Newsletter

search results

results of search on CRYSTALLOGRAPHY JOURNALS ONLINE

46 citations found for Yamauchi,

Search for Yamauchi, in the World Directory of Crystallographers

Select bibliographic records for downloading using the checkboxes or select all button

Results 1 to 20, sorted by name:


Download citation
Acta Cryst. (1993). A49, c336-c337
Download citation


Download citation
Download citation

link to html
The title compound, 4Na+·C24H12O16S84-·14H2O (Na4TCAS·14H2O), was found to crystallize in the triclinic space group P\overline 1. The X-ray structure revealed that the centrosymmetric TCAS4- anion adopts the 1,2-alternate conformation. The sodium cations are surrounded by five or six O atoms in the crystal structure. All sodium ions form centrosymmetric aqua-bridged dimers, Na([mu]-H2O)2Na, which are also coordinated by sulfonate O atoms and contribute to the formation of a three-dimensional network. The compound exists in the solid state as layers of anionic thia­calixarenes, alternating with inorganic layers that contain sodium cations and water mol­ecules. Intercalation of metal ions into the solid-state layered structure was observed.



Download citation
Acta Cryst. (2014). A70, C448
Download citation

link to html
The resorcinol hydroxylase is involved in the first step of the resorcinol catabolic pathway and catalyzes hydroxylation of resorcinol to hydroxyquinol. The enzyme belongs to the two-component flavin-diffusible monooxygenase family and acts in the coexistence of two components: an oxygenase and a flavin reductase. The oxygenase component hydroxylates the substrate using molecular oxygen and reduced flavin produced by the reductase. To understand the structural basis for the catalytic mechanism, we analyzed the crystal structure of the oxygenase component (GraA) from Rhizobium sp. strain MTP-10005. The GraA subunit has 409 amino acid residues. Apo-form crystals were obtained in the tetragonal space group I4122 by a sitting-drop vapor-diffusion method with a reservoir solution of PEG3350 and K2HPO4. Holo-form crystals were obtained in the trigonal space group P3221 by a sitting-drop vapor-diffusion method with a reservoir solution of PEG3350 and KNO3. Both structures were determined by molecular replacement and refined at 2.3 Å and 3.2 Å resolutions, respectively. GraA is a homotetramer with three molecular two-fold axes identical to crystallographic two-fold axes in the apo-form crystal. In the holo-form crystal, four tetramers exist in the asymmetric unit and each subunit binds one FAD. The subunit consists of three domains. The N-terminal domain has an [alpha]-structure mainly of antiparallel [alpha]-helices; the central domain has a [beta]-structure of two [beta]-sheets stacked together; the C-terminal domain has a four-helix-bundle structure of long antiparallel [alpha]-helices involved in tetramer formation. In the holo-form, the FAD is located in the space that is encompassed by these three domains. The loop region of 13 residues, which is disordered in the apo-form, is ordered and covers FAD of another subunit. The turn portion of the loop occludes the entrance of the putative active site.

Download citation
Acta Cryst. (2017). A73, C268
Download citation


Download citation
Download citation

link to html
The aspartate racemase from L. sakei NBRC 15893 has been crystallized by the sitting-drop vapour-diffusion method. The crystal diffracted to 2.6 Å resolution.


Download citation
Download citation

link to html
AMP-activated protein kinase (AMPK) functions as a sensor to maintain energy balance and is therefore a potential target for drug design against metabolic syndrome. The crystal structure of the complex between the phosphorylated-state mimic T172D mutant AMPK [alpha]2 kinase domain and a selective inhibitor, compound C, has been determined, revealing the unique inhibitor-binding mode of this protein kinase.

Download citation
Acta Cryst. (2014). A70, C1055
Download citation

link to html
Aspartate racemase (AspR) catalyzes the interconversion between L- and D-aspartates without PLP. The only crystal structure of the PLP-independent amino-acid racemase is now available from a hyperthermophilic archaeon. To elucidate structural features and low-temperature adaptation of the racemase group, we determined the crystal structures of AspR from Lactobacillus sakei NBRC 15893 (LsAspR), which works in the low-to-medium temperature range, and for comparison AspR from Thermococcus litoralis DSM 5473 (TlAspR), which has the maximum activity at 95 0C. LsAspR and TlAspR weree crystallized at 20 0C by the sitting-drop vapour-diffusion method using a precipitant solution of 25% (v/v) PEG-MME 550, 5% (v/v) 2-propanol and 0.1 M sodium acetate pH 4.8 and a precipitant solution of 24% (w/v) PEG1500, 0.2 M L-proline and 0.1 M HEPES pH 7.5, respectively. The structures of LsAspR and TlAspR were determined by molecular replacement and refined at 2.6 Å resolution (R=23.8%, Rfree = 31.6%) and 2.0 Å resolution (R=18.7%, Rfree = 25.0%), respectively. Both LsAspR and TlAspR molecules are homodimers with molecular two-fold axis. The subunit of each enzyme molecule comprises the N-terminal and C-terminal domains. The molecule is formed mainly by intersubunit interactions between the N-terminal [alpha]-helices and intersubunit hydrogen-bonds between the N-terminal [beta]-sheets in the dimer interface. The active-site cleft exists between both the domains. The spatial arrangement of the strictly conserved cystein residues in the cleft reveals the Cys residues involved in the enzymatic catalysis. A structural comparison of LsAspR and TlAspR reveals structural factors probably involved in thermostability of AspR. The molecular volume, intersubunit interaction, and the number of ion pairs suggest that the LsAspR molecule is more loose than that of TlAspR.

