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99 citations found for Ueno,

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Acta Cryst. (2014). A70, C569
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X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.

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Angle-resolved UV photoelectron spectra (ARUPS) were measured for thin films of perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) deposited on cleaved MoS2 surfaces. The take-off angle ([theta]) dependence of the photoelectron intensity of the highest [pi] band showed a sharp maximum at [theta] = 32-34°. A spectral feature of the binding energy at ~8.9 eV, which is believed to originate from a [pi] state, showed a remarkably different [theta] dependence from that of the [pi] band. A quantitative analysis of the observed [theta] dependencies clearly indicates that (a) the feature at ~8.9 eV originates from the oxygen 2p non-bonding states and (b) the molecules lie flat on the substrate surface.

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Angle-resolved UV photoelectron spectra were measured for thin films of chloroaluminum phthalocyanine deposited on cleaved MoS2 surfaces. The take-off angle ([theta]) dependence of the photoelectron intensity of the highest [pi] band showed a remarkable sharpening upon cooling the film, indicating that thermal excitation of molecular vibrations gives a considerable broadening of the photoelectron angular distribution. The [theta] dependence observed at ~120 K agrees well with that calculated.

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Acta Cryst. (2011). A67, C619
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A systematic approach by the molecular-replacement method with a dimeric search model using the program Phaser led to an unexpected pentameric structure of the NSP4:95–146 region of the ST3 strain of rotavirus, in contrast to the previously reported tetramers.

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The crystal of the DNA dodecamer of d(CGCGmo6AATCCGCG) containing 2'-deoxy-N6-methoxyadenosine changes from one form to another during data collection, as a phase transition ascribed to differences in humidity. It has been found as the first example that the N6-methoxyadenosine residue forms a base pair with cytosine residue in a manner identical to Watson-Crick-type pairing.

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A new cassette system for protein cryocrystallography has been developed. This system is compatible with crystal-exchange robots installed at both SPring-8 and the Photon Factory.


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The observation of O2 in a time-frozen structure using serial femtosecond rotation crystallography of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from A. xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.

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Damage-free structures of the resting state of one of the most studied copper nitrite reductases were obtained independently by X-ray free-electron laser (XFEL) and neutron crystallography, representing the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography.

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Acta Cryst. (2014). A70, C331
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BL41XU is the oldest macromolecular crystallography (MX) beamline at SPring-8 [1]. Although it has been contributing to the structure determination of difficult samples since its start of operation in 1997, the targets for the structural study is still getting more challenging and the crystal quality brought to the beamline is getting worse. Therefore, we have upgraded the focusing optics and diffractometer of BL41XU to cope with these targets. Our goal is to achieve an environment which can offer a stable beam with a photon flux of >1013 photons/s in the beam size range of 5 ~ 50[mu]m. It is a complementary specification with our micro-focus beamline BL32XU [2], and allows both micro-crystallography and data collection using crystal volume. The new optics adopts a two-step focusing with elliptical figured mirrors: the first optics is a single horizontal mirror and the second one adopts Kirkpatrick-Baez (KB) configuration. At the middle of the two focusing optics, a high precision horizontal slit is installed to define secondary source size. The beam size can be changed either by changing the secondary source size, by offsetting the sample position, or by tilting the vertical mirror. For the stable use of small beam, both KB mirror and diffractometer were equipped on the granite stage, and enclosed in a booth in which the temperature is keep stable. On the new diffractometer, we equipped PILATUS3 6M that enables rapid data collection combining with high flux beam. Together with the upgrade of hardware, software tools, which support diffraction based centering and determination of measurement condition, have been implemented in order to make full use of the renewed beamline. The upgrade was conducted in the long shut-down period between January and March of this year, and the beamline was opened for users in the middle of May after commissioning of one month. The result of commissioning and initial results will be presented. This study was supported by the MEXT of Japan.

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Acta Cryst. (2006). A62, s129
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The best practice for dose-limiting serial synchrotron rotation crystallography was examined through anomalous signal and single-wavelength anomalous diffraction phasing of mercury-bound luciferin regenerating enzyme. Sample rotation enabled accurate data collection with fewer diffraction images than without rotation, and an increase in resolution and anomalous signal was observed up to 3.4 MGy even though specific damage occurred after an accumulated dose of 1.1 MGy.

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Acta Cryst. (2011). A67, C46
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Acta Cryst. (2014). A70, C333
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Protein micro-crystallography is one of the most advanced technologies for protein structure analysis. In order to realize this, an undulator beamline, named BL32XU, was constructed at SPring-8. The beamline can provide beam with size of 0.9 x 0.9 µm and photon flux of 6E10 photons/s. The beam size can be easily changed by users from 1 to 10 µm square with the same flux density. Through three years user operation, we have established several key systems for efficient protein micro-crystallography. One of them is the software for precise positioning of micro-crystals in `raster scan'. SHIKA is a program with GUI which searches diffraction spots in a plenty of low dose diffraction images obtained in raster scan. Finally, it generates 2D map of crystal positions based on the number of spots or spot intensities. Parameters and thresholds in peak search have been empirically optimized for LCP crystals and it provides robust results. Another system is for the data collection strategy. Almost all successful data collections were conducted via `helical data collection' on BL32XU using the line-focused beam. The GUI software, named KUMA, enables estimation of an accumulated dose and suggests suitable experimental conditions for helical data collection. The system is proven to be useful for experimental phasing using tiny LCP crystals of membrane proteins[1-3]. Based on them, the rapid and automatic data collection system using protein micro-crystals is under development. The new CCD detector, Rayonix MX225HS, was installed for faster data acquisition in 10 Hz with the pixel size of 78 µm square. The new SHIKA using GPUs is under development for faster and more accurate crystal alignment. Following this step, KUMA system can suggest experimental conditions for each crystal found on the loop. We also report about the effects of higher dose rate in protein crystallography up to the order of 100 MGy/s. This work was supported by Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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An automated data-collection system named ZOO has been developed. This system enabled faster data collection, facilitated advanced data-collection and data-processing techniques, and permitted the collection of higher quality data.



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