forthcoming articles in Acta Crystallographica Section D

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.

See also Forthcoming articles in all IUCr journals.

Accepted 22 April 2015

The defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal quality improvement in reduced screens

A. Chaikuad, S. Knapp and F. von Delft

Accepted 21 April 2015

New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM

F. Fadel, Y. Zhao, R. Cachau, A. Cousido-Siah, F. X. Ruiz, K. Harlos, E. Howard, A. Mitschler and A. Podjarny

Accepted 20 April 2015

Protonation and geometry of histidine rings

M. Malinska, M. Dauter, M. Kowiel, M. Jaskolski and Z. Dauter

Synopsis: The correlation of histidine ring geometry with the protonation state was analyzed in PDB and CSD structures. In conclusion, revised stereochemical restraints for histidine are proposed.

Accepted 18 April 2015

A binding hotspot in the Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens

C. Y. Koh, L. Kallur Siddaramaiah, R. M. Ranade, J. Nguyen, T. Jian, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. M. J. Verlinde, E. Fan and W. G. J. Hol

Synopsis: A crystallographic cocktail screening campaign against 680 fragments revealed a binding hotspot in the structure of Trypanosoma cruzi histidyl-tRNA synthetase.

Accepted 17 April 2015

S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data collection strategy and a posteriori analysis of different data combinations

S. Klinke, N. Foos, J. J. Rinaldi, G. Paris, F. A. Goldbaum, P. Legrand, B. G. Guimarães and A. Thompson

Synopsis: The structure of the histidine kinase associated with the light-oxygen-voltage domain from Brucella abortus, containing 968 amino acids in the asymmetric unit, was solved using the "off edge" anomalous signal from sulfur to a resolution of 2.90 Å by combining data from several isomorphous crystals (space group P21) as well as data collected in multiple orientations of the same crystal (true redundancy), stressing the importance of the latter approach in off edge S-SAD. A second construct that has a shorter cloning artifact enabled the production of improved crystals and subsequent refinement of the structure to 2.51 Å resolution.

Accepted 15 April 2015

Full-length structure of the major autolysin LytA

Q. Li, W. Cheng, C. Morlot, X.-H. Bai, Y.-L. Jiang, W. Wang, D. I. Roper, T. Vernet, Y.-H. Dong, Y. Chen and C.-Z. Zhou

Synopsis: Full-length structure of the major autolysin LytA from Streptococcus pneumoniae combined with the enzymatic activity assays suggest that dimerization and full occupancy of all choline-binding sites are indispensable for the full activity of LytA in vivo.

Accepted 15 April 2015

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles

A. H. Van Benschoten, P. V. Afonine, T. C. Terwilliger, M. E. Wall, C. J. Jackson, N. K. Sauter, P. D. Adams, A. Urzhumtsev and J. S. Fraser

Synopsis: A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different Translation-Libration-Screw refinement strategies produce unique diffuse intensity patterns.

Accepted 15 April 2015

Two high-mobility group box domains act together to underwind and kink DNA

R. Sánchez-Giraldo, F. J. Acosta-Reyes, C. S. Malarkey, N. Saperas, M. E. A. Churchill and J. L. Campos

Synopsis: We report the crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment at a resolution of 2 Å. We find a new mode of DNA recognition for HMG box proteins, where two box A domains bind in an unusual configuration generating a highly kinked DNA structure.

Accepted 10 April 2015

Structural analysis of [alpha]-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism

X. Shen, W. Saburi, Z. Gai, K. Kato, T. Ojima-Kato, J. Yu, K. Komoda, Y. Kido, H. Matsui, H. Mori and M. Yao

Synopsis: The complex structures of HaG and its mutants revealed the substrate specificity and catalytic mechanism of HaG.

Accepted 9 April 2015

Structure of RsbX phosphatase in general stress response of Bacillus subtilis

A.-H. Teh, M. Makino, T. Hoshino, S. Baba, N. Shimizu, M. Yamamoto and T. Kumasaka

Synopsis: The PPM II phosphatase RsbX features a catalytic centre that binds two Mn2+ ions with five residues instead of the usual four as in PPM I phosphatases, with a conformational reorganization that tilts a flexible loop towards the second Mn2+ ion for the fifth residue to coordinate it.

Accepted 9 April 2015

datasw, a tool for HPLC-SAXS data analysis

A. V. Shkumatov and S. V. Strelkov

Synopsis: datasw, a novel tool for rapid processing of HPLC-SAXS data.

Accepted 8 April 2015

Structural characterization of a novel subfamily of Leucine-Rich Repeat Proteins from the human pathogen Leptospira interrogans

I. Miras, F. Saul, M. Nowakowski, P. Weber, A. Haouz, W. Shepard and M. Picardeau

Accepted 6 April 2015

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

H. M. Ginn, A. S. Brewster, J. Hattne, G. Evans, A. Wagner, J. Grimes, N. K. Sauter, G. Sutton and D. I. Stuart

Synopsis: We present an updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data, confirmed by observing anomalous density for sulfur atoms at an X-ray wavelength of 1.3 Å.