Download citation
Acta Cryst. (2011). A67, C782-C783
Download citation


Download citation
Download citation


Download citation
Acta Cryst. (2008). A64, C585-C586
Download citation



Download citation
Download citation

link to html
Focusing of an X-ray free-electron laser enables the production of ultrahigh-intensity X-ray pulses. X-ray nanobeams of a free-electron laser were generated using reflective focusing optics combined with speckle interferometry.

Download citation
Acta Cryst. (2011). A67, C106
Download citation


Download citation
Acta Cryst. (2014). A70, C1181
Download citation

link to html
In situ synchrotron X-ray powder diffraction can be one of the most powerful probes to investigate the structure evolution by a chemical reaction thanks to simultaneity of data collection. It is not, however, with ease to produce a homogeneous chemical reaction in the limited spaces, which is essential to see an atomic-scale structure evolution. We have developed an in situ capillary cell for both high-temperature H2 reduction and precise humidity control at the SPring-8 BL44B2. We successfully applied this in situ system to an electronic conductor LaSr3Fe3O10, which is transformed into an ionic conductor by the two-step chemical treatments [1]. LaSr3Fe3O10 has a triple-layer structure with a FeO6 octahedral unit. One triple layer is bonded with another layer through van der Waals interaction. Structure refinements with in situ synchrotron powder diffraction data revealed that the H2 reduction at 613 K produced in-plane oxygen vacancies, which resulted in suppression of the interlayer interaction. We found from charge density studies and Raman spectroscopy measurements that the following humidification intercalated H2O and OH- into the interlayer and intralayer, respectively. That means that H2O plays a role for suppression of three-dimensional electronic conductivity, stabilizing the intercalation structure. On the other hand, the OH- ions behave as carriers for ionic conductivity, maintaining the charge neutrality in the intralayer. Finally we determined the composition of the ionic conductor to be LaSr3Fe3O8.0 (OH) 1.2·2H2O, which indicates a transformation of LaSr3Fe3O10 into an OH- ionic conductor. In the presentation, I will discuss the OH- ionic conduction channel based on electrostatic potentials obtained from charge densities.

Download citation
Download citation

link to html
A statistical approach to correct X-ray response non-uniformity in microstrip detectors was developed and applied to a detector system, which enabled high-accuracy and high-resolution total scattering measurements in a wide range of scattering vector.

Download citation
Acta Cryst. (2014). A70, C355
Download citation

link to html
Various superionic conductors have been examined in terms of the application to electrolytes for solid fuel cells [1]. Recently we demonstrated by impedance measurements that a simple two-step chemical reaction transformed an electronic conductor NaxCoO2 into a superionic one. In the present study, we performed in situ synchrotron X-ray diffraction experiments to investigate a structural mechanism for the superionic conductivity driven by the chemical treatment of the layered oxide NaxCoO2. We developed a temperature- and humidity-controllable capillary cell under hydrogen and helium gas flow to install in the Debye-Scherrer camera at BL44B2 of SPring-8. This cell allows us to explore a structural transformation process by reduction and humidification treatments. Structural identifications and refinements with in situ diffraction data proved that Co vacancies formed by a CoO separation suppressed the electronic conductivity. Meanwhile it turned out from charge estimation in the Na layers that the superionic conductor transition originated from an ion exchange of H3O+ for Na+, which was confirmed by Raman spectroscopy measurements. In addition, charge densities clearly visualized the H3O+ ions disordering around the Na original sites, suggesting that the H3O+ behave as a carrier source. Finally it was found from electrostatic potentials that the disordering H3O+ sites were coupled through shallow potential barriers to trace a honeycomb-like ion pathway. In the presentation, I will discuss what a carrier is for the superionic-conductive phase from different viewpoints such as activation energies, concentration cell tests, and molecular dynamics simulations using the experimental structure information.

Download citation
Download citation

link to html
The molecular and crystal structure of the complex composed of 2,3,5-triphenyltetrazolium dichloro-(1,3,5-triphenylforma- zanato)cobaltate(II) is reported. Tetrahedral geometry is realized around the high spin state cobalt(II) ion in the complex.

Follow IUCr Journals
Sign up for e-alerts
Follow IUCr on Twitter
Follow us on facebook
Sign up for RSS feeds