Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 68, Part 12 (December 2012)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (Petrova et al., p. 1440).

structural communications


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Acta Cryst. (2012). F68, 1420-1426  [ doi:10.1107/S1744309112041759 ]

Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex

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

Synopsis: Crystal structures of the hexanucleotide d(CACGCG)·d(CGCGTG) were determined in the presence of Mn2+ ions in two crystal lattices and provide insights into ion interactions.

PDB references: 4dwy and 4dy8

Online 14 November 2012


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Acta Cryst. (2012). F68, 1427-1433  [ doi:10.1107/S174430911204273X ]

Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118

C. M. C. Lobley, P. Aller, A. Douangamath, Y. Reddivari, M. Bumann, L. E. Bird, J. E. Nettleship, J. Brandao-Neto, R. J. Owens, P. W. O'Toole and M. A. Walsh

Synopsis: The crystal structure of ribose 5-phosphate isomerase has been determined to 1.72 Å resolution and is presented with a brief comparison to other known ribose 5-phosphate isomerase A structures.

PDB reference: 4gmk

Online 14 November 2012


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Acta Cryst. (2012). F68, 1434-1439  [ doi:10.1107/S1744309112042972 ]

Structure of extracellular signal-regulated kinase 2 in complex with ATP and ADP

J. Zhang, P. Shapiro and E. Pozharski

Synopsis: Structures of ERK2 in complexes with ATP and with ADP are presented and are compared with the apo form of the protein in the same monoclinic crystal form and with the closest structural homolog cyclin-dependent kinase 2, for which an ATP-complex structure is available.

PDB references: 4gsb, 4gt3 and 4gva

Online 14 November 2012


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Acta Cryst. (2012). F68, 1440-1447  [ doi:10.1107/S1744309112043394 ]

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain

T. Petrova, E. Y. Bezsudnova, K. M. Boyko, A. V. Mardanov, K. M. Polyakov, V. V. Volkov, M. Kozin, N. V. Ravin, I. G. Shabalin, K. G. Skryabin, T. N. Stekhanova, M. V. Kovalchuk and V. O. Popov

Synopsis: The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 was determined at a resolution of 3.02 Å, showing a new relative arrangement of the OB-fold domain.

PDB reference: 3rr5

Online 14 November 2012


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Acta Cryst. (2012). F68, 1448-1454  [ doi:10.1107/S1744309112044168 ]

Structure of the [alpha]-1,6/[alpha]-1,4-specific glucansucrase GTFA from Lactobacillus reuteri 121

T. Pijning, A. Vujicic-Zagar, S. Kralj, L. Dijkhuizen and B. W. Dijkstra

Synopsis: A 118 kDa fragment, comprising the catalytic domain and four other domains, of the glucansucrase GTFA from L. reuteri 121, which synthesizes [alpha]-glucans with both [alpha]-1,6- and [alpha]-1,4-glycosidic linkages, was crystallized. The weakly diffracting crystals, which contained 85% solvent, were used to determine the structure at 3.6 Å resolution.

PDB reference: 4amc

Online 14 November 2012


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Acta Cryst. (2012). F68, 1455-1459  [ doi:10.1107/S1744309112045265 ]

Structure of the Rho-specific guanine nucleotide-exchange factor Xpln

K. Murayama, M. Kato-Murayama, R. Akasaka, T. Terada, S. Yokoyama and M. Shirouzu

Synopsis: The Xpln crystal structure provides structural insights into Rho GTPase binding.

PDB reference: 2z0q

Online 19 November 2012


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Acta Cryst. (2012). F68, 1460-1464  [ doi:10.1107/S1744309112045241 ]

Structure of a periplasmic glucose-binding protein from Thermotoga maritima

K. Palani, D. Kumaran, S. K. Burley and S. Swaminathan

Synopsis: The periplasmic glucose-binding protein from T. maritima consists of two domains with the ligand [beta]-D-glucose buried between them. The two domains adopt a closed conformation.

PDB reference: 2qvc

Online 19 November 2012


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Acta Cryst. (2012). F68, 1465-1471  [ doi:10.1107/S1744309112045514 ]

Complex of myoglobin with phenol bound in a proximal cavity

X. Huang, C. Wang, L. R. Celeste, L. L. Lovelace, S. Sun, J. H. Dawson and L. Lebioda

Synopsis: The structure of a complex of sperm whale myoglobin with phenol places this inhibitor of the haloperoxidase activity in a proximal cavity that is unlikely to be the halophenol binding site. The absence of phenol binding at the heme edge, where dehalogenation is likely to take place, indicates that the inhibitor and the halophenol substrates only bind in the active site in the presence of hydrogen peroxide.

