2DYT
 
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1ITK
 | | Crystal structure of catalase-peroxidase from Haloarcula marismortui | | Descriptor: | CHLORIDE ION, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... | | Authors: | Yamada, Y, Fujiwara, T, Sato, T, Igarashi, N, Tanaka, N. | | Deposit date: | 2002-01-18 | | Release date: | 2002-08-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui.
Nat.Struct.Biol., 9, 2002
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6KN7
 | | Structure of human cardiac thin filament in the calcium free state | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin, alpha skeletal muscle, ... | | Authors: | Fujii, T, Yamada, Y, Namba, K. | | Deposit date: | 2019-08-03 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (6.6 Å) | | Cite: | Cardiac muscle thin filament structures reveal calcium regulatory mechanism.
Nat Commun, 11, 2020
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6KN8
 | | Structure of human cardiac thin filament in the calcium bound state | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Actin, alpha skeletal muscle, ... | | Authors: | Fujii, T, Yamada, Y, Namba, K. | | Deposit date: | 2019-08-03 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (4.8 Å) | | Cite: | Cardiac muscle thin filament structures reveal calcium regulatory mechanism.
Nat Commun, 11, 2020
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2AE2
 | | TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE | | Descriptor: | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROTEIN (TROPINONE REDUCTASE-II), PSEUDOTROPINE | | Authors: | Yamashita, A, Kato, H, Wakatsuki, S, Tomizaki, T, Nakatsu, T, Nakajima, K, Hashimoto, T, Yamada, Y, Oda, J. | | Deposit date: | 1999-01-26 | | Release date: | 1999-02-02 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.
Biochemistry, 38, 1999
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2AE1
 | | TROPINONE REDUCTASE-II | | Descriptor: | TROPINONE REDUCTASE-II | | Authors: | Nakajima, K, Yamashita, A, Akama, H, Nakatsu, T, Kato, H, Hashimoto, T, Oda, J, Yamada, Y. | | Deposit date: | 1997-10-27 | | Release date: | 1998-11-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structures of two tropinone reductases: different reaction stereospecificities in the same protein fold.
Proc.Natl.Acad.Sci.USA, 95, 1998
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1AE1
 | | TROPINONE REDUCTASE-I COMPLEX WITH NADP | | Descriptor: | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, TROPINONE REDUCTASE-I | | Authors: | Nakajima, K, Yamashita, A, Akama, H, Nakatsu, T, Kato, H, Hashimoto, T, Oda, J, Yamada, Y. | | Deposit date: | 1997-10-23 | | Release date: | 1998-11-18 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structures of two tropinone reductases: different reaction stereospecificities in the same protein fold.
Proc.Natl.Acad.Sci.USA, 95, 1998
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1AUN
 | | PATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM | | Descriptor: | PR-5D | | Authors: | Koiwa, H, Kato, H, Nakatsu, T, Oda, J, Yamada, Y, Sato, F. | | Deposit date: | 1997-08-29 | | Release date: | 1998-03-04 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of tobacco PR-5d protein at 1.8 A resolution reveals a conserved acidic cleft structure in antifungal thaumatin-like proteins.
J.Mol.Biol., 286, 1999
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8XZ2
 | | The structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria | | Descriptor: | D-alanyl-D-alanine dipeptidase | | Authors: | Konuma, T, Takai, T, Tsuchiya, C, Nishida, M, Hashiba, M, Yamada, Y, Shirai, H, Motoda, Y, Nagadoi, A, Chikaishi, E, Akagi, K, Akashi, S, Yamazaki, T, Akutsu, H, Oe, A, Ikegami, T. | | Deposit date: | 2024-01-20 | | Release date: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria.
Protein Sci., 33, 2024
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1IPF
 | | TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE | | Descriptor: | 8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, TROPINONE REDUCTASE-II | | Authors: | Yamashita, A, Endo, M, Higashi, T, Nakatsu, T, Yamada, Y, Oda, J, Kato, H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-05-09 | | Release date: | 2003-06-03 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes
BIOCHEMISTRY, 42, 2003
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1IPE
 | | TROPINONE REDUCTASE-II COMPLEXED WITH NADPH | | Descriptor: | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, TROPINONE REDUCTASE-II | | Authors: | Yamashita, A, Endo, M, Higashi, T, Nakatsu, T, Yamada, Y, Oda, J, Kato, H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-05-09 | | Release date: | 2003-06-03 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes
BIOCHEMISTRY, 42, 2003
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8DCT
 | | Lysozyme cluster 3 dual apo structure | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, BENZAMIDINE, CHLORIDE ION, ... | | Authors: | Soares, A.S, Yamada, Y, Jakoncic, J, Schneider, D.K, Bernstein, H.J. | | Deposit date: | 2022-06-17 | | Release date: | 2022-08-17 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Serial crystallography with multi-stage merging of thousands of images.
Acta Crystallogr.,Sect.F, 78, 2022
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8DCW
 | | Lysozyme cluster 0062 (NAG and benzamidine ligands) | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, BENZAMIDINE, CHLORIDE ION, ... | | Authors: | Soares, A.S, Yamada, Y, Jakoncic, J, Schneider, D.K, Bernstein, H.J. | | Deposit date: | 2022-06-17 | | Release date: | 2022-08-17 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Serial crystallography with multi-stage merging of thousands of images.
