2PJZ
 
 | | The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066 | | Descriptor: | Hypothetical protein ST1066, SULFATE ION | | Authors: | Hirata, K, Hasegawa, K, Ebihara, A, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-04-17 | | Release date: | 2008-04-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066
To be Published
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1WUA
 | | The structure of Aplyronine A-actin complex | | Descriptor: | (8R,9R,10R,11R,14S,18S,20S,24S)-24-{(1R,2S,3R,6R,7R,8R,9S,10E)-8-(ACETYLOXY)-6-[(N,N-DIMETHYLALANYL)OXY]-11-[FORMYL(MET HYL)AMINO]-2-HYDROXY-1,3,7,9-TETRAMETHYLUNDEC-10-ENYL}-10-HYDROXY-14,20-DIMETHOXY-9,11,15,18-TETRAMETHYL-2-OXOOXACYCLOTE TRACOSA-3,5,15,21-TETRAEN-8-YL N,N,O-TRIMETHYLSERINATE, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | | Authors: | Hirata, K, Muraoka, S, Suenaga, K, Kuroda, T, Kato, K, Tanaka, H, Yamamoto, M, Takata, M, Yamada, K, Kigoshi, H. | | Deposit date: | 2004-12-03 | | Release date: | 2006-02-14 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structure basis for antitumor effect of aplyronine a
J.Mol.Biol., 356, 2006
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3WG7
 | | A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography | | 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: | Hirata, K, Shinzawa-Itoh, K, Yano, N, Takemura, S, Kato, K, Hatanaka, M, Muramoto, K, Kawahara, T, Tsukihara, T, Yamashita, E, Tono, K, Ueno, G, Hikima, T, Murakami, H, Inubushi, Y, Yabashi, M, Ishikawa, T, Yamamoto, M, Ogura, T, Sugimoto, H, Shen, J.R, Yoshikawa, S, Ago, H. | | Deposit date: | 2013-07-29 | | Release date: | 2014-04-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
Nat.Methods, 11, 2014
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6E67
 | | Structure of beta2 adrenergic receptor fused to a Gs peptide | | Descriptor: | 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one, Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera | | Authors: | Liu, X, Xu, X, Hilger, D, Tiemann, J, Liu, H, Du, Y, Hirata, K, Sun, X, Guixa-Gonzalez, R, Mathiesen, J, Hildebrand, P, Kobilka, B. | | Deposit date: | 2018-07-24 | | Release date: | 2019-06-05 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Structural Insights into the Process of GPCR-G Protein Complex Formation.
Cell, 177, 2019
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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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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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5X1B
 | | 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
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5X19
 | | 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
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7XWS
 | | Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis with small volume | | Descriptor: | ACETYL GROUP, CHLORIDE ION, Polyhedrin | | Authors: | Abe, S, Tanaka, J, Kojima, M, Hirata, K, Yamashita, K, Ueno, T. | | Deposit date: | 2022-05-27 | | Release date: | 2023-02-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Cell-free protein crystallization for nanocrystal structure determination.
Sci Rep, 12, 2022
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8J2Q
 | | Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment | | Descriptor: | Polyhedrin,Myc proto-oncogene protein | | Authors: | Kojima, M, Ueno, T, Abe, S, Hirata, K. | | Deposit date: | 2023-04-15 | | Release date: | 2024-04-17 | | Last modified: | 2024-07-03 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization.
Proc.Natl.Acad.Sci.USA, 121, 2024
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8JAE
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7Y44
 | | Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution | | 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: | Tsukihara, T, Hirata, K, Ago, H. | | Deposit date: | 2022-06-14 | | Release date: | 2022-07-20 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
Nat.Methods, 11, 2014
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3FI6
 | | apo-H49AFr with high content of Pd ions | | Descriptor: | CADMIUM ION, Ferritin light chain, PALLADIUM ION, ... | | Authors: | Abe, M, Ueno, T, Hirata, K, Suzuki, M, Abe, S, Shimizu, N, Yamaoto, M, Takata, M, Watanabe, Y. | | Deposit date: | 2008-12-11 | | Release date: | 2009-04-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Process of Accumulation of Metal Ions on the Interior Surface of apo-Ferritin: Crystal Structures of a Series of apo-Ferritins Containing Variable Quantities of Pd(II) Ions
J.Am.Chem.Soc., 131, 2009
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6LPK
 | | A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a, CHOLESTEROL, ... | | Authors: | Ihara, K, Hato, M, Nakane, T, Yamashita, K, Kimura-Someya, T, Hosaka, T, Ishizuka-Katsura, Y, Tanaka, R, Tanaka, T, Sugahara, M, Hirata, K, Yamamoto, M, Nureki, O, Tono, K, Nango, E, Iwata, S, Shirouzu, M. | | Deposit date: | 2020-01-10 | | Release date: | 2020-11-25 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Sci Rep, 10, 2020