PDB references: 3u3e, 4h07 and 4h0b

Online 19 November 2012


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Acta Cryst. (2012). F68, 1472-1476  [ doi:10.1107/S1744309112045770 ]

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

R. C. Hughes, H. McFeeters, L. Coates and R. L. McFeeters

Synopsis: P. aeruginosa peptidyl-tRNA hydrolase was cloned, expressed, purified and crystallized. The crystals obtained diffracted to 1.77 Å resolution.

PDB reference: 4fyj

Online 28 November 2012


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Acta Cryst. (2012). F68, 1477-1481  [ doi:10.1107/S174430911204571X ]

Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii

J. Badger, B. Chie-Leon, C. Logan, V. Sridhar, B. Sankaran, P. H. Zwart and V. Nienaber

Synopsis: Crystal structures of the LpxA protein from A. baumannii were solved in apo forms that were suitable for structure-based antibacterial drug discovery.

PDB references: 4e6t and 4e6u

Online 28 November 2012


crystallization communications


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Acta Cryst. (2012). F68, 1482-1487  [ doi:10.1107/S1744309112032447 ]

Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction

R. C. Hughes, L. Coates, M. P. Blakeley, S. J. Tomanicek, P. Langan, A. Y. Kovalevsky, J. M. García-Ruiz and J. D. Ng

Synopsis: Inorganic pyrophosphatase from T. thioreducans has been crystallized and the crystals were deemed to be suitable for both X-ray and neutron diffraction at room temperature.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1488-1490  [ doi:10.1107/S1744309112040638 ]

Crystallization and preliminary X-ray crystallographic analysis of quinolinate phosphoribosyltransferase from porcine kidney in complex with nicotinate mononucleotide

H.-S. Youn, M.-K. Kim, G. B. Kang, T. G. Kim, J. Y. An, J.-G. Lee, K. R. Park, Y. Lee, S.-I. Fukuoka and S. H. Eom

Synopsis: Crystals of S. scrofa quinolinate phosphoribosyltransferase purified from porcine kidney in complex with nicotinate mononucleotidewere obtained and diffraction data were collected and processed to 2.1 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1491-1493  [ doi:10.1107/S1744309112042212 ]

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana

A. Roberts, R. Gill, R. J. Hussey, H. Mikolajek, P. T. Erskine, J. B. Cooper, S. P. Wood, E. J. T. Chrystal and P. M. Shoolingin-Jordan

Synopsis: The enzyme porphobilinogen deaminase (PBGD) catalyses a key early step in the biosynthesis of haem in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. PBGD from the model plant organism A. thaliana has been expressed and the enzyme was crystallized in a form that diffracted synchrotron radiation to high resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1494-1497  [ doi:10.1107/S1744309112042236 ]

Cloning, expression, purification and crystallization of an endotoxin-biosynthesis enzyme from Neisseria meningitidis

A. Anandan, S. Piek, C. M. Kahler and A. Vrielink

Synopsis: The cloning, expression, purification and crystallization of phosphoethanolamine transferase A, an endotoxin-modifying enzyme from N. meningitidis, are reported.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1498-1502  [ doi:10.1107/S1744309112042510 ]

Crystallization and preliminary X-ray crystallographic analysis of the oxysterol-binding protein Osh3 from Saccharomyces cerevisiae

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

Synopsis: The PH domain and ORD of the oxysterol-binding protein Osh3 from S. cerevisae were crystallized and X-ray diffraction data were collected.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1503-1506  [ doi:10.1107/S1744309112042686 ]

Purification, crystallization and X-ray diffraction analysis of Trypanosoma congolense insect-stage surface antigen (TcCISSA)

M. L. Tonkin, S. D. Workman, B. A. Eyford, B. C. Loveless, J. L. Fudge, T. W. Pearson and M. J. Boulanger

Synopsis: A novel stage-specific surface protein, T. congolense insect-stage surface antigen (TcCISSA), from the African trypanosome T. congolense was recently identified by mass-spectrometric differential protein-expression analysis. To gain structure-function insight into this protein, the extracellular domain of TcCISSA was expressed, purified and crystallized and X-ray diffraction data were collected and processed to 2.7 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1507-1510  [ doi:10.1107/S1744309112042546 ]

