Access the full text.
Sign up today, get DeepDyve free for 14 days.
K. Tono, E. Nango, M. Sugahara, Changyong Song, Jaehyun Park, Tomoyuki Tanaka, Rie Tanaka, Y. Joti, T. Kameshima, S. Ono, T. Hatsui, E. Mizohata, Mamoru Suzuki, T. Shimamura, Yoshiki Tanaka, S. Iwata, M. Yabashi (2015)
Diverse application platform for hard X-ray diffraction in SACLA (DAPHNIS): application to serial protein crystallography using an X-ray free-electron laserJournal of Synchrotron Radiation, 22
T. Nakane, Y. Joti, K. Tono, M. Yabashi, E. Nango, S. Iwata, R. Ishitani, O. Nureki (2016)
Data processing pipeline for serial femtosecond crystallography at SACLA1Journal of Applied Crystallography, 49
T. Kameshima, S. Ono, T. Kudo, K. Ozaki, Y. Kirihara, Kazuo Kobayashi, Y. Inubushi, M. Yabashi, T. Horigome, A. Holland, K. Holland, D. Burt, H. Murao, T. Hatsui (2014)
Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments.The Review of scientific instruments, 85 3
R. Neutze, R. Wouts, D. Spoel, E. Weckert, J. Hajdu (2000)
Potential for biomolecular imaging with femtosecond X-ray pulsesNature, 406
D. Liebschner, P. Afonine, M. Baker, G. Bunkoczi, Vincent Chen, T. Croll, B. Hintze, L. Hung, Swati Jain, A. Mccoy, N. Moriarty, R. Oeffner, B. Poon, M. Prisant, R. Read, J. Richardson, D. Richardson, M. Sammito, O. Sobolev, Duncan Stockwell, T. Terwilliger, A. Urzhumtsev, Lizbeth Videau, Christopher Williams, P. Adams (2019)
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in PhenixActa Crystallographica. Section D, Structural Biology, 75
K. Pande, C. Hutchison, G. Groenhof, A. Aquila, J. Robinson, J. Tenboer, S. Basu, S. Boutet, D. DePonte, M. Liang, T. White, N. Zatsepin, O. Yefanov, D. Morozov, D. Oberthuer, C. Gati, G. Subramanian, Daniel James, Yun Zhao, J. Koralek, Jennifer Brayshaw, Christopher Kupitz, C. Conrad, Shatabdi Roy-Chowdhury, J. Coe, M. Metz, P. Xavier, T. Grant, J. Koglin, Gihan Ketawala, R. Fromme, V. Šrajer, Robert Henning, J. Spence, A. Ourmazd, P. Schwander, U. Weierstall, M. Frank, P. Fromme, A. Barty, H. Chapman, K. Moffat, J. Thor, Marius Schmidt (2016)
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow proteinScience, 352
T. Murakawa, H. Hayashi, T. Sunami, K. Kurihara, T. Tamada, R. Kuroki, Mamoru Suzuki, K. Tanizawa, T. Okajima (2013)
High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2.Acta crystallographica. Section D, Biological crystallography, 69 Pt 12
A. Mccoy, R. Grosse-Kunstleve, P. Adams, M. Winn, L. Storoni, R. Read (2007)
Phaser crystallographic softwareJournal of Applied Crystallography, 40
Y. Chiu, T. Okajima, T. Murakawa, M. Uchida, M. Taki, S. Hirota, Misa Kim, H. Yamaguchi, Y. Kawano, N. Kamiya, S. Kuroda, H. Hayashi, Yukio Yamamoto*, K. Tanizawa (2006)
Kinetic and structural studies on the catalytic role of the aspartic acid residue conserved in copper amine oxidase.Biochemistry, 45 13
Y. Joti, T. Kameshima, M. Yamaga, T. Sugimoto, K. Okada, T. Abe, Y. Furukawa, T. Ohata, R. Tanaka, T. Hatsui, M. Yabashi (2015)
Data acquisition system for X-ray free-electron laser experiments at SACLAJournal of Synchrotron Radiation, 22
O. Yefanov, V. Mariani, C. Gati, T. White, H. Chapman, A. Barty (2015)
