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.

Structural changes caused by radiation-induced reduction and radiolysis: the effect of X-ray absorbed dose in a fungal multicopper oxidase

E. De la Mora, J. E. Lovett, C. F. Blanford, E. F. Garman, B. Valderrama and E. Rudino-Pinera

Synopsis: Radiation-induced reduction, radiolisys of copper sites and the effect of pH values with the concomitant geometrical distortions of the active centres are analysed in several fungal Coriolopsis gallica laccase structures collected at cryotemperatures. This study emphasizes the importance of careful interpretations when the crystallographic structure of a metalloprotein is described.

Novel -structure of YLR301w from Saccharomyces cerevisiae

K.-H. Kim, H. J. Ahn, W.-K. Lee, C. Lee, M.-H. Yu and E. E. Kim

Synopsis: Structures of uncharacterized protein YLR301w

Structure of a phosphoserine aminotransferase from Mycobacterium tuberculosis

F. Coulibaly, E. Lassalle, H. M. Baker and E. N. Baker

Notes of a Protein Crystallographer: On the high resolution structure of the PDB growth rate

C. Abad-Zapatero

The S-SAD phasing study of DR6 and its solution conformation revealed by SAXS

H. Ru, L. Zhao, W. Ding, L. Jiao, N. Shaw, W. Liang, L. Zhang, L.-W. Hung, N. Matsugaki, S. Wakatsuki and Z.-J. Liu

Synopsis: Comparative analysis of sulfur phasing of death receptor 6 with data collected using 2.0 Å versus 2.7 Å wavelengths is presented. SAXS analysis of unliganded DR6 defines a dimer as the minimum physical unit in solution.

Peptide Inhibitors of Botulinum Neurotoxin Serotype A: Design, Inhibition, Co-crystal Structures, SAR and Pharmacophore Modeling

G. Kumar, D. Kumaran, S. A. Ahmed and S. Swaminathan

Synopsis: Botulinum neurotoxins have been declared as Category A agent by the Centers of Disease Control and Prevention due to its extreme poisonous nature and they are potential bioweapon and bioterrorism agents. Towards the discovery of antidote, determined structures of inhibitory peptides - enzyme complex, derived the structure activity relationship and developed the pharmacophore. PDB accession numbers: Coordinates and structure factors have been deposited to the Protein Data Bank. BALC-RRGF (3qw5), BALC-RYGC (3qw6), BALC-RRFC (3qw7) and BALC-CRGC (3qw8)

X-ray excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection

R. L. Owen, B. A. Yorke and A. R. Pearson

Synopsis: Macromolecular crystals luminesce during X-ray irradiation. This luminescence, and how it changes as a function of absorbed dose, has been characterized for several different proteins.

Beyond the detergent effect: A binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin

R. Liu, W. Bu, J. Xi, S. R. Mortazav, J. Cheung-Lau, I. Dmochowski and P. Loll

JLigand: a graphical tool for CCP4 template restraint library

A. A. Lebedev, P. Young, M. N. Isupov, O. V. Moroz, A. A. Vagin and G. N. Murshudov

Synopsis: The CCP4 template restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages.

Structure of the catalytic domain of the Clostridium thermocellum cellulase CelT

M. M. Kesavulu, J.-Y. Tsai, H.-L. Lee, P.-H. Liang and C.-D. Hsiao

Synopsis: By determining the structure of the catalytic domain of the C. thermocellum cellulase CelT, the mechanism of function of the enzyme in the absence of an accessory module and the structural elements that might be responsible for its stability have been proposed.

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase

T. Nagae, T. Kawamura, L. M. G. Chavas, K. Niwa, M. Hasegawa, C. Kato and N. Watanabe

Synopsis: Structures of 3-isopropylmalate dehydrogenase were determined at pressures ranging from 0.1 to 650 MPa. Comparison of these structures gives a detailed picture of the swelling of a cavity at the dimer interface and the generation of a new cleft on the molecular surface, which are accompanied by water penetration.

Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases

A. R. Johal, B. Schuman, J. A. Alfaro, S. Borisova, N. O. L. Seto and S. V. Evans

Synopsis: The use of the common cryoprotectants glycerol and MPD in the structure determination of the human ABO(H) blood group glycosyltransferases GTA, GTB and their chimera causes changes in the structure that could mistakenly be attributed to single point mutations.

Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex

R. Brunecky, M. Alahuhta, Y. J. Bomble, Q. Xu, J. O. Baker, S.-Y. Ding, M. E. Himmel and V. V. Lunin

Synopsis: The crystal structures of two X1 modules from the multimodular CbhA protein have been solved and it has been proposed that a possible biological function of these domains is to enhance the stability of the complex at higher temperatures.

Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme

S. G. Bell, W. Yang, J. A. Yorke, W. Zhou, H. Wang, J. Harmer, R. Copley, A. Zhang, R. Zhou, M. Bartlam, Z. Rao and L.-L. Wong

Synopsis: The crystal structure and substrate-binding and activity studies of CYP108D1, an aromatic hydrocarbon-binding cytochrome P450 monooxygenase from N. aromaticivorans DSM12444, are presented.

Towards automated crystallographic structure refinement with phenix.refine

P. V. Afonine, R. W. Grosse-Kunstleve, N. Echols, J. J. Headd, N. W. Moriarty, M. Mustyakimov, T. C. Terwilliger, A. Urzhumtsev, P. H. Zwart and P. D. Adams

Challenges and Surprises that Arise with Nucleic Acids During Model Building and Refinement

W. Scott

Synopsis: The challenges that arise with nucleic acid model building are a consequence of their simpler and more symmetric super-secondary structures are addressed.

A grid-enabled web service for low-resolution crystal structure refinement

D. J. O'Donovan, I. Stokes-Rees, Y. Nam, S. C. Blacklow, G. F. Schröder, A. T. Brunger and P. Sliz

Synopsis: The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.

Catechol-O-methyltransferase in complex with substituted 3'-deoxyribose bisubstrate inhibitors

M. Ellermann, C. Lerner, G. Burgy, A. Ehler, C. Bissantz, R. Jakob-Roetne, R. Paulini, O. Allemann, H. Tissot, D. Grünstein, M. Stihle, F. Diederich and M. G. Rudolph

Synopsis: High-resolution structures of catechol-O-methyltransferase with ribose-modified inhibitors and Mg²⁺ identify the side chain of Glu90 as crucial for hydrogen bonding to the ribose hydroxyl groups. Glu90 subtly aligns with the 2'-hydroxyl, but not the 3'-hydroxyl, group to increase binding affinity, explaining the observed activities of bisubstrate inhibitors with a 3'-desoxyribose moiety.

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

P. Dessanti, Y. Zhang, S. Allegrini, M. G. Tozzi, F. Sgarrella and S. E. Ealick

Synopsis: Adenosine phosphorylase from B. cereus shows a strong preference for adenosine over other 6-oxopurine nucleosides. Mutation of Asp204 to asparagine reduces the efficiency of adenosine cleavage but does not affect inosine cleavage, effectively reversing the substrate specificity. The structures of D204N complexes explain these observations.

Handling Ligands with Coot

J. É. Debreczeni and P. Emsley

Synopsis: Cootis a molecular graphics program designed to assist in the building of protein and other macromolecular models. The current state of ligand tools is presented.

Practical structure solution with ARCIMBOLDO

D. Rodríguez, M. Sammito, K. Meindl, I. M. de Ilarduya, M. Potratz, G. M. Sheldrick and I. Usón

Synopsis: ARCIMBOLDO combines location of small fragments with PHASER and density modification with SHELXE of all possible PHASER solutions. Its uses are explained and illustrated through practical test cases.

Crystallography on a chip

A. Zarrine-Afsar, T. R. M. Barends, C. Müller, M. R. Fuchs, L. Lomb, I. Schlichting and R. J. D. Miller

Synopsis: This article describes a new platform for self-assembly of large array of protein crystals on a surface for the purpose of high-throughput room-temperature X-ray diffraction studies.

PDB_REDO: constructive validation, more than just looking for errors

R. P. Joosten, K. Joosten, G. N. Murshudov and A. Perrakis

Synopsis: The decision-making algorithms and software used in PDB_REDO to re-refine and rebuild crystallographic protein structures in the PDB are presented and discussed.

Use of noncrystallographic symmetry for automated model building at medium to low resolution

T. Wiegels and V. S. Lamzin

Synopsis: Noncrystallographic symmetry is automatically detected and used to achieve higher completeness and accuracy of automatically built protein structures at a resolution of 2.3 Å or poorer.

Implementing an X-ray validation pipeline for the Protein Data Bank

S. Gore, S. Velankar and G. J. Kleywegt

Synopsis: The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described.

Conventions and workflows for using Situs

W. Wriggers

Synopsis: Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

A. T. Brunger, D. Das, A. M. Deacon, J. Grant, T. C. Terwilliger, R. J. Read, P. D. Adams, M. Levitt and G. F. Schröder

Synopsis: DEN refinement and automated model building with AutoBuild were used to determine the structure of a putative succinyl-diaminopimelate desuccinylase from C. glutamicum. This difficult case of molecular-replacement phasing shows that the synergism between DEN refinement and AutoBuild outperforms standard refinement protocols.

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

J. J. Headd, N. Echols, P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, N. W. Moriarty, D. C. Richardson, J. S. Richardson and P. D. Adams

Synopsis: Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.

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