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Pseudo-translational Symmetry (pseudo-translational + symmetry)
Selected AbstractsStructure of the Escherichia coli RNA polymerase , subunit C-terminal domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Samuel Lara-González The , subunit C-terminal domain (,CTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli,CTD (, subunit residues 245,329) determined to 2.0,Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P21 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, Rfree = 0.236) has improved geometry compared with prior lower resolution determinations of the ,CTD structure [Jeon et al. (1995), Science, 270, 1495,1497; Benoff et al. (2002), Science, 297, 1562,1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of ,CTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction. [source] Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubled a axisACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Arthur H. Robbins The crystal structure of human carbonic anhydrase II with a doubled a axis from that of the usually observed monoclinic unit cell has been determined and refined to 1.4,Å resolution. The diffraction data with h = 2n + 1 were systematically weaker than those with h = 2n. Consequently, the scaling of the data, structure solution and refinement were challenging. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ along a, but one of the molecules has two alternate positions related by a rotation of approximately 2°. This rotation axis is located near the edge of the central ,-sheet, causing a maximum distance disparity of 1.7,Å between equivalent atoms on the diametrically opposite side of the molecule. The crystal-packing contacts are similar to two sequential combined unit cells along a of the previously determined monoclinic unit cell. Abnormally high final Rcryst and Rfree values (20.2% and 23.7%, respectively) are not unusual for structures containing pseudo-translational symmetry and probably result from poor signal to noise in the weak h -odd data. [source] Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Megan Guelker The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,Å resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source] Crystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001D. Kumaran Single crystals of the outer surface protein C (OspC) from Borrelia burgdorferi HB19 have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 66.218, b = 46.113, c = 112.079,Å, , = 99.30°, and diffract to at least 2.2,Å resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. There are two dimers per asymmetric unit, related by a non-crystallographic twofold axis and a pseudo-translational symmetry. [source] Crystallization and preliminary X-ray analysis of d -2-hydroxyacid dehydrogenase from Haloferax mediterraneiACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009J. Domenech d -2-Hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei has been overexpressed in Escherichia coli, solubilized in 8,M urea and refolded by rapid dilution. The protein was purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate or PEG 3350 as precipitant. Two crystal forms representing the free enzyme and the nonproductive ternary complex with ,-ketohexanoic acid and NAD+ grew under these conditions. Crystals of form I diffracted to beyond 3.0,Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 66.0, b = 119.6, c = 86.2,Å, , = 96.3°. Crystals of form II diffracted to beyond 2.0,Å resolution and belonged to the triclinic space group P1, with unit-cell parameters a = 66.5, b = 75.2, c = 77.6,Å, , = 109.1, , = 107.5, , = 95.9°. The calculated values for VM and analysis of the self-rotation and self-Patterson functions suggest that the asymmetric unit in both crystal forms contains two dimers related by pseudo-translational symmetry. [source] | ||||||||||