Accurate determination of segmented X-ray detector geometry.Optics express, 23 22
J. Tenboer, S. Basu, N. Zatsepin, K. Pande, D. Milathianaki, M. Frank, M. Hunter, S. Boutet, Garth Williams, J. Koglin, D. Oberthuer, M. Heymann, Christopher Kupitz, C. Conrad, J. Coe, Shatabdi Roy-Chowdhury, U. Weierstall, Daniel James, Dingjie Wang, T. Grant, A. Barty, O. Yefanov, J. Scales, C. Gati, C. Seuring, V. Šrajer, R. Henning, P. Schwander, R. Fromme, A. Ourmazd, K. Moffat, J. Thor, J. Spence, P. Fromme, H. Chapman, Marius Schmidt (2014)
Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow proteinScience, 346
E. Mora, J. Lovett, C. Blanford, E. Garman, B. Valderrama, E. Rudiño-Piñera (2012)
Structural changes caused by radiation-induced reduction and radiolysis: the effect of X-ray absorbed dose in a fungal multicopper oxidase.Acta crystallographica. Section D, Biological crystallography, 68 Pt 5
M. Suga, F. Akita, M. Sugahara, M. Kubo, Y. Nakajima, T. Nakane, K. Yamashita, Y. Umena, M. Nakabayashi, Takahiro Yamane, T. Nakano, Mamoru Suzuki, T. Masuda, S. Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, T. Motomura, Jing-Hua Chen, Yuki Kato, T. Noguchi, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, E. Nango, Rie Tanaka, H. Naitow, Y. Matsuura, Ayumi Yamashita, Masaki Yamamoto, O. Nureki, M. Yabashi, T. Ishikawa, S. Iwata, Jian-Ren Shen (2017)
Light-induced structural changes and the site of O=O bond formation in PSII caught by XFELNature, 543
J. Stagno, Y. Liu, Y. Bhandari, C. Conrad, S. Panja, M. Swain, L. Fan, G. Nelson, C. Li, D. Wendel, T. White, J. Coe, M. Wiedorn, J. Knoška, D. Oberthuer, R. Tuckey, P. Yu, M. Dyba, S. Tarasov, U. Weierstall, T. Grant, C. Schwieters, J. Zhang, A. Ferré-D’Amaré, P. Fromme, D. Draper, M. Liang, M. Hunter, S. Boutet, K. Tan, X. Zuo, X. Ji, A. Barty, N. Zatsepin, H. Chapman, J. Spence, S. Woodson, Y. Wang (2016)
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallographyNature, 541
C. Lomelino, Jin Kim, Cheol Lee, S. Lim, J. Andring, B. Mahon, M. Chung, Chae Kim, R. McKenna (2018)
Carbonic anhydrase II microcrystals suitable for XFEL studies.Acta crystallographica. Section F, Structural biology communications, 74 Pt 6
T. Murakawa, K. Kurihara, M. Shoji, C. Shibazaki, T. Sunami, T. Tamada, N. Yano, Taro Yamada, K. Kusaka, Mamoru Suzuki, Y. Shigeta, R. Kuroki, H. Hayashi, T. Yano, K. Tanizawa, M. Adachi, T. Okajima (2020)
Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharingProceedings of the National Academy of Sciences, 117
Yoshiaki Shimazu, K. Tono, Tomoyuki Tanaka, Y. Yamanaka, T. Nakane, C. Mori, Kanako Kimura, T. Fujiwara, M. Sugahara, Rie Tanaka, R. Doak, T. Shimamura, S. Iwata, E. Nango, M. Yabashi (2019)
High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressureJournal of Applied Crystallography, 52
T. Barends, L. Foucar, A. Ardèvol, K. Nass, A. Aquila, S. Botha, R. Doak, K. Falahati, E. Hartmann, M. Hilpert, M. Heinz, M. Hoffmann, Jürgen Köfinger, J. Koglin, G. Kovácsová, M. Liang, D. Milathianaki, H. Lemke, J. Reinstein, C. Roome, R. Shoeman, Garth Williams, I. Burghardt, G. Hummer, S. Boutet, I. Schlichting (2015)
Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociationScience, 350
P. Emsley, B. Lohkamp, William Scott, K. Cowtan (2010)
