2EK7
 
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L163M) | | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION | | Authors: | Asada, Y, Taketa, M, Morikawa, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-22 | | Release date: | 2007-09-25 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L163M)
To be Published
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1GCQ
 | | CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2, VAV PROTO-ONCOGENE | | Authors: | Nishida, M, Nagata, K, Hachimori, Y, Ogura, K, Inagaki, F. | | Deposit date: | 2000-08-08 | | Release date: | 2001-08-08 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Novel recognition mode between Vav and Grb2 SH3 domains.
EMBO J., 20, 2001
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2E84
 | | Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion | | Descriptor: | High-molecular-weight cytochrome c, PROTOPORPHYRIN IX CONTAINING FE, SODIUM ION, ... | | Authors: | Shibata, N, Suto, K, Sato, M, Morimoto, Y, Kitamura, M, Higuchi, Y. | | Deposit date: | 2007-01-17 | | Release date: | 2008-01-15 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F)
To be Published
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1EQQ
 | | SINGLE STRANDED DNA BINDING PROTEIN AND SSDNA COMPLEX | | Descriptor: | 5'-R(*(5MU)P*(5MU)P*(5MU))-3', SINGLE STRANDED DNA BINDING PROTEIN | | Authors: | Matsumoto, T, Morimoto, Y, Shibata, N, Yasuoka, N, Shimamoto, N. | | Deposit date: | 2000-04-06 | | Release date: | 2003-09-23 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis
J.Biochem.(Tokyo), 127, 2000
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1GCP
 | | CRYSTAL STRUCTURE OF VAV SH3 DOMAIN | | Descriptor: | VAV PROTO-ONCOGENE | | Authors: | Nishida, M, Nagata, K, Hachimori, Y, Ogura, K, Inagaki, F. | | Deposit date: | 2000-08-08 | | Release date: | 2001-08-08 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Novel recognition mode between Vav and Grb2 SH3 domains.
EMBO J., 20, 2001
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1DIO
 | | DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA | | Descriptor: | COBALAMIN, POTASSIUM ION, PROTEIN (DIOL DEHYDRATASE), ... | | Authors: | Shibata, N, Masuda, J, Tobimatsu, T, Toraya, T, Suto, K, Morimoto, Y, Yasuoka, N. | | Deposit date: | 1999-01-27 | | Release date: | 2000-01-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase.
Structure Fold.Des., 7, 1999
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1X0P
 | | Structure of a cyanobacterial BLUF protein, Tll0078 | | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, hypothetical protein Tll0078 | | Authors: | Kita, A, Okajima, K, Morimoto, Y, Ikeuchi, M, Miki, K. | | Deposit date: | 2005-03-27 | | Release date: | 2005-06-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure of a Cyanobacterial BLUF Protein, Tll0078, Containing a Novel FAD-binding Blue Light Sensor Domain
J.Mol.Biol., 349, 2005
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1WQ5
 | | Crystal structure of tryptophan synthase alpha-subunit from Escherichia coli | | Descriptor: | GLYCEROL, SULFATE ION, Tryptophan synthase alpha chain | | Authors: | Nishio, K, Morimoto, Y, Ishizuka, M, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-22 | | Release date: | 2005-02-15 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Conformational Changes in the alpha-Subunit Coupled to Binding of the beta(2)-Subunit of Tryptophan Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase alpha-Subunit Alon
Biochemistry, 44, 2005
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7VLD
 | | Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLF
 | | Oxy-deoxy intermediate of V2 hemoglobin at 26% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLC
 | | Oxy-deoxy intermediate of V2 hemoglobin at 78% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLE
 | | Oxy-deoxy intermediate of V2 hemoglobin at 55% oxygen saturation | | Descriptor: | Extracellular A1 globin, Extracellular A2 globin, Extracellular B1 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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1V7Y
 | | Crystal structure of tryptophan synthase alpha-subunit from Escherichia coli at room temperature | | Descriptor: | SULFATE ION, Tryptophan synthase alpha chain | | Authors: | Nishio, K, Morimoto, Y, Ishizuka, M, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-12-25 | | Release date: | 2005-02-15 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Conformational Changes in the alpha-Subunit Coupled to Binding of the beta(2)-Subunit of Tryptophan Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase alpha-Subunit Alon
Biochemistry, 44, 2005
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1IWB
