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2DYT
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BU of 2dyt by Molmil
The crystal structure of Saccharomyces cerevisiae Atg3
Descriptor: Autophagy-related protein 3, SULFATE ION
Authors:Yamada, Y, Suzuki, N.N, Inagaki, F.
Deposit date:2006-09-17
Release date:2007-01-23
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation
J.Biol.Chem., 282, 2007
1ITK
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BU of 1itk by Molmil
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
6KN7
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BU of 6kn7 by Molmil
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
6KN8
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BU of 6kn8 by Molmil
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
1AE1
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BU of 1ae1 by Molmil
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
1AUN
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BU of 1aun by Molmil
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:2023-08-02
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
6I59
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BU of 6i59 by Molmil
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:2019-06-12
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
6I5C
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BU of 6i5c by Molmil
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:2020-09-23
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
8DCT
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BU of 8dct by Molmil
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
8DCU
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BU of 8dcu by Molmil
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: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
8DCV
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BU of 8dcv by Molmil
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: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
8DCW
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BU of 8dcw by Molmil
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
1IPE
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BU of 1ipe by Molmil
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
1IPF
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BU of 1ipf by Molmil
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
3H7G
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BU of 3h7g by Molmil
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
1WTN
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BU of 1wtn by Molmil
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:2011-07-13
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
1VYU
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BU of 1vyu by Molmil
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
1VYV
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BU of 1vyv by Molmil
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
1VYT
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BU of 1vyt by Molmil
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:2023-12-13
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
5H1A
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BU of 5h1a by Molmil
Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2
Descriptor: IclR transcription factor homolog, PHOSPHATE ION
Authors:Akiyama, T, Yamada, Y, Takaya, N, Ito, S, Sasaki, Y, Yajima, S.
Deposit date:2016-10-08
Release date:2017-01-18
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.
Acta Crystallogr F Struct Biol Commun, 73, 2017
1WTM
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BU of 1wtm by Molmil
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:2011-07-13
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
3J82
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BU of 3j82 by Molmil
Electron cryo-microscopy of DNGR-1 in complex with F-actin
Descriptor: ADENOSINE-5'-DIPHOSPHATE, Actin, cytoplasmic 1, ...
Authors:Hanc, P, Fujii, T, Yamada, Y, Huotari, J, Schulz, O, Ahrens, S, Kjaer, S, Way, M, Namba, K, Reis e Sousa, C.
Deposit date:2014-09-25
Release date:2015-05-20
Last modified:2019-12-18
Method:ELECTRON MICROSCOPY (7.7 Å)
Cite:Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens.
Immunity, 42, 2015
2Z44
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BU of 2z44 by Molmil
Crystal Structure of Selenomethionine-labeled ORF134
Descriptor: ORF134
Authors:Tomimoto, Y, Ihara, K, Onizuka, T, Kanai, S, Ashida, H, Yokota, A, Tanaka, S, Miyasaka, H, Yamada, Y, Kato, R, Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Crystal Structure of ORF134
To be Published
2Z46
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BU of 2z46 by Molmil
Crystal Structure of Native-ORF134
Descriptor: ORF134
Authors:Tomimoto, Y, Ihara, K, Onizuka, T, Kanai, S, Ashida, H, Yokota, A, Tanaka, S, Miyasaka, H, Yamada, Y, Kato, R, Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.97 Å)
Cite:Crystal Structure of ORF134
To be Published
2Z45
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BU of 2z45 by Molmil
Crystal Structure of Zn-bound ORF134
Descriptor: ORF134, ZINC ION
Authors:Tomimoto, Y, Ihara, K, Onizuka, T, Kanai, S, Ashida, H, Yokota, A, Tanaka, S, Miyasaka, H, Yamada, Y, Kato, R, Wakatsuki, S.
Deposit date:2007-06-12
Release date:2008-06-24
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Crystal Structure of ORF134
To be Published

 

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