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April 2009 issue
Cover illustration: View of the alcaligin outer-membrane transporter FauA superposed onto a diffraction pattern at 2.3 Å resolution (p. 326). The transmembrane ![[beta]](/logos/entities/beta_rmgif.gif)
-barrel is green coloured and the plug domain is cyan coloured.
research papers
The high-resolution crystal structure of unliganded rat profilin 2a has been determined. In addition, its post-translational modifications and ligand-binding properties have been studied.
PDB reference: rat profilin 2a, 2vk3, r2vk3sf
The crystal structures of various binary and ternary complexes of M. tuberculosis pantothenate kinase indicate possible changes in the location of ligands during enzyme action.
PDB references: MtPanK, initiation complex, 2zse, r2zsesf; intermediate complex, 2zsf, r2zsfsf; end complex, 2zsa, r2zsasf; citrate complex, 2zs7, r2zs7sf; complex with ADP and pantothenate, 2zs9, r2zs9sf; complex with CoA, 2zsd, r2zsdsf; complex with ADP (cocrystallized), 2zs8, r2zs8sf; complex with ADP (soaked), 2zsb, r2zsbsf
Using an in-house protocol for the expression, purification and crystallization of outer membrane proteins belonging to the TonB-dependent transporter family, the crystal structure of the alcaligin outer membrane protein FauA from B. pertussis was solved at 2.3 Å resolution and X-ray diffraction data were collected for three other targets.
PDB reference: FauA, 3efm, r3efmsf
The structure of the conserved methyltransferase domain of human trimethylguanosine synthase 1 bound to the cap analogue m7GpppA was solved by means of selenomethionine MAD.
PDB reference: methyltransferase domain of TGS1, 3egi, r3egisf
The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method.
PDB reference: simian immunodeficiency virus gp120 core, 3fus, r3fussf
The structure of hen egg-white lysozyme was determined using powder diffraction data recorded on an image plate by molecular replacement using human lysozyme as the search model.
Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described.
PDB reference: TM0439, 3fms, r3fmssf
A strategy is presented that increases the separation of the diffracting regions of macromolecular crystals from their damaged portions, thus increasing their survival.
short communications
The crystal structure of 2-methylpentane-2,4-diol inhibited secretory signalling glycoprotein (SPS-40) has been determined at 1.6 Å resolution. Trp78 works as a functional switch in these proteins by adopting pinched, stacked and obstructive conformations as observed in native, complexed with hexasaccharide and 2-methypentane-2,4-diol, respectively.
PDB reference: SPS-40, 2pi6, r2pi6sf
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The correlation coefficients calculated between raw powder diffraction profiles can be used to identify ligand-bound/unbound states of lysozyme.
Diaminopimelate (DAP) epimerase catalyses the interconversion of the D,L and L,L forms of diaminopimelic acid, which is a key component of the pentapeptide linker in bacterial peptidoglycan. The crystal structure of M. tuberculosis DAP epimerase is reported at a resolution of 2.6 Å.
PDB reference: DapF, 3fve, r3fvesf
Pseudo-merohedral twinning was detected in a monoclinic P21 crystal form of wild-type human brain neuroglobin.
Phase information from both MIRAS and MR was used to produce an interpretable electron-density map of the novel type II restriction endonuclease SgrAI bound to DNA. The MR solution corrected an instructive error in the initially chosen averaging transformation.
PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in Protein Data Bank file format.