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6LPJ
 | | A2AR crystallized in EROCOC17+4, LCP-SFX at 277 K | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a, CHOLESTEROL, ... | | Authors: | Ihara, K, Hato, M, Nakane, T, Yamashita, K, Kimura-Someya, T, Hosaka, T, Ishizuka-Katsura, Y, Tanaka, R, Tanaka, T, Sugahara, M, Hirata, K, Yamamoto, M, Nureki, O, Tono, K, Nango, E, Iwata, S, Shirouzu, M. | | Deposit date: | 2020-01-10 | | Release date: | 2020-11-25 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Sci Rep, 10, 2020
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6LPL
 | | A2AR crystallized in EROCOC17+4, SS-ROX at 100 K | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a, CHOLESTEROL, ... | | Authors: | Ihara, K, Hato, M, Nakane, T, Yamashita, K, Kimura-Someya, T, Hosaka, T, Ishizuka-Katsura, Y, Tanaka, R, Tanaka, T, Sugahara, M, Hirata, K, Yamamoto, M, Nureki, O, Tono, K, Nango, E, Iwata, S, Shirouzu, M. | | Deposit date: | 2020-01-11 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Sci Rep, 10, 2020
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6N48
 | | Structure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator | | Descriptor: | (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one, Camelid Antibody Fragment, ... | | Authors: | Liu, X, Masoudi, A, Kahsai, A.W, Huang, L.Y, Pani, B, Hirata, K, Ahn, S, Lefkowitz, R.J, Kobilka, B.K. | | Deposit date: | 2018-11-17 | | Release date: | 2019-06-26 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Mechanism of beta2AR regulation by an intracellular positive allosteric modulator.
Science, 364, 2019
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6OBA
 | | The beta2 adrenergic receptor bound to a negative allosteric modulator | | Descriptor: | (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol, 6-bromo-N~2~-phenylquinazoline-2,4-diamine, Beta-2 adrenergic receptor,Lysozyme,Beta-2 adrenergic receptor, ... | | Authors: | Liu, X, Stobel, A, Kaindl, J, Dengler, D, ClarK, M, Mahoney, J, Korczynska, M, Matt, R.A, Hubner, H, Xu, X, Stanek, M, Hirata, K, Shoichet, B, Sunahara, R, Gmeiner, R, Kobilka, B.K. | | Deposit date: | 2019-03-20 | | Release date: | 2020-03-25 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | An allosteric modulator binds to a conformational hub in the beta2adrenergic receptor.
Nat.Chem.Biol., 16, 2020
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7XHS
 | | Crystal structure of CipA crystal produced by cell-free protein synthesis | | Descriptor: | Cro/Cl family transcriptional regulator | | Authors: | Abe, S, Tanaka, J, Kojima, M, Kanamaru, S, Yamashita, K, Hirata, K, Ueno, T. | | Deposit date: | 2022-04-10 | | Release date: | 2023-02-01 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Cell-free protein crystallization for nanocrystal structure determination.
Sci Rep, 12, 2022
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7XHR
 | | Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis | | Descriptor: | ACETYL GROUP, CHLORIDE ION, Polyhedrin | | Authors: | Abe, S, Tanaka, J, Kojima, M, Hirata, K, Yamashita, K, Ueno, T. | | Deposit date: | 2022-04-10 | | Release date: | 2023-02-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.801 Å) | | Cite: | Cell-free protein crystallization for nanocrystal structure determination.
Sci Rep, 12, 2022
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7WYR
 | | Crystal structure of Cypovirus Polyhedra mutant fused with CLN025 | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Polyhedrin fused with CLN025 | | Authors: | Kojima, M, Abe, S, Hirata, K, Yamashita, K, Ueno, T. | | Deposit date: | 2022-02-16 | | Release date: | 2023-02-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein.
Biomater Sci, 11, 2023
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6LEE
 | | Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala67-Ala104 | | Descriptor: | Polyhedrin | | Authors: | Abe, S, Kasamatsu, M, Hirata, K, Yamashita, K, Ueno, T. | | Deposit date: | 2019-11-25 | | Release date: | 2020-12-09 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | In-Cell Engineering of Protein Crystals with Nanoporous Structures for Promoting Cascade Reactions
ACS Appl Nano Mater, 4, 2021
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5WS7
 | | Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 2-oxo-dATP | | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Nakamura, T, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2016-12-05 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
J. Biol. Chem., 292, 2017
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6L63
 | | Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-ACHC residues | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETYL GROUP, ... | | Authors: | Sengoku, T, Katoh, T, Hirata, K, Suga, H, Ogata, K. | | Deposit date: | 2019-10-26 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Ribosomal synthesis and de novo discovery of bioactive foldamer peptides containing cyclic beta-amino acids.
Nat.Chem., 12, 2020
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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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