Literature DB >> 16645781

RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation.

Go Ueno1, Hiroyuki Kanda, Raita Hirose, Koh Ida, Takashi Kumasaka, Masaki Yamamoto.   

Abstract

RIKEN Structural Genomics Beamlines, BL26B1 & BL26B2 at the SPring-8, have been constructed for the structural genomics research. The main feature of the beamline is full automation of the successive data collections to maximize the beam-time efficiency. The beamline optics adopted a standard design commonly used for the SPring-8 bending magnet beamlines. Beamline instruments are operated by centralized control system through the computer network to achieve the automatic operation. The core part of the beamline development is a sample management system composed of sample changer robots for laboratory and beamline, and a networked sample database. BL26B1 has started user operation, and the automatic operation with the sample management system has been implemented at BL26B2.

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Year:  2006        PMID： 16645781     DOI： 10.1007/s10969-005-9005-5

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN： 1345-711X


  10 in total

1.  Protein structure prediction and structural genomics.

Authors:  D Baker; A Sali
Journal:  Science       Date:  2001-10-05       Impact factor: 47.728

2.  Global efforts in structural genomics.

Authors:  R C Stevens; S Yokoyama; I A Wilson
Journal:  Science       Date:  2001-10-05       Impact factor: 47.728

3.  The TB structural genomics consortium crystallization facility: towards automation from protein to electron density.

Authors:  Bernhard Rupp; Brent W Segelke; Heike I Krupka; Tim Lekin; Johana Schäfer; Adam Zemla; Dominique Toppani; Gyorgy Snell; Thomas Earnest
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-09-26

4.  SPring-8 beamline control system.

Authors:  T Ohata; H Konishi; H Kimura; Y Furukawa; K Tamasaku; T Nakatani; T Tanabe; N Matsumoto; M Ishii; T Ishikawa
Journal:  J Synchrotron Radiat       Date:  1998-05-01       Impact factor: 2.616

5.  Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8.

Authors:  Go Ueno; Hiroyuki Kanda; Takashi Kumasaka; Masaki Yamamoto
Journal:  J Synchrotron Radiat       Date:  2005-04-14       Impact factor: 2.616

6.  Standard transport channels of X-ray beamlines at SPring-8.

Authors:  S Goto; M Yabashi; H Ohashi; H Kimura; K Takeshita; T Uruga; T Mochizuki; Y Kohmura; M Kuroda; M Yamamoto; Y Furukawa; N Kamiya; T Ishikawa
Journal:  J Synchrotron Radiat       Date:  1998-07-01       Impact factor: 2.616

7.  An automated system to mount cryo-cooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot.

Authors:  Aina E Cohen; Paul J Ellis; Mitchell D Miller; Ashley M Deacon; R Paul Phizackerley
Journal:  J Appl Crystallogr       Date:  2002-12       Impact factor: 3.304

8.  Structural genomics projects in Japan.

Authors:  S Yokoyama; H Hirota; T Kigawa; T Yabuki; M Shirouzu; T Terada; Y Ito; Y Matsuo; Y Kuroda; Y Nishimura; Y Kyogoku; K Miki; R Masui; S Kuramitsu
Journal:  Nat Struct Biol       Date:  2000-11

9.  Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.

Authors:  Tetsuya Hori; Takehiko Yokomizo; Hideo Ago; Mitsuaki Sugahara; Go Ueno; Masaki Yamamoto; Takashi Kumasaka; Takao Shimizu; Masashi Miyano
Journal:  J Biol Chem       Date:  2004-03-08       Impact factor: 5.157

10.  Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.

Authors:  Sachiko Yoshiba; Takushi Ooga; Noriko Nakagawa; Takehiko Shibata; Yorinao Inoue; Shigeyuki Yokoyama; Seiki Kuramitsu; Ryoji Masui
Journal:  J Biol Chem       Date:  2004-06-21       Impact factor: 5.157
  10 in total
  41 in total

1.  Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8.

Authors:  Sakiko Suzuki; Hisaaki Yanai; Mayumi Kanagawa; Satoko Tamura; Yuzo Watanabe; Kyotaro Fuse; Seiki Baba; Gen-ichi Sampei; Gota Kawai
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-12-24

2.  Transcriptional repression mediated by a TetR family protein, PfmR, from Thermus thermophilus HB8.

Authors:  Yoshihiro Agari; Keiko Sakamoto; Seiki Kuramitsu; Akeo Shinkai
Journal:  J Bacteriol       Date:  2012-06-29       Impact factor: 3.490

3.  Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family.

Authors:  Yoshifumi Maeda; Daiju Doubayashi; Takumi Ootake; Masaya Oki; Bunzo Mikami; Hiroyuki Uchida
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-08-26

4.  Structure of a UPF0150-family protein from Thermus thermophilus HB8.

Authors:  Nobuo Okazaki; Maki Kumei; Miho Manzoku; Seiki Kuramitsu; Mikako Shirouzu; Akeo Shinkai; Shigeyuki Yokoyama
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-02-23

5.  Purification, crystallization and preliminary X-ray diffraction study on pyrimidine nucleoside phosphorylase TTHA1771 from Thermus thermophilus HB8.

Authors:  Katsumi Shimizu; Naoki Kunishima
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-03-12

6.  Purification, crystallization and preliminary X-ray analysis of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8.

Authors:  Hisashi Mizutani; Naoki Kunishima
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-08-31

7.  High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center.

Authors:  Michihiro Sugahara; Yukuhiko Asada; Katsumi Shimizu; Hitoshi Yamamoto; Neratur K Lokanath; Hisashi Mizutani; Bagautdin Bagautdinov; Yoshinori Matsuura; Midori Taketa; Yuichi Kageyama; Naoko Ono; Yuko Morikawa; Yukiko Tanaka; Hiroki Shimada; Takanobu Nakamoto; Mitsuaki Sugahara; Masaki Yamamoto; Naoki Kunishima
Journal:  J Struct Funct Genomics       Date:  2008-08-02

8.  Structure of putative CutA1 from Homo sapiens determined at 2.05 A resolution.

Authors:  Bagautdin Bagautdinov; Yoshinori Matsuura; Svetlana Bagautdinova; Naoki Kunishima; Katsuhide Yutani
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2008-04-30

9.  Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions.

Authors:  Yoshiaki Kitamura; Akio Ebihara; Yoshihiro Agari; Akeo Shinkai; Ken Hirotsu; Seiki Kuramitsu
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

10.  Crystallization and preliminary X-ray analysis of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum.

Authors:  Koji Nishikawa; Yasuhito Shomura; Shinji Kawasaki; Youichi Niimura; Yoshiki Higuchi
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2009-12-25
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