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Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 2 (February 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The arrangement of ATP, Mg2+ and key amino-acid residues in the active sites present in T. tengcongensis DppD (p. 256) as a cartoon representation and surface. The residues coloured yellow interact with ATP and Mg2+ and form the binding pocket.

editorial


 

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Acta Cryst. (2013). D69, 141  [ doi:10.1107/S0907444913000255 ]

Expectation bias and information content

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

Synopsis: Editorial.

Online 19 January 2013


research papers


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Acta Cryst. (2013). D69, 142-149  [ doi:10.1107/S0907444912042710 ]

Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system

D. Martynowski, P. Grochulski and P. S. Howard

Synopsis: The crystal structure of the the natural fusion protein EpsAB from V. vulnificus is described.

PDB reference: 4g54

Online 16 January 2013


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Acta Cryst. (2013). D69, 150-167  [ doi:10.1107/S0907444912044423 ]

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

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

Synopsis: The potential causes of severe misinterpretation of ligand electron density in a surprisingly large number of protein-ligand structure complexes are analyzed. Techniques and tools are presented together with suggestions for good practice aimed at minimizing overinterpretation and mistakes in protein-ligand structure models.

Online 19 January 2013


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Acta Cryst. (2013). D69, 168-175  [ doi:10.1107/S0907444912045106 ]

Structure of full-length Toxascaris leonina galectin with two carbohydrate-recognition domains

M. S. Jeong, H. G. Hwang, H. S. Yu and S. B. Jang

Synopsis: The full-length crystal structure of Toxascaris leonine galectin (Tl-gal), a galectin-9 homologue protein, was determined at a resolution of 2.0 Å. The NCRD of Tl-gal resembles that of human galectin-7 and its CCRD resembles human galectin-9, but the residues in the interface and loop regions of the NCRD and CCRD are flexible and are related to interaction.

PDB reference: 4hl0

Online 16 January 2013


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Acta Cryst. (2013). D69, 176-183  [ doi:10.1107/S0907444912045374 ]

Intensity statistics in the presence of translational noncrystallographic symmetry

R. J. Read, P. D. Adams and A. J. McCoy

Synopsis: The statistical effects of translational noncrystallographic symmetry can be characterized by maximizing parameters describing the noncrystallographic symmetry in a likelihood function, thereby unmasking the competing statistical effects of twinning.

Online 16 January 2013


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Acta Cryst. (2013). D69, 184-193  [ doi:10.1107/S0907444912044630 ]

Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima

K. Awwad, A. Desai, C. Smith and M. Sommerhalter

Synopsis: A 2.15 Å resolution crystal structure of TM0159 with bound IMP and enzyme-kinetic data are presented. This noncanonical nucleoside triphosphatase from T. maritima helps to maintain a correct pool of DNA and RNA precursor molecules.

PDB reference: 3s86

Online 18 January 2013


 

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Acta Cryst. (2013). D69, 194-212  [ doi:10.1107/S090744491204454X ]

Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals

R. Oliete, J. Pous, S. Rodríguez-Puente, C. Abad-Zapatero and A. Guasch

Synopsis: The results observed for three different crystal forms of the enzyme PurE are reported and an attempt is made to infer some initial conclusions regarding the role that the solvent, the crystallization agents (mainly salts and polyethylene glycol) and interactions within the protein structures play in determining the changes in the diffraction pattern upon alteration of the external relative humidity of the crystals.

PDB references: 4ay3, 4ay4 and 4b4k

Online 19 January 2013


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Acta Cryst. (2013). D69, 213-226  [ doi:10.1107/S0907444912043697 ]

Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis

T. Koval', P. Lipovová, T. Podzimek, J. Matousek, J. Dusková, T. Skálová, A. Stepánková, J. Hasek and J. Dohnálek

Synopsis: The structure, reaction mechanism and behaviour of a promiscuous plant nuclease are described. Structure solution was achieved by a combination of MAD and MR on multiple crystal forms.

PDB references: 3sng and 4dj4

Online 16 January 2013


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Acta Cryst. (2013). D69, 227-236  [ doi:10.1107/S0907444912044903 ]

Evolution of vitamin B2 biosynthesis: eubacterial RibG and fungal Rib2 deaminases

S.-C. Chen, C.-Y. Shen, T.-M. Yen, H.-C. Yu, T.-H. Chang, W.-L. Lai and S.-H. Liaw

Synopsis: The crystal structure of B. subtilis RibG complexed with a deaminase product was determined and the yeast Rib2 structure was modelled. Subsequent mutational analysis was carried out to illustrate its distinct substrate specificity. An essential amino-binding hole which is conserved in the RNA/DNA-editing deaminases was also identified.

