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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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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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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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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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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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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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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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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6CSM
| Crystal structure of the natural light-gated anion channel GtACR1 | Descriptor: | GtACR1, OLEIC ACID, RETINAL | Authors: | Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K. | Deposit date: | 2018-03-21 | Release date: | 2018-09-05 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature, 561, 2018
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6CSN
| Crystal structure of the designed light-gated anion channel iC++ at pH8.5 | Descriptor: | CHLORIDE ION, OLEIC ACID, RETINAL, ... | Authors: | Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K. | Deposit date: | 2018-03-21 | Release date: | 2018-09-05 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature, 561, 2018
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6CSO
| Crystal structure of the designed light-gated anion channel iC++ at pH6.5 | Descriptor: | OLEIC ACID, RETINAL, iC++ | Authors: | Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K. | Deposit date: | 2018-03-21 | Release date: | 2018-09-05 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Structural mechanisms of selectivity and gating in anion channelrhodopsins. Nature, 561, 2018
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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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5WS3
| Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA | Descriptor: | N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, ... | Authors: | Suno, R, Kimura, K, Nakane, T, Yamashita, K, Wang, J, Fujiwara, T, Yamanaka, Y, Im, D, Tsujimoto, H, Sasanuma, M, Horita, S, Hirokawa, T, Nango, E, Tono, K, Kameshima, T, Hatsui, T, Joti, Y, Yabashi, M, Shimamoto, K, Yamamoto, M, Rosenbaum, D.M, Iwata, S, Shimamura, T, Kobayashi, T. | Deposit date: | 2016-12-05 | Release date: | 2017-12-13 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. Structure, 26, 2018
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5WQC
| Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8. | Descriptor: | N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, ... | Authors: | Suno, R, Hirata, K, Yamashita, K, Tsujimoto, H, Sasanuma, M, Horita, S, Yamamoto, M, Rosenbaum, D.M, Iwata, S, Shimamura, T, Kobayashi, T. | Deposit date: | 2016-11-25 | Release date: | 2017-11-29 | Last modified: | 2018-01-17 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA Structure, 26, 2018
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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: | 2024-07-17 | 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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4UB8
| Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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4UB6
| Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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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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