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Cover illustration: The presence of translational pseudosymmetry, a large number of molecules in the asymmetric unit (eight) and a poor search model complicated the structure solution of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin (p. 523). Structure solution in a second crystal form, P43, provided an improved model that along with complimentary approaches to molecular replacement facilitated determination of an initial solution. Phaser located six copies in the asymmetric unit, but generation of a 100 Å sphere of crystallographic symmetry-related molecules showed large spaces that corresponded with the presence of unoccupied density in a 2Fo - Fc composite OMIT map; together these analyses suggested the presence of additional molecules in the asymmetric unit. Two additional copies were placed manually using clear density for the FMN molecule that had been excluded from the search model and the pseudo-translational symmetry operators as guides. A 100 Å sphere of crystallographic symmetry-related molecules (pink) generated after manual placement of the final two molecules within the asymmetric unit (light blue) to analyze the final packing is shown. |
Acta Cryst. (2009). D65, 513-522 [ doi:10.1107/S0907444909005113 ]
Synopsis: The structures of two Dr adhesin (DraE) complexes with chloramphenicol derivatives, namely chloramphenicol succinate and bromamphenicol, have been solved. The structures reveal important functional groups for small-molecule binding and imply possible modifications to the molecule that would permit a more wide-ranging interaction without the toxic side effects associated with chloramphenicol.
PDB references: 2w5p, 2jkn, 2jkl and 2jkj
Online 15 May 2009
Acta Cryst. (2009). D65, 523-534 [ doi:10.1107/S0907444909010075 ]
Synopsis: Complications to molecular replacement resulting from a poor starting search model, pseudosymmetry, twinning and a high copy number in the asymmetric unit made the determination of the structure of D. desulfuricans (ATCC 29577) flavodoxin in two crystal forms challenging.
Online 15 May 2009
Acta Cryst. (2009). D65, 535-542 [ doi:10.1107/S0907444909010282 ]
Synopsis: An algorithm and program for simulation of X-ray data frames is described.
Online 15 May 2009
Acta Cryst. (2009). D65, 543-552 [ doi:10.1107/S0907444909010270 ]
Synopsis: The crystal structure of the G81A mutant form of the chimera of (S)-mandelate dehydrogenase and of its complexes with two of its substrates reveal productive and non-productive modes of binding for the catalytic reaction. The structure also indicates the role of G81A in lowering the redox potential of the flavin co-factor leading to an 
200-fold slower catalytic rate of substrate oxidation.
PDB references: 3giy, 2a7p and 2a85
Online 15 May 2009
Acta Cryst. (2009). D65, 553-559 [ doi:10.1107/S0907444909010725 ]
Synopsis: Lattice patterns containing alternating strong and weak reflections can be identified by a targeted search for the weak signals, permitting a wider range of diffraction patterns to be indexed automatically.
Online 15 May 2009
Acta Cryst. (2009). D65, 560-566 [ doi:10.1107/S0907444909011329 ]
Synopsis: Eukaryotic proliferating cell nuclear antigen (PCNA), an essential accessory factor in DNA replication and repair, is a ring-shaped homotrimer. A novel nontrimeric structure of E113G-mutant PCNA protein is reported, which shows that this protein forms alternate subunit interactions. It is concluded that the charged side chain of Glu113 promotes normal trimer formation by destabilizing these alternate subunit interactions.
Online 15 May 2009
Acta Cryst. (2009). D65, 567-573 [ doi:10.1107/S0907444909011548 ]
Synopsis: X-ray and neutron crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing.
Online 15 May 2009
Acta Cryst. (2009). D65, 574-581 [ doi:10.1107/S090744490901169X ]
Synopsis: The crystal structure of Sda, a DNA-replication/damage checkpoint inhibitor of sporulation in B. subtilis, has been solved via the MAD method. The subunit arrangement in the crystal has enabled a reappraisal of previous biophysical data, resulting in a new model for the behaviour of the protein in solution.
PDB reference: 3fyr
Online 15 May 2009
Acta Cryst. (2009). D65, 582-601 [ doi:10.1107/S0907444909012098 ]
Synopsis: Ten measures of experimental electron-density-map quality are examined and the skewness of electron density is found to be the best indicator of actual map quality. A Bayesian approach to estimating map quality is developed and used in the PHENIX AutoSol wizard to make decisions during automated structure solution.
Online 15 May 2009
Acta Cryst. (2009). D65, 602-610 [ doi:10.1107/S0907444909011871 ]
Synopsis: Structural conservation in the ATPase centers of RadA, Rad51 and RecA recombinases suggests conformational switching between high and low-affinity states for DNA in concert with cycles ATP hydrolysis. Such iteration would be advantageous for DNA strand exchange by optimizing the pairing between single-stranded and double-stranded DNA substrates.
PDB references: 3etl, 3ew9 and 3ewa
Online 15 May 2009
Acta Cryst. (2009). D65, 611-617 [ doi:10.1107/S0907444909011950 ]
Synopsis: The structure of the highly redox-capable laccase from Trametes hirsuta is presented and compared with related laccase structures.
PDB reference: 3fpx
Online 15 May 2009
Acta Cryst. (2009). D65, 618-622 [ doi:10.1107/S0907444909013171 ]
Synopsis: The P. falciparum nucleosome assembly protein structure was determined by SAD/SIR/SIRAS phasing methods using low-resolution iodide anomalous scattering data.
Online 15 May 2009
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