PDB reference: 4g3m

Online 19 January 2013


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Acta Cryst. (2013). D69, 237-246  [ doi:10.1107/S0907444912045040 ]

Structure of the C-terminal half of human XPB helicase and the impact of the disease-causing mutation XP11BE

E. Hilario, Y. Li, Y. Nobumori, X. Liu and L. Fan

Synopsis: The crystal structure of the C-terminal half of human XPB helicase was determined to 1.8 Å resolution. A disease-causing mutation (XP11BE) at the C-terminus produces a less soluble XPB mutant, significantly reducing the cellular level of the TFIIH complex.

PDB reference: 4ern

Online 19 January 2013


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Acta Cryst. (2013). D69, 247-255  [ doi:10.1107/S0907444912045039 ]

Structure of the oncoprotein Rcl bound to three nucleotide analogues

A. Padilla, C. Amiable, S. Pochet, P.-A. Kaminski and G. Labesse

Synopsis: High-resolution crystal structures of the oncoprotein Rcl in complexes with apoptotic nucleotides have been solved by molecular replacement using combined information from NMR, SAXS and fold recognition.

PDB references: 4fyh, 4fyi and 4fyk

Online 19 January 2013


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Acta Cryst. (2013). D69, 256-265  [ doi:10.1107/S0907444912045180 ]

Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain

X. Li, W. Zhuo, J. Yu, J. Ge, J. Gu, Y. Feng, M. Yang, L. Wang and N. Wang

Synopsis: The crystal structure of DppD, the nucleotide-binding domain of a dipeptide ABC transporter from T. tengcongensis, bound with an iron-sulfur cluster is reported at 2.89 Å resolution.

PDB reference: 4fwi

Online 19 January 2013


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Acta Cryst. (2013). D69, 266-275  [ doi:10.1107/S0907444912045520 ]

Identification of quercitrin as an inhibitor of the p90 S6 ribosomal kinase (RSK): structure of its complex with the N-terminal domain of RSK2 at 1.8 Å resolution

U. Derewenda, M. Artamonov, G. Szukalska, D. Utepbergenov, N. Olekhnovich, H. I. Parikh, G. E. Kellogg, A. V. Somlyo and Z. S. Derewenda

Synopsis: The crystal structure of quercitrin, a naturally occurring flavonol glycoside, has been determined in a complex with the N-terminal kinase domain of murine RSK2. The structure revealed that quercitrin inhibits the RSK2 kinase in the same fashion as another known inhibitor, SL0101.

PDB reference: 4gue

Online 19 January 2013


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Acta Cryst. (2013). D69, 276-283  [ doi:10.1107/S0907444912045829 ]

Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus

V. E. Fadouloglou, M. Kapanidou, A. Agiomirgianaki, S. Arnaouteli, V. Bouriotis, N. M. Glykos and M. Kokkinidis

Synopsis: The structure of a polysaccharide deacetylase from B. cereus has been determined using an adventurous molecular-replacement procedure.

PDB reference: 4hd5

Online 19 January 2013


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Acta Cryst. (2013). D69, 284-297  [ doi:10.1107/S0907444912046008 ]

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

S. O. Dahms, M. Kuester, C. Streb, C. Roth, N. Sträter and M. E. Than

Synopsis: A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data.

Online 19 January 2013


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Acta Cryst. (2013). D69, 298-307  [ doi:10.1107/S0907444912045532 ]

Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity

A. Lipski, H. Watzlawick, S. Ravaud, X. Robert, M. Rhimi, R. Haser, R. Mattes and N. Aghajari

Synopsis: X-ray structures of Rhizobium sp. sucrose isomerase mutants have improved the understanding of the enzyme mechanism and have allowed the factors that govern the hydrolytic activity of this industrially important enzyme to be pinpointed.

PDB references: 4h2c, 4gin, 4gi6, 4gi8, 4gia and 4gi9

Online 19 January 2013


short communications


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Acta Cryst. (2013). D69, 308-312  [ doi:10.1107/S090744491204543X ]

Structure determination from a single high-pressure-frozen virus crystal

A. Burkhardt, A. Wagner, M. Warmer, R. Reimer, H. Hohenberg, J. Ren, E. E. Fry, D. I. Stuart and A. Meents

Synopsis: High-pressure-freezing allowed low-temperature data collection from a single virus crystal for which no standard cryoprotection could be established.

Online 19 January 2013


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