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PDB: 248 件

7QY4
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As isolated MSOX movie series dataset 5 (2 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain)
分子名称: COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ...
著者Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S.
登録日2022-01-27
公開日2022-08-03
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
7QXK
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As isolated MSOX movie series dataset 1 (0.4 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain)
分子名称: COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ...
著者Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S.
登録日2022-01-26
公開日2022-08-03
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
7QYC
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As isolated MSOX movie series dataset 20 (8 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain)
分子名称: COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ...
著者Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S.
登録日2022-01-27
公開日2022-08-03
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
3AOI
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RNA polymerase-Gfh1 complex (Crystal type 2)
分子名称: Anti-cleavage anti-GreA transcription factor Gfh1, DNA (5'-D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*CP*GP*CP*AP*T)-3'), DNA-directed RNA polymerase subunit alpha, ...
著者Tagami, S, Sekine, S, Kumarevel, T, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2010-09-30
公開日2010-12-08
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (4.3 Å)
主引用文献Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
Nature, 468, 2010
3AOH
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RNA polymerase-Gfh1 complex (Crystal type 1)
分子名称: Anti-cleavage anti-GreA transcription factor Gfh1, DNA (5'-D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*AP*CP*CP*GP*CP*CP*GP*CP*AP*T)-3'), DNA-directed RNA polymerase subunit alpha, ...
著者Tagami, S, Sekine, S, Kumarevel, T, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
登録日2010-09-28
公開日2010-12-08
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (4.1 Å)
主引用文献Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
Nature, 468, 2010
5D9D
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Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
著者Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
登録日2015-08-18
公開日2015-09-23
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.701 Å)
主引用文献An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9B
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Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION
著者Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
登録日2015-08-18
公開日2015-09-23
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献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)
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
著者Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
登録日2015-08-18
公開日2015-09-23
最終更新日2023-09-06
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
4EFM
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Crystal structure of H-Ras G12V in complex with GppNHp (state 1)
分子名称: GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
著者Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T.
登録日2012-03-30
公開日2012-05-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants
Febs Lett., 586, 2012
4EFL
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Crystal structure of H-Ras WT in complex with GppNHp (state 1)
分子名称: GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
著者Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T.
登録日2012-03-30
公開日2012-05-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants
Febs Lett., 586, 2012
6M5E
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Human serum albumin with cyclic peptide dalbavancin
分子名称: (2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid, 10-METHYLUNDECANOIC ACID, 2-amino-2-deoxy-beta-D-altropyranuronic acid, ...
著者Ito, S, Senoo, A, Nagatoishi, S, Ohue, M, Yamamoto, M, Tsumoto, K, Wakui, N.
登録日2020-03-10
公開日2020-11-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
J.Med.Chem., 63, 2020
8JRD
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Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A
分子名称: 1,2-ETHANEDIOL, COENZYME A, DI(HYDROXYETHYL)ETHER, ...
著者Waki, T, Imaizumi, R, Nakata, S, Yanai, T, Takeshita, K, Sakai, N, Kataoka, K, Yamamoto, M, Nakayama, T, Yamashita, S.
登録日2023-06-16
公開日2024-06-19
最終更新日2024-07-17
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Structural insights into catalytic promiscuity of chalcone synthase from Glycine max (L.) Merr.: Coenzyme A-induced alteration of product specificity.
Biochem.Biophys.Res.Commun., 718, 2024
8KGA
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SlNDPS1-AtcPT4 Chimera
分子名称: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, Dimethylallylcistransferase CPT1, ...
著者Suenaga-Hiromori, M, Ishii, T, Imaizumi, R, Takeshita, K, Yanai, T, Matsuura, H, Sakai, N, Yamaguchi, H, Yanbe, F, Waki, T, Tozawa, Y, Miyagi-Inoue, Y, Yamamoto, M, Kataoka, K, Nakayama, T, Yamashita, S, Takahashi, S.
登録日2023-08-18
公開日2024-08-21
実験手法X-RAY DIFFRACTION (2.182 Å)
主引用文献Biosynthesising various rubber-like polymers by reconstituting prenyltransferases on Hevea rubber particles: molecular and structural bases of the versatile system
To Be Published
8KGB
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SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP
分子名称: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2, ...
著者Suenaga-Hiromori, M, Ishii, T, Imaizumi, R, Takeshita, K, Yanai, T, Matsuura, H, Sakai, N, Yamaguchi, H, Yanbe, F, Waki, T, Tozawa, Y, Miyagi-Inoue, Y, Yamamoto, M, Kataoka, K, Nakayama, T, Yamashita, S, Takahashi, S.
登録日2023-08-18
公開日2024-08-21
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.32 Å)
主引用文献A versatile system for enzymatic synthesis of natural and unnatural polyisoprenoids on rubber particles
To Be Published
6M5D
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Human serum albumin (apo form)
分子名称: PHOSPHATE ION, Serum albumin
著者Ito, S, Senoo, A, Nagatoishi, S, Yamamoto, M, Tsumoto, K, Wakui, N.
登録日2020-03-10
公開日2020-11-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural Basis for the Binding Mechanism of Human Serum Albumin Complexed with Cyclic Peptide Dalbavancin.
J.Med.Chem., 63, 2020
4UB8
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Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser
分子名称: 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, ...
著者Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R.
登録日2014-08-12
公開日2014-12-03
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
4UB6
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Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser
分子名称: 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, ...
著者Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R.
登録日2014-08-12
公開日2014-12-03
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
4EFN
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Crystal structure of H-Ras Q61L in complex with GppNHp (state 1)
分子名称: GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
著者Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T.
登録日2012-03-30
公開日2012-05-16
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants
Febs Lett., 586, 2012
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
分子名称: (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, ...
著者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.
登録日2017-01-25
公開日2017-08-09
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献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
分子名称: (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, ...
著者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.
登録日2017-01-25
公開日2017-08-09
最終更新日2017-12-06
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献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
分子名称: (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, ...
著者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.
登録日2017-01-25
公開日2017-08-09
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
1EH1
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RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS
分子名称: RIBOSOME RECYCLING FACTOR
著者Toyoda, T, Tin, O.F, Ito, K, Fujiwara, T, Kumasaka, T, Yamamoto, M, Garber, M.B, Nakamura, Y.
登録日2000-02-18
公開日2000-11-15
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.
RNA, 6, 2000
5Y5M
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SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state)
分子名称: NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE
著者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.
登録日2017-08-09
公開日2018-08-08
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
5Y5H
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SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA
分子名称: GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ...
著者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.
登録日2017-08-09
公開日2017-12-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献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)
分子名称: NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE
著者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.
登録日2017-08-09
公開日2017-12-06
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017

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