Acta Crystallogr.,Sect.F, 78, 2022
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8DCU
 | | Lysozyme cluster 0028 (benzamidine ligand) | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, BENZAMIDINE, CHLORIDE ION, ... | | Authors: | Soares, A.S, Yamada, Y, Jakoncic, J, Schneider, D.K, Bernstein, H.J. | | Deposit date: | 2022-06-17 | | Release date: | 2022-08-17 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Serial crystallography with multi-stage merging of thousands of images.
Acta Crystallogr.,Sect.F, 78, 2022
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8DCV
 | | Lysozyme cluster 0043, NAG ligand | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, BENZAMIDINE, CHLORIDE ION, ... | | Authors: | Soares, A.S, Yamada, Y, Jakoncic, J, Schneider, D.K, Bernstein, H.J. | | Deposit date: | 2022-06-17 | | Release date: | 2022-08-17 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Serial crystallography with multi-stage merging of thousands of images.
Acta Crystallogr.,Sect.F, 78, 2022
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6I59
 | | Long wavelength native-SAD phasing of Sen1 helicase | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-DIPHOSPHATE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Basu, S, Olieric, V, Matsugaki, N, Kawano, Y, Takashi, T, Huang, C.Y, Leonarski, F, Yamada, Y, Vera, L, Olieric, N, Basquin, J, Wojdyla, J.A, Diederichs, K, Yamamoto, M, Bunk, O, Wang, M. | | Deposit date: | 2018-11-13 | | Release date: | 2019-03-13 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
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3H7G
 | | Apo-FR with AU ions | | Descriptor: | CADMIUM ION, Ferritin light chain, GLYCEROL, ... | | Authors: | Abe, M, Ueno, T, Abe, S, Suzuki, M, Goto, T, Toda, Y, Akita, T, Yamada, Y, Watanabe, Y. | | Deposit date: | 2009-04-27 | | Release date: | 2009-09-15 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin
Chem.Commun.(Camb.), 32, 2009
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1WTN
 | | The structure of HEW Lysozyme Orthorhombic Crystal Growth under a High Magnetic Field | | Descriptor: | CHLORIDE ION, Lysozyme C | | Authors: | Saijo, S, Yamada, Y, Sato, T, Tanaka, N, Matsui, T, Sazaki, G, Nakajima, K, Matsuura, Y. | | Deposit date: | 2004-11-25 | | Release date: | 2004-12-14 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.13 Å) | | Cite: | Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.
Acta Crystallogr.,Sect.D, 61, 2005
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6I5C
 | | Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Basu, S, Olieric, V, Matsugaki, N, Kawano, Y, Takashi, T, Huang, C.Y, Leonarski, F, Yamada, Y, Vera, L, Olieric, N, Basquin, J, Wojdyla, J.A, Diederichs, K, Yamamoto, M, Bunk, O, Wang, M. | | Deposit date: | 2018-11-13 | | Release date: | 2019-03-13 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
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1VYU
 | | Beta3 subunit of Voltage-gated Ca2+-channel | | Descriptor: | CALCIUM CHANNEL BETA-3 SUBUNIT | | Authors: | Chen, Y.-H, Li, M.-H, Zhang, Y, He, L.-L, Yamada, Y, Fitzmaurice, A, Yang, S, Zhang, H, Liang, T, Yang, J. | | Deposit date: | 2004-05-07 | | Release date: | 2004-06-15 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural Basis of the Alpha(1)-Beta Subunit Interaction of Voltage-Gated Ca(2+) Channels
Nature, 429, 2004
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1VYV
 | | beta4 subunit of Ca2+ channel | | Descriptor: | CALCIUM CHANNEL BETA-4SUBUNIT | | Authors: | Chen, Y.-H, Li, M.-H, Zhang, Y, He, L.-L, Yamada, Y, Fitzmaurice, A, Yang, S, Zhang, H, Liang, T, Yang, J. | | Deposit date: | 2004-05-07 | | Release date: | 2004-06-15 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural Basis of the Alpha(1)-Beta Subunit Interaction of Voltage-Gated Ca(2+) Channels
Nature, 429, 2004
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1VYT
 | | beta3 subunit complexed with aid | | Descriptor: | CALCIUM CHANNEL BETA-3 SUBUNIT, VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT | | Authors: | Chen, Y.-H, Li, M.-H, Zhang, Y, He, L.-L, Yamada, Y, Fitzmaurice, A, Yang, S, Zhang, H, Tong, L, Yang, J. | | Deposit date: | 2004-05-07 | | Release date: | 2004-06-15 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural Basis of the Alpha(1)-Beta Subunit Interaction of Voltage-Gated Ca(2+) Channels
Nature, 429, 2004
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8IX6
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8IQA
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1WTM
 | | X-ray structure of HEW Lysozyme Orthorhombic Crystal formed in the Earth's magnetic field | | Descriptor: | CHLORIDE ION, Lysozyme C | | Authors: | Saijo, S, Yamada, Y, Sato, T, Tanaka, N, Matsui, T, Sazaki, G, Nakajima, K, Matsuura, Y. | | Deposit date: | 2004-11-25 | | Release date: | 2004-12-14 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.
Acta Crystallogr.,Sect.D, 61, 2005
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