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5D9B
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BU of 5d9b by Molmil
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
5D9D
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BU of 5d9d by Molmil
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
5D9C
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BU of 5d9c by Molmil
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
5GTQ
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BU of 5gtq by Molmil
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
5XFE
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BU of 5xfe by Molmil
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
3B07
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BU of 3b07 by Molmil
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
3A6J
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BU of 3a6j by Molmil
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
3A6D
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BU of 3a6d by Molmil
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
3A6F
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BU of 3a6f by Molmil
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
3A6K
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BU of 3a6k by Molmil
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
3A6E
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BU of 3a6e by Molmil
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
3A6L
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BU of 3a6l by Molmil
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
3A6H
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BU of 3a6h by Molmil
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
3A6G
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BU of 3a6g by Molmil
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
8CKA
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BU of 8cka by Molmil
Deinococcus radidurans HPI S-layer
Descriptor: Hexagonally packed intermediate-layer surface protein
Authors:von Kuegelgen, A, Yamashita, K, Murshudov, G, Bharat, T.
Deposit date:2023-02-14
Release date:2023-04-19
Last modified:2023-04-26
Method:ELECTRON MICROSCOPY (2.54 Å)
Cite:Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans.
Proc.Natl.Acad.Sci.USA, 120, 2023
5X1B
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BU of 5x1b by Molmil
CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center
Descriptor: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
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
5X19
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BU of 5x19 by Molmil
CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center
Descriptor: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
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:2023-11-22
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
5X1F
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BU of 5x1f by Molmil
CO bound cytochrome c oxidase without pump laser irradiation at 278K
Descriptor: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ...
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:2023-11-22
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
7OWG
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BU of 7owg by Molmil
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
2A6W
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BU of 2a6w by Molmil
Crystal structure of Emp46p carbohydrate recognition domain (CRD), metal-free form
Descriptor: Emp46p
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S.
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
2A71
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BU of 2a71 by Molmil
Crystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form
Descriptor: Emp47p
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S.
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
2A6Y
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BU of 2a6y by Molmil
Crystal structure of Emp47p carbohydrate recognition domain (CRD), tetragonal crystal form
Descriptor: Emp47p (form1), SULFATE ION
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S.
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.42 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
2A6V
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BU of 2a6v by Molmil
Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form
Descriptor: 1,2-ETHANEDIOL, Emp46p, POTASSIUM ION
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S.
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
2A6Z
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BU of 2a6z by Molmil
Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1
Descriptor: Emp47p (form2)
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S.
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
2A6X
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BU of 2a6x by Molmil
Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant
Descriptor: 1,2-ETHANEDIOL, Emp46p, POTASSIUM ION
Authors:Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2005-07-04
Release date:2006-01-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006

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