Accepted 1 April 2015

Structural bases for N-glycan processing by mannoside phosphorylase

S. Ladevèze, G. Cioci, P. Roblin, L. Mourey, S. Tranier and G. Potocki-Véronèse

Synopsis: Crystal structures of the GH130 enzyme Uhgb_MP in the apo form and in complex with mannose and N-acetylglucosamine are described and the structural determinants of the functional specificities of enzymes involved in N-glycan breakdown by human gut bacteria are identified.

Accepted 1 April 2015

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA de­hydrogenase fold

M. Schürmann, R. Meijers, T. R. Schneider, A. Steinbüchel and M. Cianci

Synopsis: AcdDPN7 is a novel desulfinase, which catalyzes the sulfur abstraction in the catabolic pathway of 3,3'-dithiodipropionic acid (DTDP). The crystal structures of the native AcdDPN7 at 1.89 Å resolution and the native AcdDPN7 soaked with the substrate analog succinyl-CoA at 2.30 Å resolution revealed an acyl-CoA dehydrogenase fold with Arg84 as a key residue in the desulfination reaction.

Accepted 27 March 2015

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

I. Shabalin, Z. Dauter, M. Jaskolski, W. Minor and A. Wlodawer

Synopsis: Models of crystal structures deposited in the Protein Data Bank for protein complexes of cisplatin and carboplatin appear to have troubling crystallographic problems and to exhibit significant departures from the known principles of chemistry. They may serve as examples of what should be improved in the deposition and presentation of macromolecular models and how to handle deposition of the results of re-refinement of crystallographic data.

Accepted 26 March 2015

Structure of the bovine COPI [delta] subunit [mu] homology domain at 2.15 Å resolution

A. Lahav, H. Rozenberg, A. Parnis, D. Cassel and N. Adir

Synopsis: The crystal structure of the [mu] homology domain of the [delta] subunit of the bovine COPI complex was determined to 2.15 Å resolution. The structure reveals important aspects of interdomain flexibility that relate to the function of COPI.

Accepted 25 March 2015

The solvent component of macromolecular crystals

C. X. Weichenberger, P. V. Afonine, K. Kantardjieff and B. Rupp

Synopsis: On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity.

Accepted 24 March 2015

The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer

M. Vostrukhina, A. Popov, E. Brunstein, M. A. Lanz, R. Baumgartner, C. Bieniossek, M. Schacherl and U. Baumann

Synopsis: The hexameric structure of truncated A. aeolicus FtsH shows a molecular architecture that forms two rings, in which the ATPase ring possesses twofold symmetry and the protease ring possesses sixfold symmetry. The importance of a dynamic [beta]-strand in the active site and a conserved glycine in the linker region is demonstrated in the full-length protein by site-directed mutagenesis.

Accepted 23 March 2015

Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe

H. Lv, Y. Zhu, Y. Qiu, L. Niu, M. Teng and X. Li

Synopsis: The crystal structure of fission yeast Dis3l2 displays an open conformation that differs from that in the mouse Dis3l2-RNA complex.

Accepted 23 March 2015

The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native [alpha]-globin haem pocket

C. F. Dickson, D. A. Jacques, R. T. Clubb, J. M. Guss and D. A. Gell

Synopsis: S. aureus steals iron in the form of haem from human haemoglobin (Hb). The crystal structure of the S. aureus Hb receptor IsdH in complex with Hb shows that the receptor induces a conformational change in the globin haem pocket that may promote haem transfer.

Accepted 17 March 2015

Bond distances in polypeptide backbones depend on the local conformation

R. Improta, L. Vitagliano and L. Esposito

Synopsis: Statistical surveys of the protein structure database combined with quantum-mechanical calculations reveal a systematic dependence of bond distances on conformation. Interestingly, the variability of backbone C-O and C-N distances is not directly related to peptide-bond planarity.

Accepted 16 March 2015

The structure of the giant haemoglobin from Glossoscolex paulistus

J. F. Ruggiero Bachega, F. Vasconcelos Maluf, B. Andi, H. D'Muniz Pereira, M. Falsarella Carazzollea, A. M. Orville, M. Tabak, J. Brandão-Neto, R. C. Garratt and E. Horjales Reboredo

Synopsis: The structure of the giant haemoglobin from G. paulistus was determined.

Accepted 13 March 2015

In meso in situ serial X-ray crystallography of soluble and membrane proteins

C.-Y. Huang, V. Olieric, P. Ma, E. Panepucci, K. Diederichs, M. Wang and M. Caffrey

Synopsis: A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing.

Accepted 1 March 2015

Structure determination of an integral membrane protein at room temperature from crystals in situ

D. Axford, J. Foadi, N.-J. Hu, H. G. Choudhury, S. Iwata, K. Beis, G. Evans and Y. Alguel

Synopsis: The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated.

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