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February 2006 issue
Cover illustration: Selective fluorescent staining of nucleic acid-containing crystals. A comparison of core Pol II protein crystals in the free form (P) and in complex with an 80-mer RNA inhibitor (C) is shown. On the right, a transmission light microscopic image reveals all crystals. On the left, a fluorescence image shows selective staining of nucleic acid complex crystals after incubation with SYBR-Gold (p. 146).
research papers
A systematic study of the specific radiation damage caused by different rates of X-ray irradiation is presented. The results suggest a small dose-rate related effect.
The crystal structure of human dCK in complex with clofarabine reveals the structural basis of activation by purine-nucleoside prodrugs.
PDB reference: dCK–clofarabine–ADP, 2a7q, r2a7qsf
The crystal structure of T. gondii adenosine kinase in complex with an ATP analog at 1.1 Å resolution reveals that ATP binding and the formation of the induced anion hole can occur before adenosine binding.
PDB reference: AK–AMP-PCP, 2abs, 2abssf
A highly sensitive and specific fluorescence-based assay for the rapid detection of nucleic acids in crystals of macromolecular complexes is described.
The structure of the manganese form of prostaglandin H2 synthase-1 reveals that metal substitution has no effect on the enzyme's structure; however, the manganese is displaced farther out of the porphyrin plane than is the native iron.
PDB reference: MnIII-reconstituted ovine PGHS-1, 2ayl, r2aylsf
The structure of the uropathogenic E. coli invasin DraD containing a C-terminal extension of 13 amino acids has been solved at 1.05 Å resolution. It forms dimers through the exchange of the C-terminal donor strands, resulting in a variant of the immunoglobulin fold.
PDB reference: DraD invasin, 2axw, r2axwsf
The X-ray crystal structure of the previously unknown bacteriophage P22 lysozyme was determined ab initio by direct methods using the program SIR2002. The asymmetric unit contained 2268 non-H protein atoms, making this one of the largest structures determined to date by ab initio direct methods.
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The structures of Dsk2 UBL, Dsk2 UBA and their complex are described. The complex explains the reduced affinity of the UBA domain for UBL compared with that for ubiquitin.
A manual intervention-free automatic refinement software package (LAFIRE) has been developed for high-throughput protein-structure analysis. This program begins from an initial model that can be approximate, fragmentary or even only main-chain and performs a whole refinement process to provide a final model including water molecules.
New crystal structures of glutathione transferase A1-1 show that the C-terminal region of the apo form can be ordered and helix-like. They also show how glutathione is bound in the absence of a second substrate and provide insight into the binding of a decarboxylated glutathione conjugate.
The highly pseudosymmetric crystal structure of HTLV-1 protease could be solved using low-sequence-identity models with Phaser but, with a single exception, not with standard application of other molecular-replacement programs.
PDB reference: HTLV-1 protease, 2b7f, r2b7fsf
short communications
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The high-resolution structure of thioredoxin from the parasite T. vaginalis has been determined. The redox-active disulfide has been partially photoreduced by the intense synchrotron radiation used in the analysis. Comparisons with human thioredoxin are presented.
PDB reference: thioredoxin, 2f51, r2f51sf
international union of crystallography
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