Features and development of CootActa Crystallographica Section D: Biological Crystallography, 66
M. Sugahara, E. Mizohata, E. Nango, Mamoru Suzuki, Tomoyuki Tanaka, T. Masuda, Rie Tanaka, T. Shimamura, Yoshiki Tanaka, C. Suno, K. Ihara, D. Pan, K. Kakinouchi, S. Sugiyama, M. Murata, Tsuyoshi Inoue, K. Tono, Changyong Song, Jaehyun Park, T. Kameshima, T. Hatsui, Y. Joti, M. Yabashi, S. Iwata (2014)
Grease matrix as a versatile carrier of proteins for serial crystallographyNature Methods, 12
H. Yumoto, H. Mimura, T. Koyama, S. Matsuyama, K. Tono, T. Togashi, Y. Inubushi, Takahiro Sato, Takashi Tanaka, T. Kimura, H. Yokoyama, Jangwoo Kim, Y. Sano, Y. Hachisu, M. Yabashi, H. Ohashi, H. Ohmori, T. Ishikawa, K. Yamauchi (2012)
Focusing of X-ray free-electron laser pulses with reflective opticsNature Photonics, 7
M. Sugahara, T. Nakane, T. Masuda, Mamoru Suzuki, S. Inoue, Changyong Song, Rie Tanaka, T. Nakatsu, E. Mizohata, F. Yumoto, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, O. Nureki, K. Numata, E. Nango, S. Iwata (2017)
Hydroxyethyl cellulose matrix applied to serial crystallographyScientific Reports, 7
H. Chapman, P. Fromme, A. Barty, T. White, R. Kirian, A. Aquila, M. Hunter, J. Schulz, D. DePonte, U. Weierstall, R. Doak, F. Maia, Andrew Martin, I. Schlichting, L. Lomb, N. Coppola, R. Shoeman, S. Epp, R. Hartmann, D. Rolles, A. Rudenko, L. Foucar, N. Kimmel, G. Weidenspointner, P. Holl, M. Liang, M. Barthelmess, C. Caleman, S. Boutet, M. Bogan, J. Krzywiński, C. Bostedt, S. Bajt, L. Gumprecht, B. Rudek, B. Erk, C. Schmidt, A. Hömke, C. Reich, D. Pietschner, L. Strüder, G. Hauser, H. Gorke, J. Ullrich, S. Herrmann, G. Schaller, F. Schopper, H. Soltau, K. Kühnel, M. Messerschmidt, J. Bozek, S. Hau-Riege, M. Frank, C. Hampton, R. Sierra, D. Starodub, Garth Williams, J. Hajdu, N. Tîmneanu, M. Seibert, M. Seibert, J. Andreasson, A. Rocker, Olof Jönsson, M. Svenda, S. Stern, K. Nass, R. Andritschke, C. Schröter, F. Krasniqi, M. Bott, K. Schmidt, Xiaoyu Wang, I. Grotjohann, J. Holton, T. Barends, R. Neutze, S. Marchesini, R. Fromme, S. Schorb, D. Rupp, M. Adolph, T. Gorkhover, I. Andersson, H. Hirsemann, G. Potdevin, H. Graafsma, B. Nilsson, J. Spence (2011)
Femtosecond X-ray protein nanocrystallographyNature, 470
S. Kishishita, T. Okajima, Misa Kim, H. Yamaguchi, S. Hirota, Shinnichiro Suzuki, S. Kuroda, K. Tanizawa, M. Mure (2003)
Role of copper ion in bacterial copper amine oxidase: spectroscopic and crystallographic studies of metal-substituted enzymes.Journal of the American Chemical Society, 125 4
Y. Gevorkov, O. Yefanov, A. Barty, T. White, V. Mariani, W. Brehm, A. Tolstikova, R. Grigat, H. Chapman (2019)
XGANDALF – extended gradient descent algorithm for lattice findingActa Crystallographica. Section A, Foundations and Advances, 75
