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X-ray dynamical diffraction phenomena at a Bragg angle near [pi]/2 are studied. The X-ray transmissivity as well as the reflectivity from the (991) lattice plane of a silicon thin plate is observed. It agrees fairly well with the diffraction pattern calculated on the basis of the Darwin approach. The possibility is discussed whether a set of two crystal plates arranged face to face, in which the diffraction condition with a Bragg angle near [pi]/2 is satisfied, may be used as a very high resolution monochromator.

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A novel purification method of the oxygen-sensor domain of R. meliloti FixL, dynamic light-scattering studies of its solution and preliminary crystallographic data are reported.

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Acta Cryst. (2011). A67, C241
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The Burgers vectors of dislocations in a Czochralski-grown LiNbO3 crystal have been determined by using Lang X-ray diffraction topography. Dislocations with Burgers vectors of both 1/6<2\bar 201> and 1/3<\bar 1101> types (in hexagonal indices) are observed. The direction of the two Burgers vectors is thus identified to be along the line from one Nb (or Li) to the nearest Nb (or Li), and along the line from one Nb (or Li) to the second neighbours respectively.


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The periplasmic form of dipeptidyl aminopeptidase IV from P. mexicana WO24 was crystallized in complex with the tripeptide Lys-Pro-Tyr. X-ray diffraction data were collected to 1.90 Å resolution.

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Acta Cryst. (2014). A70, C1058
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Dipeptidyl aminopeptidase (DAP or DPP, EC 3.4.14) catalyses the removal of dipeptides from the amino termini of peptides and proteins. In microorganisms, we have reported the identification, purification, and characterization of DAP BI, DAP BII, DAP BIII, and DAP IV (bacterial DPP4), POP from Pseudoxanthomonas mexicana WO24, and demonstrated that DAP BI, DAP BIII, DAP IV and POP belong to the POP family and they are classified into the clan SC, family S9 in the MEROPS database. On the basis of the enzymological data we obtained, we proposed that bacterial DAPs should be classified in a manner different from that of mammalian DPPs, except for the DAP IV. The DAP IV liberates dipeptides from the free amino terminus and has a specificity for both proline and hydroxyproline residues in the penultimate position of peptides. Here, we report the first structure of the bacterial DPP IV (P. mexicana WO24 DAP IV) complexed with an inhibitor at 2.2 Å resolution. The subunit structure is composed of two domains, the N-terminal eight-bladed [beta]-propeller domain and the C-terminal alpha/beta/alpha sandwich catalytic domain. These structural features are conserved with clan SC S9 family. However, the N-terminal domain contains a unique helix region that extends over the active site acting as a lid, gating substrate or product access. Based upon the structural data, as well as molecular modeling, a model suggesting that the unique helix region is conserved in some kind of bacterial DPP4s except for mammalian DPP4s and some bacterial DPP4s. Some asaccharolytic and anaerobic bacteria can be used protein or peptides as an energy source. Therefore, these bacteria secrete many types of proteases and peptidases. Especially, the elucidation of degradation mechanisms of collagen, including proline and hydroxyproline, are very important from the point of view of host tissue breakdown in pathogens. Our findings suggest that different ligand recognition mechanisms from the bacterial DPP IV to mammalian DPP4 raise the possibility of an antimicrobial development targeting DPP IV from bacteria.

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Acta Cryst. (2014). A70, C1059
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The peptidase family S46 that contains the dipeptidyl aminopeptidase BII (DAP BII) from Pseudoxanthomonas mexicana WO24 is the only exopeptidase family in clan PA peptidases. Our present phylogenetic and experimental studies indicated that the catalytic triad of DAP BII is composed of His 86, Asp 224 and Ser 657 and implied that unknown large helical domains involved in exopeptidase activity[1]. However, three-dimensional structure of a family S46 peptidase has not yet been reported. Thus, the crystal structure of DAP BII is essential not only to understand the catalytic mechanism of family S46 peptidases but also to clarify the structural origin of the exo-type peptidase activities of these enzymes. Recently, we have successfully crystallized the DAP BII and collected X-ray diffraction data to 2.3 Å resolution from the crystal. This crystal belonging to space group P212121, with unit-cell parameters a = 76.55 Å, b = 130.86 Å, c = 170.87 Å[2]. Structural analysis by the multi-wavelength anomalous diffraction method is underway[3]. Here, we report the first crystallization and structural analysis of the DAP BII from P. mexicana WO24 as family S46 peptidase. Other enzymes that belong to this family are DPP7 and DPP11 from Porphyromonas gingivalis, DPP11 from Porphyromonas endodontalis (periodontal pathogen) and DPP11 from Shewanella putrefaciens (multidrug resistance associated opportunistic pathogen). These gram-negative bacterial pathogens are known to asaccharolytic. Especially, Porphyromonas gingivalis is known to utilize dipeptides, instead of free amino acids, as energy source and cellular material. Since S46 peptidases are not found in mammals, we expect our study will be useful for the discovery of specific inhibitors to S46 peptidases from these pathogens.

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