Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 69, Part 3 (March 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Structure of Vibrio cholerae ribosome hibernation promoting factor (De Bari & Berry, p. 228).

structural communications


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Acta Cryst. (2013). F69, 215-222  [ doi:10.1107/S1744309112044818 ]

Crystallographic structure determination of B10 mutants of Vitreoscilla hemoglobin: role of Tyr29 (B10) in the structure of the ligand-binding site

S. Ratakonda, A. Anand, K. Dikshit, B. C. Stark and A. J. Howard

Synopsis: The crystal structures of two mutants at position 29 of the dimeric hemoglobin from Vitreoscilla are reported, together with a discussion of the significance of these mutations.

PDB references: 3tm3, 3tld and 3tm9

Online 22 February 2013


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Acta Cryst. (2013). F69, 223-227  [ doi:10.1107/S1744309113000973 ]

High-resolution crystal structure of human Dim2/TXNL4B

T. Jin, F. Guo, Y. Wang and Y. Zhang

Synopsis: The high-resolution crystal structure of human Dim2/TXNL4B indicated that a region previously reported to be responsible for its interaction with Prp6 is unlikely to facilitate this interaction.

PDB reference: 4in0

Online 22 February 2013


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Acta Cryst. (2013). F69, 228-236  [ doi:10.1107/S1744309113000961 ]

Structure of Vibrio cholerae ribosome hibernation promoting factor

H. De Bari and E. A. Berry

Synopsis: The X-ray crystal structure of ribosome hibernation promoting factor from V. cholerae has been determined at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt.

PDB reference: 4hei

Online 22 February 2013


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Acta Cryst. (2013). F69, 237-242  [ doi:10.1107/S174430911300153X ]

Arginine 116 stabilizes the entrance to the metal ion-binding site of the MntC protein

M. Kanteev and N. Adir

Synopsis: The structures of wild-type MntC and of an R116A mutant have been determined to 2.7 and 3.5 Å resolution, respectively. The role of Arg116 in the outer shell of the active site is described.

PDB references: 3ujp and 3v63

Online 22 February 2013


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Acta Cryst. (2013). F69, 243-247  [ doi:10.1107/S1744309113002352 ]

Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase

V. A. Rao, S. M. Shepherd, R. Owen and W. N. Hunter

Synopsis: The crystal structure of inosine 5'-monophosphate dehydrogenase from P. aeruginosa has been determined to 2.25 Å resolution.

PDB reference: 3zfh

Online 22 February 2013


crystallization communications


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Acta Cryst. (2013). F69, 248-252  [ doi:10.1107/S1744309112049925 ]

Purification, crystallization and preliminary X-ray crystallographic analysis of squid heavy meromyosin

E. O'Neall-Hennessey, L. Reshetnikova, V. S. Senthil Kumar, H. Robinson, A. G. Szent-Györgyi and C. Cohen

Synopsis: In various muscles, the two heads of myosin together with part of its [alpha]-helical coiled coil make up the minimal unit that is regulated. Reported here, for the first time, is the growth of three-dimensional crystals of such a heavy meromyosin, purified from squid, and their X-ray diffraction to near-atomic resolution (up to ~5 Å).

Online 22 February 2013


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Acta Cryst. (2013). F69, 253-256  [ doi:10.1107/S1744309112052141 ]

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis

S. Correale, A. Ruggiero, E. Pedone and R. Berisio

Synopsis: In this study, the L,D-transpeptidase LdtMt1 was cloned, expressed and crystallized. Multiwavelength anomalous dispersion experiments have been carried out to obtain experimental phases using data at 2.9 Å resolution from a selenomethionine derivative.

Online 22 February 2013


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Acta Cryst. (2013). F69, 257-262  [ doi:10.1107/S1744309113001504 ]

New crystal forms of NTPDase1 from the bacterium Legionella pneumophila

M. Zebisch, P. Schäfer, P. Lauble and N. Sträter

Synopsis: The soluble NTPDase1 from L. pneumophila was crystallized in six crystal forms and the structure was solved using a sulfur SAD approach.

Online 22 February 2013


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Acta Cryst. (2013). F69, 263-266  [ doi:10.1107/S1744309113001693 ]

Purification, crystallization and preliminary crystallographic analysis of the marine [alpha]-amylase AmyP

J. Yu, C. Wang, Y. Hu, Y. Dong, Y. Wang, X. Tu, H. Peng and X. Zhang

Synopsis: A new marine derived [alpha]-amylase AmyP, classified into a new subfamily of GH13, was recombinantly expressed, crystallized and preliminarily analyzed.

