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Journal Articles

Single-crystal structure analysis of non-deuterated triglycine sulfate by neutron diffraction at 20 and 298 K; A New disorder model for the 298 K structure

Terasawa, Yukana*; Ohara, Takashi; Sato, Sota*; Yoshida, Satoshi*; Asahi, Toru*

Acta Crystallographica Section E; Crystallographic Communications (Internet), 78(3), p.306 - 312, 2022/03

Journal Articles

Structure of the {U$$_{13}$$} polyoxo cluster U$$_{13}$$O$$_{8}$$Cl$$_{x}$$(MeO)$$_{38-x}$$ (x = 2.3, MeO = methoxide)

Fichter, S.*; Radoske, T.*; Ikeda, Atsushi

Acta Crystallographica Section E; Crystallographic Communications (Internet), 77(8), p.847 - 852, 2021/08

Journal Articles

Incommensurately modulated crystal structure of $$alpha$$'(O'3)-type sodium cobalt oxide Na$$_{x}$$CoO$$_{2}$$ (${it x}$ $$sim$$ 0.78)

Miyazaki, Yuzuru*; Igawa, Naoki; Yubuta, Kunio*

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 77(3), p.371 - 377, 2021/06

 Times Cited Count:0 Percentile:0.02(Chemistry, Multidisciplinary)

Crystal structure of $$alpha$$'(O'3)-type layered sodium cobalt oxide Na$$_{x}$$CoO$$_{2}$$ (${it x}$ $$sim$$ 0.78) was analyzed using the (3+1)-dimensional superspace approach to the neutron diffraction data. The crystal structure is described based on the superspace group ${it C}$2 = ${it m}$(${it p}$0${it q}$)00, wherein the positions of Na atoms are most significantly modulated in the monoclinic ${it a}$-direction to form an ordered arrangement. Such a positional modulation causes a quasi-periodic shift of Na atoms from the centers of the NaO$$_{6}$$ polyhedra between undulated CoO$$_{2}$$ sheets, changing the form of the NaO$$_{6}$$ polyhedron from an octahedral coordination (O) to a trigonal prismatic one (P). Where the Na atoms are most significantly shifted, the neighboring Na atoms are located at almost touching distances and yielding Na-deficient sites. As a result, a typical sequence of NaO$$_{6}$$ octahedra with -O-O-O-P-$${it V}$$$$_{mathrm Na}$$-P- along the a-axis is realized.

Journal Articles

Crystal structure of a high-pressure phase of magnesium chloride hexahydrate determined by ${it in-situ}$ X-ray and neutron diffraction methods

Yamashita, Keishiro*; Komatsu, Kazuki*; Hattori, Takanori; Machida, Shinichi*; Kagi, Hiroyuki*

Acta Crystallographica Section C; Structural Chemistry (Internet), 75(12), p.1605 - 1612, 2019/12

 Times Cited Count:1 Percentile:21.27(Chemistry, Multidisciplinary)

A crystal structure of a high-pressure phase of magnesium chloride hexahydrate (MgCl$$_{2}$$ $$cdot$$ 6H$$_{2}$$O-II) and its deuterated counterpart (MgCl$$_{2}$$ $$cdot$$ 6D$$_{2}$$O-II) have been identified for the first time by in-situ single-crystal X-ray and powder neutron diffraction. The crystal structure was analyzed by the Rietveld method for the neutron diffraction pattern based on the initial structure determined by single-crystal X-ray diffraction. This high-pressure phase has a similar framework to that in the known ambient-pressure phase, but exhibits some structural changes with symmetry reduction caused by a subtle modification in the hydrogen-bond network around the Mg(H$$_{2}$$O)$$_{6}$$ octahedra. These structural features reflect the strain in the high-pressure phases of MgCl$$_{2}$$ hydrates.

