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Journal Articles

The Hydrogen-bond network in sodium chloride tridecahydrate; Analogy with ice VI

Yamashita, Keishiro*; Nakayama, Kazuya*; Komatsu, Kazuki*; Ohara, Takashi; Munakata, Koji*; Hattori, Takanori; Sano, Asami; Kagi, Hiroyuki*

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 79(5), p.414 - 426, 2023/10

https://doi.org/10.1107/S2052520623007199
 Times Cited Count：0 Percentile：0.02(Chemistry, Multidisciplinary)

The structure of a recently-found hyperhydrated form of sodium chloride, NaCl$$cdot$$ 13H(D)$$_{2}$$O, has been determined by ${it in situ}$ single-crystal neutron diffraction at 1.7 GPa and 298 K. It has large hydrogen-bond networks and some water molecules have distorted bonding features such as bifurcated hydrogen bonds and five-coordinated water molecules. The hydrogen-bond network has similarities to ice VI in terms of network topology and disordered hydrogen bonds. Assuming the equivalence of network components connected by pseudo symmetries, the overall network structure of this hydrate can be expressed by breaking it down into smaller structural units which correspond to the ice VI network structure. This hydrogen-bond network contains orientational disorder of water molecules in contrast to the known salt hydrates. Here, we present an example for further insights into a hydrogen-bond network containing ionic species.

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

https://doi.org/10.1107/S205252062100370X
 Times Cited Count：0 Percentile：0.01(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

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

https://doi.org/10.1107/S2052520619007923
 Times Cited Count：7 Percentile：58.9(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

https://doi.org/10.1107/S2059798318012081
 Times Cited Count：13 Percentile：74.07(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

https://doi.org/10.1107/S2059798315021269
 Times Cited Count：5 Percentile：37.86(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

https://doi.org/10.1107/S1399004715009438
 Times Cited Count：1 Percentile：11.43(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

https://doi.org/10.1107/S1399004714027734
 Times Cited Count：7 Percentile：50.76(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

https://doi.org/10.1107/S205252061500027X
 Times Cited Count：19 Percentile：79.64(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

https://doi.org/10.1107/S1399004713033609
 Times Cited Count：12 Percentile：63.07(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

https://doi.org/10.1107/S0907444913023196
 Times Cited Count：14 Percentile：68.77(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

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

https://doi.org/10.1107/S0907444910053382
 Times Cited Count：28 Percentile：88.53(Biochemical Research Methods)

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

https://doi.org/10.1107/S0907444910034967
 Times Cited Count：2 Percentile：30.11(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.

Journal Articles

Neutron structure analysis using the IBARAKI biological crystal diffractometer (iBIX) at J-PARC

Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Niimura, Nobuo*; Ohara, Takashi*; Kurihara, Kazuo; Yamada, Taro*; Onishi, Yuki*; Tomoyori, Katsuaki*; Yokoyama, Takeshi*

Acta Crystallographica Section D, 66(11), p.1194 - 1197, 2010/11

https://doi.org/10.1107/S0907444910033020
 Times Cited Count：49 Percentile：94.6(Biochemical Research Methods)

The IBARAKI Biological Crystal Diffractometer (iBIX), a new diffractometer for protein crystallography at the next-generation neutron source at J-PARC (Japan Proton Accelerator Research Complex), has been constructed and has been operational since December 2008. Preliminary structure analyses of organic crystals showed that iBIX has high performance even at 120 kW operation and the first full data set is being collected from a protein crystal.

Journal Articles

A Neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 ${AA}$ resolution

Yagi, Daichi*; Yamada, Taro*; Kurihara, Kazuo; Onishi, Yuki*; Yamashita, Masahiro*; Tamada, Taro; Tanaka, Ichiro*; Kuroki, Ryota; Niimura, Nobuo*

Acta Crystallographica Section D, 65(9), p.892 - 899, 2009/09

https://doi.org/10.1107/S0907444909018885
 Times Cited Count：17 Percentile：80.39(Biochemical Research Methods)

A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7 ${AA}$ resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7 ${AA}$ resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences in hydrogen-bond strengths for the $$alpha$$-helices and $$beta$$-sheets were inferred from determination of the hydrogen-bond lengths and the H/D-exchange ratios of the backbone amide H atoms. The correlation between the B factors and hydrogen-bond lengths of the hydration water molecules was also determined.

Journal Articles

Neutron diffraction analysis of deuterium transfer in chiral $$beta$$-thiolactam formation in the crystalline state

Hosoya, Takaaki*; Uekusa, Hidehiro*; Ohashi, Yuji*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 62(1), p.153 - 160, 2006/02

https://doi.org/10.1107/S0108768105038656
 Times Cited Count：5 Percentile：48.75(Chemistry, Multidisciplinary)

Since N,N-dibenzyl-1-cyclohexenecarbothioamide is photoisomerized to the optically active $$beta$$-thiolactam with the retention of the single-crystal form, the mechanism of chirality induction was identified by X-ray crystal structure analyses during the process of the reaction. In order to clarify the mechanism of hydrogen transfer in the reaction, the H atomsof the benzyl groups were replaced with deuterium atoms. The crystal structure after photoisomerization was analyzed by neutron diffraction. One of four deuterium atoms of the two benzyl groups is transferred to the C atom of the cyclohexene ring. The absolute configuration of the -C$$^{*}$$HD- group(chiral methylene) in the photoproduct r-thiolactam revealed that the deuterium atom occupies the equatorial position. This suggests that the deuterium atom is not transferred from the benzyl group of a neighbouring molecule, but from one of the benzyl groups within the molecule.

