2ZZL
 
 | | Structure of bacteriorhodopsin's M intermediate at pH 7 | | Descriptor: | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose, ... | | Authors: | Yamamoto, M, Kouyama, T. | | Deposit date: | 2009-02-18 | | Release date: | 2009-10-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Crystal Structures of Different Substates of Bacteriorhodopsin's M Intermediate at Various pH Levels.
J.Mol.Biol., 2009
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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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7QXK
 | | As isolated MSOX movie series dataset 1 (0.4 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | Authors: | Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2022-01-26 | | Release date: | 2022-08-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7QYC
 | | As isolated MSOX movie series dataset 20 (8 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | Authors: | Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2022-01-27 | | Release date: | 2022-08-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7QY4
 | | As isolated MSOX movie series dataset 5 (2 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | Authors: | Rose, S.L, Baba, S, Okumura, H, Antonyuk, S.V, Sasaki, D, Tosha, T, Kumasaka, T, Eady, R.R, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2022-01-27 | | Release date: | 2022-08-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119, 2022
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8X37
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP | | Descriptor: | DIMETHYLALLYL S-THIOLODIPHOSPHATE, MAGNESIUM ION, Neryl-diphosphate synthase 1 | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-04-17 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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8X36
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B) | | Descriptor: | 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, DIMETHYLALLYL S-THIOLODIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-04-17 | | Method: | X-RAY DIFFRACTION (2.28 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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8X35
 | | Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A) | | Descriptor: | 1,2-ETHANEDIOL, 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Imaizumi, R, Matsuura, H, Yanai, T, Takeshita, K, Misawa, S, Yamaguchi, H, Sakai, N, Miyagi-Inoue, Y, Suenaga-Hiromori, M, Kataoka, K, Nakayama, T, Yamamoto, M, Takahashi, S, Yamashita, S. | | Deposit date: | 2023-11-12 | | Release date: | 2024-02-07 | | Last modified: | 2024-04-17 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato.
Chembiochem, 25, 2024
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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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5H6M
 | | DNA targeting ADP-ribosyltransferase Pierisin-1 | | Descriptor: | 1,2-ETHANEDIOL, Pierisin-1 | | Authors: | Oda, T, Hirabayashi, H, Shikauchi, G, Takamura, R, Hiraga, K, Minami, H, Hashimoto, H, Yamamoto, M, Wakabayashi, K, Sugimura, T, Shimizu, T, Sato, M. | | Deposit date: | 2016-11-14 | | Release date: | 2017-08-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1
J. Biol. Chem., 292, 2017
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5H6J
 | | DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-NAD+ | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, Pierisin-1 | | Authors: | Oda, T, Hirabayashi, H, Shikauchi, G, Takamura, R, Hiraga, K, Minami, H, Hashimoto, H, Yamamoto, M, Wakabayashi, K, Sugimura, T, Shimizu, T, Sato, M. | | Deposit date: | 2016-11-14 | | Release date: | 2017-08-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1
J. Biol. Chem., 292, 2017
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4EFM
 | | Crystal structure of H-Ras G12V in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | 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
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4EFN
 | | Crystal structure of H-Ras Q61L in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | 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
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4EFL
 | | Crystal structure of H-Ras WT in complex with GppNHp (state 1) | | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | | Authors: | Muraoka, S, Shima, F, Araki, M, Inoue, T, Yoshimoto, A, Ijiri, Y, Seki, N, Tamura, A, Kumasaka, T, Yamamoto, M, Kataoka, T. | | Deposit date: | 2012-03-30 | | Release date: | 2012-05-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | 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
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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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6ZAW
 | | Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | | 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 (1.3 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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6ZAX
 | | Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy) | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | 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 (1.48 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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6ZAU
 | | Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | 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 (1.3 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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8ILL
 | | Crystal structure of a highly photostable and bright green fluorescent protein at pH5.6 | | Descriptor: | CHLORIDE ION, alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose, green fluorescent protein | | Authors: | Ago, H, Ando, R, Hirano, M, Shimozono, S, Miyawaki, A, Yamamoto, M. | | Deposit date: | 2023-03-03 | | Release date: | 2023-10-04 | | Last modified: | 2024-04-17 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | StayGold variants for molecular fusion and membrane-targeting applications.
Nat.Methods, 2023
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6ZAS
 | | Damage-free as-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, SULFATE ION | | 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 (1.3 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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8ILK
 | | Crystal structure of a highly photostable and bright green fluorescent protein at pH8.5 | | Descriptor: | CHLORIDE ION, Green FLUORESCENT PROTEIN | | Authors: | Ago, H, Ando, R, Hirano, M, Shimozono, S, Miyawaki, A, Yamamoto, M. | | Deposit date: | 2023-03-03 | | Release date: | 2023-10-04 | | Last modified: | 2024-04-17 | | Method: | X-RAY DIFFRACTION (1.56 Å) | | Cite: | StayGold variants for molecular fusion and membrane-targeting applications.
Nat.Methods, 2023
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6ZAT
 | | Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.0 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 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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