Journal Articles

Structure change of monoclinic ZrO$$_{2}$$ baddeleyite involving softenings of bulk modulus and atom vibrations

Fukui, Hiroshi*; Fujimoto, Manato*; Akahama, Yuichi*; Sano, Asami; Hattori, Takanori

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 75(4), p.742 - 749, 2019/08

 Times Cited Count:2 Percentile:38.26(Chemistry, Multidisciplinary)

Monoclinic ZrO$$_{2}$$ baddeleyite exhibits anomalous softenings of bulk modulus and atom vibrations with compression. We have investigated the pressure evolution of the structure by neutron powder diffraction combined with ab-initio calculations. The present results showed that the anomalous pressure response of the bulk modulus is related not to the change in the bonding characters but to the deformation of an oxygen sublattice, especially one of layers made of oxygens in the crystallographic $$a$$* plane. The layer consists of two parallelograms; one is rotating with little distortion and the other is being distorted with increasing pressure. This deformation of this layer makes one of Zr-O distances long, resulting in the softening of some atom vibrational modes.

Journal Articles

Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer

Yano, Naomine*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*

Acta Crystallographica Section D; Structural Biology (Internet), 74(11), p.1041 - 1052, 2018/11

 Times Cited Count:7 Percentile:68.69(Biochemical Research Methods)

Journal Articles

A Technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography

Chatake, Toshiyuki*; Fujiwara, Satoru

Acta Crystallographica Section D; Structural Biology (Internet), 72(1), p.71 - 82, 2016/01

 Times Cited Count:3 Percentile:31.37(Biochemical Research Methods)

Journal Articles

High-resolution crystal structures of the solubilized domain of porcine cytochrome $$b_{5}$$

Hirano, Yu; Kimura, Shigenobu*; Tamada, Taro

Acta Crystallographica Section D, 71(7), p.1572 - 1581, 2015/07

 Times Cited Count:1 Percentile:13.8(Biochemical Research Methods)

Mammalian microsomal cytochrome $$b_{5}$$ has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome $$b_{5}$$ from porcine liver were determined at sub-angstrom resolution (0.76-0.95 ${AA}$) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.

Journal Articles

Structure of a highly acidic $$beta$$-lactamase from the moderate halophile ${it Chromohalobacter}$ sp.560 and the discovery of a Cs$$^{+}$$-selective binding site

Arai, Shigeki; Yonezawa, Yasushi*; Okazaki, Nobuo*; Matsumoto, Fumiko*; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu*; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide*; et al.

Acta Crystallographica Section D, 71(3), p.541 - 554, 2015/03

 Times Cited Count:4 Percentile:40.84(Biochemical Research Methods)

The crystal structure of halophilic $$beta$$-lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr$$^{2+}$$ and Cs$$^{+}$$ ions were identified by anomalous X-ray diffraction. The location of one Cs$$^{+}$$ specific binding site was identified on HaBLA even in the presence of 9-fold molar excess of Na$$^{+}$$ (90 mM Na$$^{+}$$ /10 mM Cs$$^{+}$$). This Cs$$^{+}$$ binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs$$^{+}$$ by the cation-$$pi$$ interaction. The observation of a selective and high-affinity Cs$$^{+}$$ binding site provides important information that is useful for designing artificial Cs$$^{+}$$ binding sites useful in bioremediation of radioactive isotopes.

Journal Articles

Crystal structure of magnesium dichloride decahydrate determined by X-ray and neutron diffraction under high pressure

Komatsu, Kazuki*; Shinozaki, Ayako*; Machida, Shinichi*; Matsubayashi, Takuto*; Watanabe, Mao*; Kagi, Hiroyuki*; Sano, Asami; Hattori, Takanori

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 71(1), p.74 - 80, 2015/02

 Times Cited Count:11 Percentile:70.55(Chemistry, Multidisciplinary)

Magnesium dichloride decahydrate (MgCl$$_{2}$$10H$$_{2}$$O) and its deuterated counterpart (MgCl$$_{2}$$10D$$_{2}$$O) are identified for the first time by in-situ powder synchrotron X-ray and spallation neutron diffraction. These substances are crystallized from a previously unidentified nanocrystalline compound, which originates from an amorphous state at low temperature. A combination of a recently developed autoindexing procedure and the charge-flipping method reveals that the crystal structure of MgCl 10H$$_{2}$$O consists of an ABCABC... sequence of Mg(H$$_{2}$$O)$$_{6}$$ octahedra. The Cl$$^{-}$$ anions and remaining water molecules unconnected to the Mg$$^{2+}$$ cations bind the octahedra, similar to other water-rich magnesium dichloride hydrates. The D positions in MgCl$$_{2}$$10D$$_{2}$$O, determined by the difference Fourier methods using the neutron powder diffraction patterns at 2.5 GPa, show the features such as bifurcated hydrogen bonds and tetrahedrally coordinated O atoms.