 | | Crystal structure of diol dehydratase | | Descriptor: | COBALAMIN, DIOL DEHYDRATASE alpha chain, DIOL DEHYDRATASE beta chain, ... | | Authors: | Shibata, N, Masuda, J, Morimoto, Y, Yasuoka, N, Toraya, T. | | Deposit date: | 2002-05-01 | | Release date: | 2003-05-01 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Biochemistry, 41, 2002
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7FBO
 | | geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BezA, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Tsutsumi, H, Moriwaki, Y, Terada, T, Shimizu, K, Katsuyama, Y, Ohnishi, Y. | | Deposit date: | 2021-07-12 | | Release date: | 2021-12-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Angew.Chem.Int.Ed.Engl., 61, 2022
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2Z6V
 | | Crystal structure of sulfotransferase STF9 from Mycobacterium avium | | Descriptor: | PALMITIC ACID, Putative uncharacterized protein, SULFATE ION | | Authors: | Hassain, M.M, Moriizumi, Y, Tanaka, S, Kimura, M, Kakuta, Y. | | Deposit date: | 2007-08-09 | | Release date: | 2008-09-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of sulfotransferase STF9 from Mycobacterium avium
To be Published
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2ZFO
 | | Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins | | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B1, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-01-08 | | Release date: | 2008-04-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins
Proteins, 73, 2008
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2ZS1
 | | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin | | Descriptor: | CHLORIDE ION, Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-09-02 | | Release date: | 2008-10-21 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Biochemistry, 47, 2008
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2ZS0
 | | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin | | Descriptor: | CALCIUM ION, CHLORIDE ION, Extracellular giant hemoglobin major globin subunit A1, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-09-02 | | Release date: | 2008-10-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Biochemistry, 47, 2008
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3AJ9
 | | X-ray analysis of Crystal of Proteinase K Obtained from D2O Solution Using PEG 8000 | | Descriptor: | CALCIUM ION, GLYCEROL, Proteinase K | | Authors: | Chatake, T, Ishikawa, T, Morimoto, Y. | | Deposit date: | 2010-05-27 | | Release date: | 2011-06-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K
Acta Crystallogr.,Sect.F, 67, 2011
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3AJ8
 | | X-ray analysis of Crystal of Proteinase K Obtained from H2O Solution Using PEG 8000 | | Descriptor: | CALCIUM ION, GLYCEROL, Proteinase K | | Authors: | Chatake, T, Ishikawa, T, Morimoto, Y. | | Deposit date: | 2010-05-27 | | Release date: | 2011-06-22 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K
Acta Crystallogr.,Sect.F, 67, 2011
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7FBH
 | | geranyl pyrophosphate C6-methyltransferase BezA | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BezA, ... | | Authors: | Tsutsumi, H, Moriwaki, Y, Terada, T, Shimizu, K, Katsuyama, Y, Ohnishi, Y. | | Deposit date: | 2021-07-10 | | Release date: | 2021-12-01 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Angew.Chem.Int.Ed.Engl., 61, 2022
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2DH6
 | | Crystal structure of E. coli Apo-TrpB | | Descriptor: | SULFATE ION, tryptophan synthase beta subunit | | Authors: | Nishio, K, Morimoto, Y, Ogasahara, K, Yasuoka, N, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-03-23 | | Release date: | 2007-04-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding
Febs J., 277, 2010
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6K8G
 | | H/D exchanged Hen egg-white lysozyme | | Descriptor: | CHLORIDE ION, Lysozyme C, SODIUM ION | | Authors: | Kita, A, Morimoto, Y. | | Deposit date: | 2019-06-11 | | Release date: | 2020-06-17 | | Last modified: | 2024-04-03 | | Method: | NEUTRON DIFFRACTION (2 Å), X-RAY DIFFRACTION | | Cite: | Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state.
J.Appl.Crystallogr., 53, 2020
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2DH5
 | | Crystal structure of E. coli Holo-TrpB | | Descriptor: | GLYCEROL, PYRIDOXAL-5'-PHOSPHATE, SULFATE ION, ... | | Authors: | Nishio, K, Morimoto, Y, Ogasahara, K, Yutani, K, Tsukihara, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-03-23 | | Release date: | 2007-04-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding
Febs J., 277, 2010
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