Literature DB >> 34605440

Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase.

Takeshi Murakawa1, Mamoru Suzuki2, Toshi Arima3, Michihiro Sugahara3, Tomoyuki Tanaka3, Rie Tanaka3, So Iwata3, Eriko Nango3, Kensuke Tono3, Hideyuki Hayashi4, Kenji Fukui1, Takato Yano1, Katsuyuki Tanizawa5, Toshihide Okajima4.   

Abstract

Recent advances in serial femtosecond X-ray crystallography (SFX) using X-ray free-electron lasers have paved the way for determining radiation-damage-free protein structures under nonfreezing conditions. However, the large-scale preparation of high-quality microcrystals of uniform size is a prerequisite for SFX, and this has been a barrier to its widespread application. Here, a convenient method for preparing high-quality microcrystals of a bacterial quinoprotein enzyme, copper amine oxidase from Arthrobacter globiformis, is reported. The method consists of the mechanical crushing of large crystals (5-15 mm3), seeding the crushed crystals into the enzyme solution and standing for 1 h at an ambient temperature of ∼26°C, leading to the rapid formation of microcrystals with a uniform size of 3-5 µm. The microcrystals diffracted X-rays to a resolution beyond 2.0 Å in SFX measurements at the SPring-8 Angstrom Compact Free Electron Laser facility. The damage-free structure determined at 2.2 Å resolution was essentially identical to that determined previously by cryogenic crystallography using synchrotron X-ray radiation.

Entities:  

Keywords:  X-ray free-electron lasers; copper amine oxidase; microcrystals; radiation-damage-free protein structure; serial femtosecond X-ray crystallography

Mesh:

Substances:

Year:  2021        PMID: 34605440      PMCID: PMC8488853          DOI: 10.1107/S2053230X21008967

Source DB:  PubMed          Journal:  Acta Crystallogr F Struct Biol Commun        ISSN: 2053-230X            Impact factor:   1.072


  32 in total

1.  Potential for biomolecular imaging with femtosecond X-ray pulses.

Authors:  R Neutze; R Wouts; D van der Spoel; E Weckert; J Hajdu
Journal:  Nature       Date:  2000-08-17       Impact factor: 49.962

2.  Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.

Authors:  Michihiro Suga; Fusamichi Akita; Michihiro Sugahara; Minoru Kubo; Yoshiki Nakajima; Takanori Nakane; Keitaro Yamashita; Yasufumi Umena; Makoto Nakabayashi; Takahiro Yamane; Takamitsu Nakano; Mamoru Suzuki; Tetsuya Masuda; Shigeyuki Inoue; Tetsunari Kimura; Takashi Nomura; Shinichiro Yonekura; Long-Jiang Yu; Tomohiro Sakamoto; Taiki Motomura; Jing-Hua Chen; Yuki Kato; Takumi Noguchi; Kensuke Tono; Yasumasa Joti; Takashi Kameshima; Takaki Hatsui; Eriko Nango; Rie Tanaka; Hisashi Naitow; Yoshinori Matsuura; Ayumi Yamashita; Masaki Yamamoto; Osamu Nureki; Makina Yabashi; Tetsuya Ishikawa; So Iwata; Jian-Ren Shen
Journal:  Nature       Date:  2017-02-20       Impact factor: 49.962

3.  Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Authors:  Kunio Hirata; Kyoko Shinzawa-Itoh; Naomine Yano; Shuhei Takemura; Koji Kato; Miki Hatanaka; Kazumasa Muramoto; Takako Kawahara; Tomitake Tsukihara; Eiki Yamashita; Kensuke Tono; Go Ueno; Takaaki Hikima; Hironori Murakami; Yuichi Inubushi; Makina Yabashi; Tetsuya Ishikawa; Masaki Yamamoto; Takashi Ogura; Hiroshi Sugimoto; Jian-Ren Shen; Shinya Yoshikawa; Hideo Ago
Journal:  Nat Methods       Date:  2014-05-11       Impact factor: 28.547

4.  Role of copper ion in bacterial copper amine oxidase: spectroscopic and crystallographic studies of metal-substituted enzymes.

Authors:  Sei'ichiro Kishishita; Toshihide Okajima; Misa Kim; Hiroshi Yamaguchi; Shun Hirota; Shinnichiro Suzuki; Shun'ichi Kuroda; Katsuyuki Tanizawa; Minae Mure
Journal:  J Am Chem Soc       Date:  2003-01-29       Impact factor: 15.419

5.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

6.  X-ray snapshots of quinone cofactor biogenesis in bacterial copper amine oxidase.

Authors:  Misa Kim; Toshihide Okajima; Seiichiro Kishishita; Megumi Yoshimura; Asako Kawamori; Katsuyuki Tanizawa; Hiroshi Yamaguchi
Journal:  Nat Struct Biol       Date:  2002-08

7.  Data acquisition system for X-ray free-electron laser experiments at SACLA.

Authors:  Yasumasa Joti; Takashi Kameshima; Mitsuhiro Yamaga; Takashi Sugimoto; Kensuke Okada; Toshinori Abe; Yukito Furukawa; Toru Ohata; Ryotaro Tanaka; Takaki Hatsui; Makina Yabashi
Journal:  J Synchrotron Radiat       Date:  2015-04-17       Impact factor: 2.616

8.  Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laser.

Authors:  Kensuke Tono; Eriko Nango; Michihiro Sugahara; Changyong Song; Jaehyun Park; Tomoyuki Tanaka; Rie Tanaka; Yasumasa Joti; Takashi Kameshima; Shun Ono; Takaki Hatsui; Eiichi Mizohata; Mamoru Suzuki; Tatsuro Shimamura; Yoshiki Tanaka; So Iwata; Makina Yabashi
Journal:  J Synchrotron Radiat       Date:  2015-04-16       Impact factor: 2.616

9.  XGANDALF - extended gradient descent algorithm for lattice finding.

Authors:  Yaroslav Gevorkov; Oleksandr Yefanov; Anton Barty; Thomas A White; Valerio Mariani; Wolfgang Brehm; Aleksandra Tolstikova; Rolf Rainer Grigat; Henry N Chapman
Journal:  Acta Crystallogr A Found Adv       Date:  2019-08-30       Impact factor: 2.290

10.  Recent developments in CrystFEL.

Authors:  Thomas A White; Valerio Mariani; Wolfgang Brehm; Oleksandr Yefanov; Anton Barty; Kenneth R Beyerlein; Fedor Chervinskii; Lorenzo Galli; Cornelius Gati; Takanori Nakane; Alexandra Tolstikova; Keitaro Yamashita; Chun Hong Yoon; Kay Diederichs; Henry N Chapman
Journal:  J Appl Crystallogr       Date:  2016-03-29       Impact factor: 3.304

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