Journal Articles

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium ${it Halomonas}$ sp.593

Arai, Shigeki; Yonezawa, Yasushi*; Ishibashi, Matsujiro*; Matsumoto, Fumiko*; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Acta Crystallographica Section D, 70(3), p.811 - 820, 2014/03

 Times Cited Count:9 Percentile:60.02(Biochemical Research Methods)

In order to clarify the structural basis of halophilic characteristics of an alkaline phosphatase derived from the moderate halophile ${it Halomonas}$ sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1${AA}$ resolution by X-ray crystallography. Structural properties of surface negative charge and core hydrophobicity are shown to be intermediate between halophile and non-halophile characteristics, and may explain the unique functional adaptation to a wide-range of salt concentration.

Journal Articles

High-resolution crystal structure of copper amine oxidase from ${it Arthrobacter globiformis}$; Assignment of bound diatomic molecules as O$$_{2}$$

Murakawa, Takeshi*; Hayashi, Hideyuki*; Sunami, Tomoko; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Suzuki, Mamoru*; Tanizawa, Katsuyuki*; Okajima, Toshihide*

Acta Crystallographica Section D, 69(12), p.2483 - 2494, 2013/12

 Times Cited Count:9 Percentile:60.68(Biochemical Research Methods)

The crystal structure of a Cu amine oxidase from ${it Arthrobacter globiformis}$ was determined at 1.08 ${AA}$ resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight $$sim$$200) as a cryoprotectant. The final crystallographic $$R$$-factor and $$R$$$$_{rm free}$$ value are 13.0% and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior including the active site, which resulted in the marked reduction of the overall ${it B}$ factor and consequently led to a sub-atomic resolution structure for a relatively large protein with a monomer molecular weight of $$sim$$70,000. About 40% of all the presumed hydrogen atoms were observed as clear electron densities in the $$F$$$$_{rm o}$$ - $$F$$$$_{rm c}$$ difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site that contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely molecular oxygen, are bound to the protein, one of which is located in the region that has been previously proposed as an entry route for the substrate dioxygen from the central cavity of the dimer interface to the active site.

Journal Articles

Crystallization and preliminary X-ray diffraction analysis of tetrathionate hydrolase from ${it Acidithiobacillus ferrooxidans}$

Kanao, Tadayoshi*; Kosaka, Megumi*; Yoshida, Kyoya*; Nakayama, Hisayuki*; Tamada, Taro; Kuroki, Ryota; Yamada, Hidenori; Takada, Jun*; Kamimura, Kazuo*

Acta Crystallographica Section F, 69(6), p.692 - 694, 2013/06

 Times Cited Count:9 Percentile:60.68(Biochemical Research Methods)

Tetrathionate hydrolase (4THase) from the iron- and sulfur-oxidizing bacterium ${it Acidithiobacillus ferrooxidans}$ catalyses the disproportionate hydrolysis of tetrathionate to elemental sulfur, thiosulfate and sulfate. The gene encoding 4THase (${it Af-tth}$) was expressed as inclusion bodies in recombinant ${it Escherichia coli}$. Recombinant ${it Af}$-Tth was activated by refolding under acidic conditions and was then purified to homogeneity. The recombinant protein was crystallized in 20 m${it M}$ glycine buffer pH 10 containing 50 m${it M}$ sodium chloride and 33%(${it v/v}$) PEG 1000 using the hanging-drop vapour-diffusion method. The crystal was a hexagonal cylinder with dimensions of 0.2 $$times$$ 0.05 $$times$$ 0.05 mm. X-ray crystallographic analysis showed that the crystal diffracted to 2.15 ${AA}$ resolution and belongs to space group ${it P}$3$$_{1}$$ or ${it P}$3$$_{2}$$, with unit-cell parameters ${it a}$ = ${it b}$ = 92.1, ${it c}$ = 232.6 ${AA}$.

