5D9B
 
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, 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: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | 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
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5D9D
 | | Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, 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: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2024-03-20 | | 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
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5D9C
 | | Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, 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: | 2015-08-18 | | Release date: | 2015-09-23 | | Last modified: | 2023-09-06 | | 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
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5GTQ
 | | Luciferin-regenerating enzyme at cryogenic temperature | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | 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 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.13 Å) | | Cite: | Luciferin-regenerating enzyme at cryogenic temperature
To Be Published
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5XFE
 | | Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, 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: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
IUCrJ, 4, 2017
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3B07
 | | Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Gamma-hemolysin component A, Gamma-hemolysin component B | | Authors: | Yamashita, K, Kawai, Y, Tanaka, Y, Yao, M, Tanaka, I. | | Deposit date: | 2011-06-06 | | Release date: | 2011-10-12 | | Last modified: | 2023-11-01 | | 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
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3A6J
 | | E122Q mutant creatininase complexed with creatine | | Descriptor: | Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-09-02 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6D
 | | Creatininase complexed with 1-methylguanidine | | Descriptor: | 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6G
 | | 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: | 2023-11-01 | | 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
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3A6F
 | | W174F mutant creatininase, Type II | | Descriptor: | CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6K
 | | The E122Q mutant creatininase, Mn-Zn type | | Descriptor: | CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-09-02 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6E
 | | W174F mutant creatininase, type I | | Descriptor: | CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6L
 | | E122Q mutant creatininase, Zn-Zn type | | Descriptor: | CHLORIDE ION, Creatinine amidohydrolase, ZINC ION | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-09-02 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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3A6H
 | | W154A mutant creatininase | | Descriptor: | CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | 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
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7OWG
 | | human DEPTOR in a complex with mutant human mTORC1 A1459P | | Descriptor: | DEP domain-containing mTOR-interacting protein, Regulatory-associated protein of mTOR, Serine/threonine-protein kinase mTOR, ... | | Authors: | Heimhalt, M, Berndt, A, Wagstaff, J, Anandapadamanaban, M, Perisic, O, Maslen, S, McLaughlin, S, Yu, W.-H, Masson, G.R, Boland, A, Ni, X, Yamashita, K, Murshudov, G.N, Skehel, M, Freund, S.M, Williams, R.L. | | Deposit date: | 2021-06-18 | | Release date: | 2021-09-08 | | Last modified: | 2022-02-23 | | Method: | ELECTRON MICROSCOPY (4.7 Å) | | Cite: | Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.
Elife, 10, 2021
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5ONX
 | | Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2017-08-04 | | Release date: | 2017-11-29 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.
IUCrJ, 5, 2018
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5ONY
 | | As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2017-08-04 | | Release date: | 2017-11-29 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.
IUCrJ, 5, 2018
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8W7N
 | | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis | | Descriptor: | Pesticidal crystal protein Cry1Aa, UNKNOWN ATOM OR ION | | Authors: | Tanaka, J, Abe, S, Hayakawa, T, Kojima, M, Yamashita, K, Hirata, K, Ueno, T. | | Deposit date: | 2023-08-31 | | Release date: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis.
Biochem.Biophys.Res.Commun., 685, 2023
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7V93
 | | Cryo-EM structure of the Cas12c2-sgRNA binary complex | | Descriptor: | cas12c2, sgRNA | | Authors: | Kurihara, N, Hirano, H, Tomita, A, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2021-08-24 | | Release date: | 2022-04-13 | | Last modified: | 2022-06-01 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structure of the type V-C CRISPR-Cas effector enzyme.
Mol.Cell, 82, 2022
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7V94
 | | Cryo-EM structure of the Cas12c2-sgRNA-target DNA ternary complex | | Descriptor: | Cas12c2, sgRNA, target DNA (non target strand), ... | | Authors: | Kurihara, N, Hirano, H, Tomita, A, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2021-08-24 | | Release date: | 2022-04-13 | | Last modified: | 2022-06-01 | | Method: | ELECTRON MICROSCOPY (2.6 Å) | | Cite: | Structure of the type V-C CRISPR-Cas effector enzyme.
Mol.Cell, 82, 2022
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5IP3
 | | Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex | | Descriptor: | DNA (5'-D(P*TP*TP*TP*TP*T)-3'), DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3'), DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3'), ... | | Authors: | Komoda, K, Narita, M, Yamashita, K, Tanaka, I, Yao, M. | | Deposit date: | 2016-03-09 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
J. Virol., 91, 2017
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5IP2
 | | Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex | | Descriptor: | Nucleoprotein, RNA (5'-D(P*UP*UP*U)-3'), RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | | Authors: | Komoda, K, Narita, M, Yamashita, K, Tanaka, I, Yao, M. | | Deposit date: | 2016-03-09 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
J. Virol., 91, 2017
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5IP1
 | | Tomato spotted wilt tospovirus nucleocapsid protein | | Descriptor: | Nucleoprotein | | Authors: | Komoda, K, Narita, M, Yamashita, K, Tanaka, I, Yao, M. | | Deposit date: | 2016-03-09 | | Release date: | 2017-03-22 | | Last modified: | 2018-03-21 | | Method: | X-RAY DIFFRACTION (2.703 Å) | | Cite: | Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus.
J. Virol., 91, 2017
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6ZAV
 | | NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX) | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2020-06-05 | | Release date: | 2021-01-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.19 Å) | | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
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6ZAR
 | | As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX) | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2020-06-05 | | Release date: | 2021-01-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
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