Journal Articles

A Neutron crystallographic analysis of a rubredoxin mutant at 1.6 ${AA}$ resolution

Chatake, Toshiyuki*; Kurihara, Kazuo; Tanaka, Ichiro*; Tsyba, I.*; Bau, R.*; Jenney, F. E. Jr.*; Adams, M. W. W.*; Niimura, Nobuo

Acta Crystallographica Section D, 60(8), p.1364 - 1373, 2004/08

https://doi.org/10.1107/S090744490401176X
 Times Cited Count：34 Percentile：88.89(Biochemical Research Methods)

A neutron diffraction study has been carried out at 1.6 ${AA}$ resolution on a mutant rubredoxin from ${it Pyrococcus furiosus}$ using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of JAERI. In order to study the unusual thermostability of rubredoxin from ${it P. furiosus}$, the hydrogen-bonding patterns were compared between the native and a 'triple-mutant' variant where three residues were changed so that they are identical to those in a mesophilic rubredoxin. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. The H/D-exchange ratios in the protein were also studied. The results suggest that the backbone amide bonds near the four Cys residues of the FeS$$_{4}$$ redox center are most resistant to H/D exchange. In addition, the 1.6 ${AA}$ resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds.

Journal Articles

More rapid evaluation of biomacromolecular crystals for diffraction experiments

Arai, Shigeki; Chatake, Toshiyuki; Suzuki, Nobuhiro*; Mizuno, Hiroshi*; Niimura, Nobuo

Acta Crystallographica Section D, 60(6), p.1032 - 1039, 2004/06

https://doi.org/10.1107/S0907444904006559
 Times Cited Count：17 Percentile：76.04(Biochemical Research Methods)

The parameters used for evaluating biomacromolecular crystal quality (${it R}$$$_{merge}$$, ${it I}$/$$sigma$$(${it I}$), maximum resolution and mosaicity) strongly depend on the diffraction experimental conditions. In this paper we describe the distinctive features of the relative Wilson plot method, and we show that the overall B-factor obtained from this plot is given as a more appropriate to characterize protein crystals. The relative Wilson plot has been applied to the characterization of crystals of a B-DNA decamer d(CCATTAATGG), and crystals of the proteins DsrD (dissimilatory sulfite reductase D) and hen egg-white lysozyme (HEWL) which we have studied by neutron diffraction. We have found that the crystal qualities of the B-DNA decamer and DsrD significantly depend on the regions of the crystallization phase diagram from which samples were taken. However, in the case of HEWL, crystal quality appears to be independent on the region of the crystallization phase diagram.

Journal Articles

Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium $textit{Desulfovibrio vulgaris}$

Chatake, Toshiyuki; Mizuno, Nobuhiro*; Voordown, G.*; Higuchi, Yoshiki*; Arai, Shigeki; Tanaka, Ichiro; Niimura, Nobuo

Acta Crystallographica Section D, 59(Part2), p.2306 - 2309, 2003/12

https://doi.org/10.1107/S0907444903020596
 Times Cited Count：19 Percentile：75.55(Biochemical Research Methods)

Issimilatory sulfite reductase D (DsrD) from $textit{Desulfovibrio vulgaris}$ has been crystallized for a neutron diffraction study. The initial crystals obtained were too small for the neutron experiment. In order to obtain a larger crystal (1 mm$$^{3}$$), a combination of two techniques was used to find the optimum crystallization conditions: a crystallization phase diagram, followed by crystal-quality assessment via X-ray diffraction. Using conditions determined in this manner, a large single crystal (1.7 mm$$^{3}$$) of the DsrD protein was subsequently grown in D$$_{2}$$O solution by the macro-seeding technique. The neutron diffraction experiment was carried out using the BIX-3 diffractometer at the Japan Atomic Energy Research Institute (JAERI), and the diffraction data up to 2.4 AA resolution could be collected from this crystal.

Journal Articles

Crystallization of a large single crystal of a B-DNA decamer for a neutron diffraction experiment by the phase-diagram technique

Arai, Shigeki; Chatake, Toshiyuki; Minezaki, Yoshiaki*; Niimura, Nobuo

Acta Crystallographica Section D, 58(Part 1), p.151 - 153, 2002/01

https://doi.org/10.1107/S0907444901017401
 Times Cited Count：23 Percentile：81.54(Biochemical Research Methods)

no abstracts in English

Journal Articles

Structure of magnetite(Fe$$_{3}$$O$$_{4}$$)below the verwey transition temperature

; T.F.Koetzle*; *; *; *; *

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 38(8), p.2121 - 2133, 1982/00

https://doi.org/10.1107/S0567740882008176
 Times Cited Count：252 Percentile：99.48(Chemistry, Multidisciplinary)

no abstracts in English

23 (Records 1-20 displayed on this page)