Journal Articles

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function; Resolution limit due to the quantum noise

Tokuhisa, Atsushi*; Taka, Junichiro*; Kono, Hidetoshi; Go, Nobuhiro*

Acta Crystallographica Section A, 68(3), p.366 - 381, 2012/05

 Times Cited Count:18 Percentile:82.22(Chemistry, Multidisciplinary)

Journal Articles

Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from ${it Thermus thermophilus}$ HB8

Okazaki, Nobuo; Adachi, Motoyasu; Tamada, Taro; Kurihara, Kazuo; Oga, Takushi*; Kamiya, Nobuo*; Kuramitsu, Seiki*; Kuroki, Ryota

Acta Crystallographica Section F, 68(1), p.49 - 52, 2012/01

 Times Cited Count:1 Percentile:20.29(Biochemical Research Methods)

Journal Articles

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of GK0767, the copper-containing nitrite reductase from Geobacillus kaustophilus

Fukuda, Yota*; Tamada, Taro; Takami, Hideto*; Suzuki, Shinichiro*; Inoue, Tsuyoshi*; Nojiri, Masaki

Acta Crystallographica Section F, 67(6), p.692 - 695, 2011/06

 Times Cited Count:5 Percentile:32.82(Biochemical Research Methods)

Journal Articles

Crystallization and preliminary X-ray diffraction studies of the catalytic domain of a novel chitinase, a member of GH family 23, from the moderately thermophilic bacterium ${it Ralstonia}$ sp. A-471

Okazaki, Nobuo; Arimori, Takao; Nakazawa, Masami*; Miyatake, Kazutaka*; Ueda, Mitsuhiro*; Tamada, Taro

Acta Crystallographica Section F, 67(4), p.494 - 497, 2011/04

 Times Cited Count:3 Percentile:43.75(Biochemical Research Methods)

Journal Articles

X-ray and neutron protein crystallographic analysis of the trypsin-BPTI complex

Kawamura, Kenji*; Yamada, Taro*; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Tanaka, Ichiro*; Takahashi, Haruyuki*; Niimura, Nobuo*

Acta Crystallographica Section D, 67(2), p.140 - 148, 2011/02

 Times Cited Count:23 Percentile:87.3(Biochemical Research Methods)

Journal Articles

Purification, crystallization and preliminary X-ray diffraction analysis of DNA damage response A protein from ${it Deinococcus radiodurans}$

Yamada, Mitsugu; Sato, Katsuya; Narumi, Issei

Acta Crystallographica Section F, 66(12), p.1614 - 1616, 2010/12

 Times Cited Count:1 Percentile:17.42(Biochemical Research Methods)

DNA damage response A protein (DdrA) from ${it Deinococcus radiodurans}$ has been suggested to be involved in DNA repair processes through binding to 3' ends of single-stranded DNA, thereby protecting the ends from nuclease digestion. In this study, a recombinant C-terminal truncated form of ${it D. radiodurans}$ DdrA (DdrA157), comprising of the first 157 residues of DdrA, was expressed in ${it E. coli}$, purified and crystallized. Single crystals of DdrA157 were obtained by a hanging drop method at 293 K. The crystal belonged to the monoclinic space group ${it P}$2$$_{1}$$, with unit-cell parameters ${it a}$ = 46.31, ${it b}$ = 180.26, ${it c}$ = 114.17 ${AA}$, ${it $beta$}$ = 90.02$$^{circ}$$. The crystal was expected to contain fourteen molecules in the asymmetric unit. Diffraction data were collected to 2.35 ${AA}$ resolution at beamline BL-5 of the Photon Factory and initial phase determinations were attempted by a molecular-replacement method using the human Rad52 structure.

Journal Articles

Towards investigation of the inhibitor-recognition mechanisms of drug-target proteins by neutron crystallography

Kuroki, Ryota; Okazaki, Nobuo; Adachi, Motoyasu; Ohara, Takashi; Kurihara, Kazuo; Tamada, Taro

Acta Crystallographica Section D, 66(11), p.1126 - 1130, 2010/11

 Times Cited Count:2 Percentile:32.06(Biochemical Research Methods)

It is generally known that enzymes represent important drug-target proteins. Elucidation of the catalytic function and the molecular-recognition mechanisms of enzymes provides important information for structure-based drug design. Neutron crystallography provides accurate information on the locations of H atoms that are essential in enzymatic function and molecular recognition. Recent examples are described of the structure determination of the drug-target proteins human immunodeficiency virus protease and porcine pancreatic elastase in complex with transition-state analogue inhibitors using the neutron diffractometers for biological crystallography (BIX-3 and BIX-4) installed at the JRR-3 research reactor.

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