB subunit of mosquito-larvicidal binary toxin from B. sphaericus has been crystallized. The crystal could diffract to a resolution of 1.75 Å and belongs to space group P6222.

Online 31 January 2013


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Acta Cryst. (2013). F69, 174-177  [ doi:10.1107/S1744309113000055 ]

Crystallization and preliminary X-ray crystallographic analyses of Thermus thermophilus backtracked RNA polymerase

Y. Murayama, S.- Sekine and S. Yokoyama

Synopsis: Backtracked bacterial RNA polymerase (RNAP) complexes were reconstituted by assembling Thermus thermophilus RNAP with nucleic acid scaffolds. The complexes were crystallized, and their X-ray diffraction data were collected and analyzed.

Online 31 January 2013


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Acta Cryst. (2013). F69, 178-183  [ doi:10.1107/S1744309113000134 ]

Crystallization and preliminary structure determination of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501

N. Goessweiner-Mohr, L. Grumet, T. Pavkov-Keller, R. Birner-Gruenberger, E. Grohmann and W. Keller

Synopsis: This paper reports the successful purification, crystallization and preliminary structure solution of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501.

Online 31 January 2013


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Acta Cryst. (2013). F69, 184-187  [ doi:10.1107/S1744309113000766 ]

Crystallization and preliminary X-ray characterization of an NAD(P)-dependent butanol dehydrogenase A from Geobacillus thermodenitrificans NG80-2

Y. Ji, G. Mao, Y. Wang and M. Bartlam

Synopsis: ADH2, an NAD(P)-dependent butanol dehydrogenase A, is part of the terminal oxidation pathway in the long-chain alkane-degrading G. thermodenitrificans NG80-2. The expression, purification, crystallization and preliminary crystallographic analysis of ADH2 are reported.

Online 31 January 2013


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Acta Cryst. (2013). F69, 188-190  [ doi:10.1107/S1744309113001267 ]

Crystallization of the acyl-CoA thioesterase TesB from Yersinia pestis

C. M. D. Swarbrick, E. I. Patterson and J. K. Forwood

Synopsis: The expression, purification, crystallization and diffraction of the acyl-CoA thioesterase TesB from Y. pestis are reported. X-ray crystallographic diffraction data to 2.0 Å resolution were collected at the Australian Synchrotron.

Online 31 January 2013


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Acta Cryst. (2013). F69, 191-194  [ doi:10.1107/S1744309113001620 ]

Overproduction, purification, crystallization and preliminary X-ray characterization of the C-terminal family 65 carbohydrate-binding module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens

I. Venditto, A. Baslé, A. S. Luís, M. J. Temple, L. M. A. Ferreira, C. M. G. A. Fontes, H. J. Gilbert and S. Najmudin

Synopsis: The C-terminal carbohydrate-binding module (CBM65B) of family 5 glycoside hydrolase endoglucanase 5A (Cel5A) of E. cellulosolvens has been co-crystallized with cellohexaose and xyloglucan heptasaccharide and various data collected to 1.42-3.5 Å resolution.

Online 31 January 2013


laboratory communications


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Acta Cryst. (2013). F69, 195-200  [ doi:10.1107/S1744309112044387 ]

Visualizing ligand molecules in twilight electron density

C. X. Weichenberger, E. Pozharski and B. Rupp

Synopsis: A software script is presented for facilitating the analysis and visual inspection of ligand molecules in the context of the electron-density maps calculated from experimental data associated with protein structures determined by X-ray crystallography.

Online 19 January 2013


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Acta Cryst. (2013). F69, 201-208  [ doi:10.1107/S1744309112048634 ]

Some practical guidelines for UV imaging in the protein crystallization laboratory

S. Desbois, S. A. Seabrook and J. Newman

Synopsis: The use of UV imaging as a means of locating protein crystals is a fairly new tool, however not suitable for all protein crystallization trials. Practical examples of the strengths and some of the pitfalls of the technology are presented.

Online 26 January 2013


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Acta Cryst. (2013). F69, 209-214  [ doi:10.1107/S1744309112051858 ]

Optimization of protein buffer cocktails using Thermofluor

L. Reinhard, H. Mayerhofer, A. Geerlof, J. Mueller-Dieckmann and M. S. Weiss

Synopsis: The Thermofluor assay constitutes a quick and easy-to-perform high-throughput method with which it is possible to identify protein-stabilizing buffer compositions or small-molecule additives.

Online 31 January 2013


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