Purification, crystallization and preliminary X-ray analysis of two hydrogen sulfide-producing enzymes from Fusobacterium nucleatum

Y. Kezuka, N. Abe, Y. Yoshida and T. Nonaka

Synopsis: Two homologous hydrogen sulfide-producing enzymes, Fn1220 and Cdl, from F. nucleatum (which actively produces hydrogen sulfide) were overproduced, purified and crystallized. The crystals obtained were characterized by X-ray diffraction.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1511-1514  [ doi:10.1107/S1744309112042650 ]

Crystallization of domains involved in self-assembly of the S-layer protein SbsC

A. Đordic, E. M. Egelseer, M. Tesarz, U. B. Sleytr, W. Keller and T. Pavkov-Keller

Synopsis: Three different truncation constructs of the S-layer protein SbsC containing domains crucial for self-assembly could be crystallized. Native data were collected for the three crystal forms from crystals that diffracted to 3.4, 2.8 and 1.5 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1515-1517  [ doi:10.1107/S1744309112042819 ]

Expression, crystallization and preliminary X-ray crystallographic analysis of cystathionine [gamma]-synthase (XometB) from Xanthomonas oryzae pv. oryzae

H.-P.-T. Ngo, J.-K. Kim, S.-H. Kim, T.-V. Pham, T.-H. Tran, D.-D. Nguyen, J.-G. Kim, S. Chung, Y.-J. Ahn and L.-W. Kang

Synopsis: Cystathionine [gamma]-synthase (CGS) catalyzes the [gamma]-replacement reaction of O-succinylhomoserine and L-cysteine to form L-cystathionine and succinate. As an antibacterial drug target, CGS from X. oryzae pv. oryzae (XometB) was cloned, purified and crystallized, and a preliminary X-ray crystallography analysis of the XometB crystal was performed.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1518-1520  [ doi:10.1107/S1744309112042832 ]

Crystallization and preliminary X-ray crystallographic analysis of human Apaf-1-interacting protein

W. Kang and J. K. Yang

Synopsis: Apaf-1-interacting protein (APIP) inhibits cell death involving caspase-1 and caspase-9. APIP was crystallized and X-ray diffraction data were collected to 2.40 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1521-1524  [ doi:10.1107/S1744309112043333 ]

Crystallization and preliminary X-ray characterization of Epstein-Barr virus BHRF1 in complex with a benzoylurea peptidomimetic

S. Caria, S. Chugh, D. Nhu, G. Lessene and M. Kvansakul

Synopsis: The expression and purification of Epstein-Barr virus BHRF1 as well as its co-crystallization with a peptidomimetic are described.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1525-1528  [ doi:10.1107/S1744309112043813 ]

Molecular cloning, expression, purification and crystallographic analysis of zebrafish THEM2

H. Li, F. Gao, S. Yu, M. Jia and W. Gong

Synopsis: The THEM2 protein from zebrafish has successfully been expressed, purified and crystallized. Diffraction data were collected to a resolution of 1.8 Å.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1529-1533  [ doi:10.1107/S1744309112043989 ]

Purification, crystallization and preliminary X-ray crystallographic analysis of the CIDE-N domain of Fsp27

X. Wang, B. Zhang, D. Xu, J. Gao, L. Wang, Z. Wang, Y. Shan and X. Yu

Synopsis: The CIDE-N domain of Fsp27 expressed in E. coli was purified as a monomer and identified by LC/MS/MS. Crystals of the Fsp27 CIDE-N domain were grown in sitting-drop mode and diffracted to 1.92 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1534-1537  [ doi:10.1107/S1744309112044041 ]

Crystallization of the DdrB-DNA complex from Deinococcus radiodurans

S. Sugiman-Marangos and M. Junop

Synopsis: DdrB from D. radiodurans has been crystallized in complex with ssDNA and diffraction data have been collected to 2.3 Å resolution.

Online 14 November 2012


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Acta Cryst. (2012). F68, 1538-1541  [ doi:10.1107/S1744309112044417 ]

Crystallization and preliminary X-ray diffraction analysis of the invertase from Saccharomyces cerevisiae

M. A. Sainz-Polo, A. Lafraya, A. Polo, J. Marín-Navarro, J. Polaina and J. Sanz-Aparicio

Synopsis: The invertase from S. cerevisiae was overexpressed, purified and crystallized, and its preliminary X-ray diffraction analysis is reported at 3.3 Å resolution.

