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Preview: Forthcoming article in Acta Crystallographica Section D: Biological Crystallography

Forthcoming article in Acta Crystallographica Section D Structural Biology



Acta Crystallographica Section D: Structural Biology welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. Reports o



 



Structural basis for regulation of chemotaxis by MapZ in the presence of c-di-GMP
We report the structure of CheR1 in complex with c-di-GMP bound MapZ and reveal the complex biochemical process which involves CheR1, MapZ, SAH/SAM and c-di-GMP.



Binding of hydroxycitrate to human ATP-citrate lyase
Hydroxycitrate was co-crystallized with the amino-terminal portion of human ATP-citrate lyase to learn how this competitive inhibitor binds. Crystals diffracting to high resolution were obtained by adding cleavage sites in the protein to remove a disordered linker. This strategy could be useful with other proteins that do not crystallize well.



AUSPEX: a graphical tool for X-ray diffraction data analysis
AUSPEX is a new software tool for the statistical analysis of single-crystal X-ray diffraction data. It can be used to identify problems in the data resulting from the experiment itself, image processing, data scaling or conversion.



Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition
An in-depth analysis oF PEG-bound C-terminal SH3 domain of myosin IB from E. histolytica has been performed, which reveals the mode of ligand recognition and will be helpful in identification of probable binding partners of E. histolytica myosin IB.



An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences
This paper reviews the recent advances in computational template-based structural modelling and proposes the subclustering of protein domain superfamilies to guide the template-selection process.



Protein–ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation
The applicability of the ligand-soaking method in serial femtosecond crystallography has been examined to examine the feasibility of pharmaceutical applications of X-ray free-electron lasers.



Toscana virus nucleoprotein oligomer organization observed in solution
The nucleoprotein of Toscana virus forms mainly open fivefold oligomers consistent with the encapsidation mechanism of phlebovirus RNA both in solution and under physiological conditions.



The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases
The crystal structure of the class D carbapenemase OXA-143 from A. baumannii shows that a conserved valine residue on the protein surface controls access of the deacylating water molecule to the active site of the enzyme. Analysis of the structures of other class D carbapenemases implicates movement of juxtaposed surface valine and leucine residues in a universal deacylation mechanism for these enzymes.



Activity inhibition and crystal polymorphism induced by active-site metal swapping
The effect of ion swapping on the activity of an Arenaviridae exonuclease is reported.



Factors affecting the amplitude of the τ angle in proteins: a revisitation
Statistical surveys of protein structures reveal that the backbone conformation in terms of (φ, ψ) is the most important factor in τ-angle modulation.



DNA conformational transitions inferred from re-evaluation of m|Fo| − D|Fc| electron-density maps
A re-evaluation of m|Fo| − D|Fc| electron-density maps revealed that potential conformational transitions of 27% of DNA phosphates are found in previous crystallographic data. The analysis suggests that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI transitions.



Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein from Salmonella typhimurium
A seemingly reasonable solution was obtained for the structure of a presumed mutant of an S. typhimurium survival protein (SurE) by molecular replacement using the wild-type SurE structure as the phasing model. Although the crystal was of glycerol dehydrogenase, as subsequently demonstrated using the MarathonMR protocol, the initial structure appeared to be reasonable because of a partial similarity in the arrangement of secondary-structural elements in the two proteins.



Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering
Solutions of lysozyme in heavy water with added precipitants were studied by small-angle neutron scattering at lysozyme concentrations of 40, 20 and 10 mg ml−1 and at temperatures of 10, 20 and 30°C. In addition to protein monomers, dimeric and octameric oligomers were also found in solution at the maximal concentration near the optimal crystallization conditions. The volume fraction of octamers decreases on deviation from the optimal temperature and on decreasing the protein concentration. In the absence of the precipitant, only monomers and a minor fraction of dimers are present in solution.



Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase
The crystal structure of the cofactor-independent dioxygenase DpgC was refined and the new structure was used to probe the basis for dioxygen binding using site-directed mutagenesis.



Rapid cadmium SAD phasing at the standard wavelength (1 Å)
Single-wavelength anomalous dispersion (SAD) phasing experiments were successfully carried out at the standard wavelength of 1 Å by using cadmium ions as anomalous scatterers.



Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites
YfeA, a substrate-binding protein that is important for the virulence of Yersinia pestis, has two polyspecific metal-binding sites that may play different roles during infection. A flexible lobe at the carboxy-terminus suggests that structural rearrangement is required for metal transfer to binding partners.