Author results

5D9B
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LUCIFERIN-REGENERATING ENZYME SOLVED BY SIRAS USING XFEL (REFINED AGAINST NATIVE DATA)
Descriptor:Luciferin regenerating enzyme, MAGNESIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL
Authors:Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9C
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LUCIFERIN-REGENERATING ENZYME SOLVED BY SIRAS USING XFEL (REFINED AGAINST HG DERIVATIVE DATA)
Descriptor:Luciferin regenerating enzyme, MAGNESIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ...
Authors:Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9D
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LUCIFERIN-REGENERATING ENZYME SOLVED BY SAD USING SYNCHROTRON RADIATION AT ROOM TEMPERATURE
Descriptor:Luciferin regenerating enzyme, MAGNESIUM ION, MERCURY (II) ION, ...
Authors:Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Method:X-RAY DIFFRACTION (1.701 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5XFE
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LUCIFERIN-REGENERATING ENZYME SOLVED BY SAD USING XFEL (REFINED AGAINST 11,000 PATTERNS)
Descriptor:Luciferin regenerating enzyme, MERCURY (II) ION, MAGNESIUM ION, ...
Authors:Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.
Deposit date:2017-04-10
Release date:2017-08-30
Last modified:2017-10-25
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
IUCrJ, 4, 2017
5GTQ
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LUCIFERIN-REGENERATING ENZYME AT CRYOGENIC TEMPERATURE
Descriptor:Luciferin regenerating enzyme, MERCURY (II) ION, MAGNESIUM ION, ...
Authors:Yamashita, K., Murai, T., Yamamoto, M., Gomi, K., Kajiyama, N., Kato, H., Nakatsu, T.
Deposit date:2016-08-23
Release date:2016-11-09
Method:X-RAY DIFFRACTION (1.13 Å)
Cite:Luciferin-regenerating enzyme at cryogenic temperature
To Be Published
3B07
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CRYSTAL STRUCTURE OF OCTAMERIC PORE FORM OF GAMMA-HEMOLYSIN FROM STAPHYLOCOCCUS AUREUS
Descriptor:Gamma-hemolysin component B, Gamma-hemolysin component A, (4S)-2-METHYL-2,4-PENTANEDIOL
Authors:Yamashita, K., Kawai, Y., Tanaka, Y., Yao, M., Tanaka, I.
Deposit date:2011-06-06
Release date:2011-10-12
Last modified:2011-12-21
Method:X-RAY DIFFRACTION (2.495 Å)
Cite:Crystal structure of the octameric pore of staphylococcal gamma-hemolysin reveals the beta-barrel pore formation mechanism by two components
Proc.Natl.Acad.Sci.USA, 108, 2011
3A6D
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CREATININASE COMPLEXED WITH 1-METHYLGUANIDINE
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6E
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W174F MUTANT CREATININASE, TYPE I
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6F
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W174F MUTANT CREATININASE, TYPE II
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6G
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W154F MUTANT CREATININASE
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6H
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W154A MUTANT CREATININASE
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6J
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E122Q MUTANT CREATININASE COMPLEXED WITH CREATINE
Descriptor:Creatinine amidohydrolase, ZINC ION, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6K
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THE E122Q MUTANT CREATININASE, MN-ZN TYPE
Descriptor:Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION, ...
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6L
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E122Q MUTANT CREATININASE, ZN-ZN TYPE
Descriptor:Creatinine amidohydrolase, ZINC ION, CHLORIDE ION
Authors:Nakajima, Y., Yamashita, K., Ito, K., Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2014-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
5X19
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CO BOUND CYTOCHROME C OXIDASE AT 100 MICRO SEC AFTER PUMP LASER IRRADIATION TO RELEASE CO FROM O2 REDUCTION CENTER
Descriptor:Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, Cytochrome c oxidase subunit 3, ...
Authors:Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.
Deposit date:2017-01-25
Release date:2017-08-09
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
5X1B
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CO BOUND CYTOCHROME C OXIDASE AT 20 NSEC AFTER PUMP LASER IRRADIATION TO RELEASE CO FROM O2 REDUCTION CENTER
Descriptor:Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, Cytochrome c oxidase subunit 3, ...
Authors:Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.
Deposit date:2017-01-25
Release date:2017-08-09
Last modified:2017-12-06
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
5X1F
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CO BOUND CYTOCHROME C OXIDASE WITHOUT PUMP LASER IRRADIATION AT 278K
Descriptor:Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, Cytochrome c oxidase subunit 3, ...
Authors:Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.
Deposit date:2017-01-25
Release date:2017-08-09
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
5Y5H
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SF-ROX STRUCTURE OF CYTOCHROME P450NOR (NO-BOUND STATE) DETERMINED AT SACLA
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ...
Authors:Tosha, T., Nomura, T., Nishida, T., Yamagiwa, R., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Yamashita, A., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5I
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TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: 20 MS AFTER PHOTO-IRRADIATION OF CAGED NO IN THE PRESENCE OF NADH (NO-BOUND STATE), LIGHT DATA
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ...
Authors:Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5J
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TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: DARK-2 DATA IN THE PRESENCE OF NADH (RESTING STATE)
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL
Authors:Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Method:X-RAY DIFFRACTION (2 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5K
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TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR : 20 MS AFTER PHOTO-IRRADIATION OF CAGED NO IN THE ABSENCE OF NADH (NO-BOUND STATE), LIGHT DATA
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE
Authors:Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5L
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TIME-RESOLVED SFX STRUCTURE OF CYTOCHROME P450NOR: DARK-2 DATA IN THE ABSENCE OF NADH (RESTING STATE)
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE
Authors:Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5M
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SFX STRUCTURE OF CYTOCHROME P450NOR: A COMPLETE DARK DATA WITHOUT PUMP LASER (RESTING STATE)
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE
Authors:Tosha, T., Nomura, T., Nishida, T., Saeki, N., Okubayashi, K., Yamagiwa, R., Sugahara, M., Nakane, T., Yamashita, K., Hirata, K., Ueno, G., Kimura, T., Hisano, T., Muramoto, K., Sawai, H., Takeda, H., Mizohata, E., Yamashita, A., Kanematsu, Y., Takano, Y., Nango, E., Tanaka, R., Nureki, O., Ikemoto, Y., Murakami, H., Owada, S., Tono, K., Yabashi, M., Yamamoto, M., Ago, H., Iwata, S., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2018-08-08
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5F
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STRUCTURE OF CYTOCHROME P450NOR IN NO-BOUND STATE: DAMAGED BY LOW-DOSE (0.72 MGY) X-RAY
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ...
Authors:Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Last modified:2018-09-19
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5G
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STRUCTURE OF CYTOCHROME P450NOR IN NO-BOUND STATE: DAMAGED BY LOW-DOSE (0.72 MGY) X-RAY
Descriptor:NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ...
Authors:Tosha, T., Nomura, T., Nishida, T., Ueno, G., Murakami, H., Yamashita, K., Hirata, K., Yamamoto, M., Ago, H., Sugimoto, H., Shiro, Y., Kubo, M.
Deposit date:2017-08-09
Release date:2017-12-06
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017