Online 19 November 2012


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Acta Cryst. (2012). F68, 1542-1544  [ doi:10.1107/S1744309112044612 ]

Cloning, purification, crystallization and preliminary crystallographic study of calcium-binding protein 5 from Entamoeba histolytica

S. Kumar, R. Zaidi and S. Gourinath

Synopsis: Calcium-binding protein 5 from E. histolytica was cloned, expressed in E. coli and purified. The purified protein crystallized in space group C222 and the crystals diffracted to 2 Å resolution.

Online 19 November 2012


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Acta Cryst. (2012). F68, 1545-1549  [ doi:10.1107/S1744309112045447 ]

Crystallization and preliminary X-ray analysis of the open form of human ecto-5'-nucleotidase (CD73)

K. M. Knapp, M. Zebisch and N. Sträter

Synopsis: The crystallization of human ecto-5'-nucleotidase (CD73) paves the way for detailed studies of the domain motion between the open and closed forms. It will also enable the structure-based design of inhibitors targeting the open form.

Online 19 November 2012


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Acta Cryst. (2012). F68, 1550-1553  [ doi:10.1107/S1744309112045551 ]

Crystallization and preliminary X-ray data analysis of the pXO1 plasmid-partitioning factor TubZ from Bacillus cereus

S. Hoshino, T. Maki and I. Hayashi

Synopsis: B. cereus TubZ was cocrystallized with GDP and diffraction data were collected to 2.1 Å resolution.

Online 19 November 2012


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Acta Cryst. (2012). F68, 1554-1556  [ doi:10.1107/S1744309112044375 ]

A preliminary X-ray study of transketolase from Burkholderia pseudomallei

M.-S. Kim, A. Lim, S. W. Yang, D. Lee, J. Park and D. H. Shin

Synopsis: The transketolase TktA from B. pseudomallei has been cloned, expressed, purified and crystallized. Synchrotron X-ray data were collected to 2.0 Å resolution.

Online 28 November 2012


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Acta Cryst. (2012). F68, 1557-1559  [ doi:10.1107/S174430911204657X ]

Preliminary crystallographic analysis of the Megavirus superoxide dismutase

A. Lartigue, N. Philippe, S. Jeudy and C. Abergel

Synopsis: The preliminary crystallographic analysis of the Megavirus chilensis superoxide dismutase Mg277 is reported. The crystals belonged to space group P41212 or P43212, with one dimer per asymmetric unit.

Online 28 November 2012


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Acta Cryst. (2012). F68, 1560-1563  [ doi:10.1107/S1744309112047070 ]

Crystallization and preliminary X-ray diffraction analysis of mevalonate kinase from Methanosarcina mazei

N. Zhuang, K. H. Seo, C. Chen, J. Zhou, S. W. Kim and K. H. Lee

Synopsis: Recombinant mevalonate kinase from M. mazei has been crystallized. Diffraction data were collected to 2.08 Å resolution.

Online 28 November 2012


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Acta Cryst. (2012). F68, 1564-1567  [ doi:10.1107/S1744309112047598 ]

Cloning, expression, purification, crystallization and preliminary X-ray analysis of a fructokinase from Vibrio cholerae O395

R. Paul, S. Nath and U. Sen

Synopsis: A fructokinase from V. cholerae O395 has been cloned, expressed, purified and crystallized in the apo form; the crystals belonged to the orthorhombic space group P21212 and diffracted to 2.45 Å resolution. Fructokinase with ADP and fructose bound has also been crystallized and the crystals diffracted to a resolution of 1.75 Å.

Online 28 November 2012


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Acta Cryst. (2012). F68, 1568-1570  [ doi:10.1107/S1744309112046453 ]

Expression, purification, crystallization and preliminary X-ray analysis of NAD(P)H-dependent carbonyl reductase specifically expressed in thyroidectomized chicken fatty liver

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

Synopsis: An NAD(P)H-dependent carbonyl reductase specifically expressed in thyroidectomized chicken fatty liver was successfully isolated and crystallized.

Online 28 November 2012


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Acta Cryst. (2012). F68, 1571-1576  [ doi:10.1107/S1744309112045563 ]

Production, purification, crystallization and structure determination of H-1 Parvovirus

S. Halder, H.-J. Nam, L. Govindasamy, M. Vogel, C. Dinsart, N. Salomé, R. McKenna and M. Agbandje-McKenna

Synopsis: The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported.

Online 28 November 2012


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