Online 22 February 2013


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Acta Cryst. (2013). F69, 267-269  [ doi:10.1107/S1744309113001668 ]

Crystallization and preliminary X-ray crystallographic studies of DnaJ from Streptococcus pneumoniae

S. Zhao, L. Jin, S. Niu, W. Yang, S. Zhang, Z. Guo, H. Zhang, A. Huang, Y. Yin and D. Wang

Synopsis: DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported.

Online 22 February 2013


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Acta Cryst. (2013). F69, 270-274  [ doi:10.1107/S1744309113001917 ]

Production, crystallization and X-ray diffraction analysis of two nanobodies against the Duffy binding-like (DBL) domain DBL6[epsilon]-FCR3 of the Plasmodium falciparum VAR2CSA protein

A. Vuchelen, E. Pardon, J. Steyaert, B. Gamain, R. Loris, N. A. J. van Nuland and S. Ramboarina

Synopsis: Two nanobodies generated against the VAR2CSA DBL6[epsilon]-FCR3 domain involved in pregnancy-associated malaria were selected, expressed, purified and crystallized.

Online 22 February 2013


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Acta Cryst. (2013). F69, 275-279  [ doi:10.1107/S174430911300184X ]

Expression, purification, crystallization and preliminary X-ray diffraction analysis of a lactococcal bacteriophage small terminase subunit

B. Ren, T. M. Pham, R. Surjadi, C. P. Robinson, T. Le, P. S. Chandry, T. S. Peat and W. J. McKinstry

Synopsis: The small terminase subunit from a lactococcal 936 bacteriophage (strain 454) has been expressed, purified, crystallized and X-ray diffraction data collected to 2.4 Å resolution.

Online 22 February 2013


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Acta Cryst. (2013). F69, 280-283  [ doi:10.1107/S1744309113002388 ]

Crystallization and X-ray crystallographic analysis of the cap-binding domain of influenza A virus H1N1 polymerase subunit PB2

Y. Liu, G. Meng, M. Luo and X. Zheng

Synopsis: Substrate-free cap-binding domain of influenza A virus H1N1 polymerase subunit PB2 has been crystallized to show the structural details and clarify whether obvious conformational changes exist between the substrate-free and substrate-bound cap-binding domain.

Online 22 February 2013


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Acta Cryst. (2013). F69, 284-287  [ doi:10.1107/S1744309113002467 ]

Differences in crystallization of two LinB variants from Sphingobium japonicum UT26

O. Degtjarik, R. Chaloupkova, P. Rezacova, M. Kuty, J. Damborsky and I. Kuta Smatanova

Synopsis: To study enzyme functionality, two haloalkane dehalogenase variants LinB32 and LinB70 carrying single-point and double-point mutations were constructed and crystallized in different crystallization conditions. Both LinB variants and their complexes with halogenated substrates diffracted to resolutions ranging from 1.6 to 2.8 Å.

Online 22 February 2013


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Acta Cryst. (2013). F69, 288-291  [ doi:10.1107/S1744309113002522 ]

Crystallization and preliminary X-ray crystallographic analysis of recombinant [beta]-mannosidase from Aspergillus niger

G. Demo, B. Fliedrová, L. Weignerová and M. Wimmerová

Synopsis: [beta]-Mannosidase from Aspergillus niger was crystallized in the presence of D-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to the space group P1 with unit-cell parameters a= 62.37, b = 69.73, c = 69.90 Å, [alpha] = 108.20, [beta] = 101.51, [gamma] = 103.20°.

Online 23 February 2013


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Acta Cryst. (2013). F69, 292-294  [ doi:10.1107/S1744309113002686 ]

Crystallization and preliminary X-ray crystallographic studies of cPOP1

K. H. Do and H. H. Park

Synopsis: The cellular pyrin domain-only protein 1 (cPOP1) was crystallized. The crystals were found to belong to the cubic space group P213 with unit-cell parameters a = b = c = 94.12 Å, [alpha] = [beta] = [gamma] = 90.00°. The crystals were obtained at 293 K and diffracted to a resolution of 3.6 Å.

Online 23 February 2013


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Acta Cryst. (2013). F69, 295-301  [ doi:10.1107/S1744309113002716 ]

Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase

D. Sartmatova, T. Nash, N. Schormann, M. Nuth, R. Ricciardi, S. Banerjee and D. Chattopadhyay

Synopsis: The crystallization of three recombinant mutants of Vaccinia virus uracil DNA glycosylase is reported.