T. Ishikawa, H. Aoyagi, T. Asaka, Y. Asano, N. Azumi, T. Bizen, H. Ego, K. Fukami, T. Fukui, Y. Furukawa, S. Goto, H. Hanaki, T. Hara, T. Hasegawa, T. Hatsui, A. Higashiya, T. Hirono, N. Hosoda, M. Ishii, T. Inagaki, Y. Inubushi, T. Itoga, Y. Joti, M. Kago, T. Kameshima, H. Kimura, Y. Kirihara, A. Kiyomichi, Toshiaki Kobayashi, C. Kondo, T. Kudo, H. Maesaka, X. Maréchal, T. Masuda, S. Matsubara, Takahiro Matsumoto, T. Matsushita, S. Matsui, M. Nagasono, N. Nariyama, H. Ohashi, T. Ohata, T. Ohshima, S. Ono, Y. Otake, C. Saji, T. Sakurai, Takahiro Sato, K. Sawada, T. Seike, K. Shirasawa, T. Sugimoto, Shinsuke Suzuki, S. Takahashi, H. Takebe, K. Takeshita, K. Tamasaku, Hitoshi Tanaka, R. Tanaka, Takashi Tanaka, T. Togashi, K. Togawa, Atsushi Tokuhisa, H. Tomizawa, K. Tono, S. Wu, M. Yabashi, M. Yamaga, A. Yamashita, K. Yanagida, Chaoji Zhang, T. Shintake, H. Kitamura, N. Kumagai (2012)
A compact X-ray free-electron laser emitting in the sub-ångström regionNature Photonics, 6
A. Royant, E. Nango, T. Nakane, Tomoyuki Tanaka, T. Arima, R. Neutze, S. Iwata (2016)
A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 290 ns after photoexcitation
T. White, V. Mariani, W. Brehm, O. Yefanov, A. Barty, K. Beyerlein, F. Chervinskii, L. Galli, C. Gati, T. Nakane, A. Tolstikova, K. Yamashita, C. Yoon, K. Diederichs, H. Chapman (2016)
Recent developments in CrystFEL 1Journal of Applied Crystallography, 49
J. Olmos, S. Pandey, J. Martin-Garcia, George Calvey, Andrea Katz, J. Knoška, Christopher Kupitz, M. Hunter, M. Liang, D. Oberthuer, O. Yefanov, M. Wiedorn, M. Heyman, M. Holl, K. Pande, A. Barty, Mitchell Miller, S. Stern, Shatabdi Roy-Chowdhury, J. Coe, Nirupa Nagaratnam, James Zook, Jacob Verburgt, Tyler Norwood, I. Poudyal, David Xu, J. Koglin, M. Seaberg, Yun Zhao, S. Bajt, T. Grant, V. Mariani, G. Nelson, G. Subramanian, E. Bae, R. Fromme, R. Fung, P. Schwander, M. Frank, T. White, U. Weierstall, N. Zatsepin, J. Spence, P. Fromme, H. Chapman, L. Pollack, L. Tremblay, A. Ourmazd, G. Phillips, Marius Schmidt (2017)
Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallographyBMC Biology, 16
K. Hirata, K. Shinzawa-Itoh, N. Yano, S. Takemura, Koji Kato, Miki Hatanaka, K. Muramoto, Takako Kawahara, T. Tsukihara, E. Yamashita, K. Tono, G. Ueno, T. Hikima, H. Murakami, Y. Inubushi, M. Yabashi, T. Ishikawa, Masaki Yamamoto, T. Ogura, H. Sugimoto, Jian-Ren Shen, S. Yoshikawa, H. Ago (2014)
Determination of damage-free crystal structure of an X-ray–sensitive protein using an XFELNature Methods, 11
T. Halsted, K. Yamashita, C. Gopalasingam, R. Shenoy, K. Hirata, H. Ago, G. Ueno, M. Blakeley, R. Eady, S. Antonyuk, Masaki Yamamoto, S. Hasnain (2019)
Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallographyIUCrJ, 6
R. Matsuzaki, T. Fukui, H. Sato, Y. Ozaki, K. Tanizawa (1994)
Generation of the topa quinone cofactor in bacterial monoamine oxidase by cupric ion‐dependent autooxidation of a specific tyrosyl residueFEBS Letters, 351
T. Halsted, K. Yamashita, K. Hirata, H. Ago, G. Ueno, T. Tosha, R. Eady, S. Antonyuk, Masaki Yamamoto, S. Hasnain (2018)
An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductaseIUCrJ, 5
A. Barty, R. Kirian, F. Maia, M. Hantke, C. Yoon, T. White, H. Chapman (2014)
Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction dataJournal of Applied Crystallography, 47
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.
Acta Crystallographica Section F: Structural Biology Communications – Wiley
Published: Oct 1, 2021
Keywords: serial femtosecond X‐ray crystallography
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.