Kensaku Hamada

FUNDAMENTAL DESIGN OF THE HIGH ENERGY UNDULATOR PILOT BEAMLINE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE SPRING-8

The SPring‐8 project team adopted our proposal for public beamline as one of two pilot beamlines for standardizing the beamline elements. The light source of this beamline is an in‐vacuum‐type undulator of magnetic periodicity of 3.2 cm, which emits highly brilliant x rays in a wide energy range between 9 and 38 keV. The highest power emitted from the light source is 5 kW. The corresponding power density is 300 kW/mrad2. To handle the tremendous power density, grazing incidence diffraction with variable glancing angle will be used for the first crystal of a fixed‐exit double‐crystal monochromator. To focus the high energy x rays up to 38 keV, two supermirrors (Ovonic Synthetic Materials Co.) will be installed in vertical and horizontal directions independently to get a quasi‐isotropic and small beam profile at a focal position. In the experimental station, the sample crystals will be mounted on the κ‐type goniostat, and the Weissenberg photographs will be recorded by on‐line mode on an imaging plate detec...

In-house simultaneous collection of small-angle X-ray scattering, wide-angle X-ray diffraction and Raman scattering data from polymeric materials

An in-house X-ray scattering system, which can simultaneously measure small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD) data, as well Raman scattering data, has been developed to study the phase transitions of polymeric materials. To date, these types of measurements have been limited to synchrotron radiation. The present system is an in-house SAXS system combined with a WAXD detector and a Raman spectrometer. A rotating-anode X-ray generator and multilayer optic are employed to provide a high-flux X-ray beam. Two two-dimensional hybrid pixel detectors are utilized for the rapid-scan time-resolved SAXS and WAXD measurements. The Raman unit consists of a compact probe with a near-infrared excitation laser operating at a wavelength of 1064 nm. This long-wavelength laser produces less fluorescence than conventional excitation lasers with wavelengths of 532 or 785 nm. The performance of this system was tested by investigating the thermally induced ferroelectric phase transition of vinylidene fluoride–trifluoroethylene (VDF-TrFE) copolymers. It has been demonstrated that the combination of SAXS, WAXD and Raman techniques gives useful information for revealing the relationship between the structural change in the crystal lattice and the morphological change in the lamellar stacking mode in polymer samples of complicated hierarchical structure.

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida

Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the β‐proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate‐binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.

Cloning, structural analysis and expression of the gene encoding aspartate aminotransferase from the thermophilic cyanobacterium Phormidium lapideum.

The aspartate aminotransferase gene from the thermophilic cyanobacterium Phormidium lapideum was cloned and expressed in Escherichia coli. The ORF of 1167 nucleotides encodes a protein of 388 amino acids having a molecular weight of 42,099. A molecular model of PIAspAT shows structural features similar to those of the Thermus thermophilus AspAT.

Expression, purification, crystallization and preliminary X-ray studies of geranylgeranyl diphosphate synthase from Thermus thermophilus HB8

Geranylgeranyl diphosphate (GGPP) synthase from Thermus thermophilus HB8 was expressed in Escherichia coli, purified to homogeneity and crystallized both as the recombinant native protein and its selenomethionine (SeMet) derivative. Well diffracting crystals of these proteins were obtained belonging to the tetragonal space group P4(1) or P4(3), with unit-cell parameters a = b = 139.88, c = 73.37 A. There were two homodimers in the asymmetric unit. A native data set was collected to 1.55 A resolution and a data set suitable for MAD phasing was collected to 2.40 A resolution on beamline BL40B2 at SPring-8.

Crystal structure of the solute-binding protein BxlE from Streptomyces thermoviolaceus OPC-520 complexed with xylobiose

BxlE from Streptomyces thermoviolaceus OPC-520 is a xylo-oligosaccharide (mainly xylobiose)-binding protein that serves as the initial receptor for the bacterial ABC-type xylo-oligosaccharide transport system. To determine the ligand-binding mechanism of BxlE, X-ray structures of ligand-free (open form) and ligand (xylobiose)-bound (closed form) BxlE were determined at 1.85 Å resolution. BxlE consists of two globular domains that are linked by two β-strands, with the cleft at the interface of the two domains creating the ligand-binding pocket. In the ligand-free open form, this pocket consists of a U-shaped and negatively charged groove located between the two domains. In the xylobiose-bound closed form of BxlE, both the N and C domains move to fold the ligand without conformational changes in either domain. Xylobiose is buried in the groove and wrapped by the N-domain mainly via hydrogen bond interactions and by the C-domain primarily via non-polar interactions with Trp side chains. In addition to the concave shape matching the binding of xylobiose, an inter-domain salt bridge between Asp-47 and Lys-294 limits the space in the ligand-binding site. This domain-stabilized mechanism of ligand binding to BxlE is a unique feature that is not observed with other solute-binding proteins.

Special articles on zeolite chemistry and technology. Structure and adsorption characteristics of natural clinoptilolite treated with hydrochloric acid.

クリノプチロライトを 0.45 から 10mol・dm-3の塩酸で処理した。3mol・dm-3までは, X線粉末法での結晶化度にはいちじるしい変化はなかった。IRスペクトルには, わずかな変化が認められた。5mol・dm-3では結晶構造がかなり崩壊し, 10mol・dm-3 で無定形を示した。低濃度の塩酸処理で, Na, Ca, Kは急激に減少し, とくに Na, K は二価イオンに比較して容易に脱離した。窒素ガスの飽和単分子吸着量はオリジナル試料の 11.3ml・g-1 が, 0.9mol・dm-3処理で 53ml・g-1 と5倍に増加した。吸着量の増加は内部吸着量に依存している。Dubinin-Radushkevitch プロットから, オリジナル試料はメソ, マクロボアがかなり存在しているが, 酸処理により粒子が均一化しミクロボアが支配的になることが示唆された。窒素ガスの場合, Dubinin-Astakhov の式から算出した吸着特性エネルギーは酸処理により 1.9倍 も増大した。細孔内での吸着分子と陽イオンとの相互作用が増加したことを示している。メタノール蒸気は窒素ガスに比較し多く吸着した。Clausius-Clapeyron の式から算出した被覆率の高い状態での吸着熱は, オリジナルがもっとも高く, 酸処理により減少した。また, 吸着特性エネルギーは窒素ガスに比較して 4～6倍 も大きな値を示した。湿潤熱は, 水>メタノール>ベンゼン>シクロヘキサンの順に低い値を示し, 酸処理により急激に減少した。