Online 23 February 2013


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Acta Cryst. (2013). F69, 302-305  [ doi:10.1107/S1744309113002881 ]

Crystallization and preliminary X-ray diffraction analysis of the complex between a human anti-alpha toxin antibody fragment and alpha toxin

V. Oganesyan, A. Barnes, C. Tkaczyk, A. Ferguson, H. Wu and W. Dall'Acqua

Synopsis: Crystals of the complex between the Fab fragment of a human anti-alpha toxin antibody and alpha toxin have been obtained. Diffraction data sets were collected to 2.56 Å resolution.

Online 23 February 2013


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Acta Cryst. (2013). F69, 306-312  [ doi:10.1107/S1744309113003060 ]

Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus

R. A. North, S. A. Kessans, S. C. Atkinson, H. Suzuki, A. J. A. Watson, B. R. Burgess, L. M. Angley, A. O. Hudson, A. Varsani, M. D. W. Griffin, A. J. Fairbanks and R. C. J. Dobson

Synopsis: N-Acetylneuraminate lyase, an enzyme involved in the bacterial uptake and metabolism of sialic acid, is a promising target for antibiotic development against pathogenic bacteria. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylneuraminate lyase from methicillin-resistant S. aureus to 1.70 Å resolution are reported.

Online 27 February 2013


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Acta Cryst. (2013). F69, 313-315  [ doi:10.1107/S1744309113003667 ]

Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330

N. Aggarwal, P. K. Mandal, N. Gautham and A. Chadha

Synopsis: The expression, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies on C. parapsilosis carbonyl reductase are reported.

Online 27 February 2013


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Acta Cryst. (2013). F69, 316-319  [ doi:10.1107/S1744309113003758 ]

Crystallization and preliminary X-ray analysis of human leukocyte cell-derived chemotaxin 2 (LECT2)

H. Zheng, T. Miyakawa, Y. Sawano, S. Yamagoe and M. Tanokura

Synopsis: Diffraction data to 1.94 Å limiting resolution were collected from a crystal of selenomethionine-substituted LECT2.

Online 27 February 2013


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Acta Cryst. (2013). F69, 320-323  [ doi:10.1107/S1744309113001164 ]

Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants

Q. Wan, A. Kovalevsky, Q. Zhang, S. Hamilton-Brehm, R. Upton, K. L. Weiss, M. Mustyakimov, D. Graham, L. Coates and P. Langan

Synopsis: The wild-type protein and four active-site mutants of xylanase II from Trichoderma reesei that catalyzes the hydrolysis of glycosidic bonds in xylan have successfully been crystallized. The crystallization of several structures including ligand-free and protein ligand complexes containing the substrate (xylohexaose) or product (xylotriose) are detailed.

Online 27 February 2013


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Acta Cryst. (2013). F69, 324-327  [ doi:10.1107/S1744309113003382 ]

Crystallization and preliminary X-ray crystallographic analysis of the human CKIP-1 pleckstrin homology domain

P. Li, Y. Xu, X. Li and M. Bartlam

Synopsis: Crystals of an S84D/S86D/S88D triple mutant of the casein kinase 2 interacting protein-1 (CKIP-1) pleckstrin homology domain were obtained and diffraction data were collected and processed to 1.7 Å resolution.

Online 27 February 2013


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Acta Cryst. (2013). F69, 328-331  [ doi:10.1107/S1744309113003837 ]

Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase from Escherichia coli

X. Li, X. Han, T.-P. Ko, C.-C. Chen, Z. Zhu, E. Hua, R.-T. Guo and C.-H. Huang

Synopsis: Here, Escherichia coli octaprenyl pyrophosphate synthase was expressed, purified and crystallized. The crystals were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.2 Å resolution.

Online 27 February 2013


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Acta Cryst. (2013). F69, 332-335  [ doi:10.1107/S1744309113003424 ]

Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8

A. Matsumoto, Y. Shimizu, C. Takemoto, T. Ueda, T. Uchiumi and K. Ito

Synopsis: Peptidyl-tRNA hydrolase from T. thermophilus has been expressed, purified and crystallized. The crystals diffracted X-rays to atomic resolution (beyond 1.0 Å resolution).

Online 27 February 2013


laboratory communications


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Acta Cryst. (2013). F69, 336-341  [ doi:10.1107/S1744309113000791 ]

A simple and effective calibration method to determine the accuracy of liquid-handling nano-dispenser devices

S. Rodríguez-Puente, J. Linacero-Blanco and A. Guasch

Synopsis: A simple fluorescence-based calibration method that can be used to monitor the precision and accuracy of any liquid-handling nano-dispenser device is presented.

Online 23 February 2013


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