2YVK
 
 | | Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis | | Descriptor: | 5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE, Methylthioribose-1-phosphate isomerase | | Authors: | Tamura, H, Inoue, T, Kai, Y, Matsumura, H. | | Deposit date: | 2007-04-13 | | Release date: | 2008-01-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism
Protein Sci., 17, 2008
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2YRF
 | | Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion | | Descriptor: | Methylthioribose-1-phosphate isomerase, SULFATE ION | | Authors: | Tamura, H, Inoue, T, Kai, Y, Matsumura, H. | | Deposit date: | 2007-04-02 | | Release date: | 2008-01-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism
Protein Sci., 17, 2008
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2ZVI
 | | Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis | | Descriptor: | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase | | Authors: | Tamura, H, Yadani, T, Kai, Y, Inoue, T, Matsumura, H. | | Deposit date: | 2008-11-07 | | Release date: | 2009-09-01 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis
Acta Crystallogr.,Sect.D, 65, 2009
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2ZWO
 | | Crystal structure of Ca2 site mutant of Pro-S324A | | Descriptor: | CALCIUM ION, Tk-subtilisin | | Authors: | Takeuchi, Y, Tanaka, S, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2008-12-17 | | Release date: | 2009-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon.
Biochemistry, 48, 2009
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2ZWP
 | | Crystal structure of Ca3 site mutant of Pro-S324A | | Descriptor: | CALCIUM ION, Tk-subtilisin | | Authors: | Takeuchi, Y, Tanaka, S, Matsumura, H, Koga, Y, Takano, K, Kanaya, S. | | Deposit date: | 2008-12-17 | | Release date: | 2009-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon.
Biochemistry, 48, 2009
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2CZR
 | | Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA | | Descriptor: | GLYCEROL, TBP-interacting protein, ZINC ION | | Authors: | Yamamoto, T, Matsuda, T, Inoue, T, Matsumura, H, Morikawa, M, Kanaya, S, Kai, Y. | | Deposit date: | 2005-07-15 | | Release date: | 2006-02-14 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA
Protein Sci., 15, 2006
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2E2G
 | | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | | Deposit date: | 2006-11-13 | | Release date: | 2007-11-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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2E2M
 | | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (sulfinic acid form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Abe, M, Matsumura, H, Hagihara, Y, Goto, T, Yamaguchi, T, Inoue, T. | | Deposit date: | 2006-11-14 | | Release date: | 2007-11-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
Proc.Natl.Acad.Sci.Usa, 105, 2008
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1UAT
 | | The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J | | Descriptor: | Azurin iso-2, COPPER (II) ION, SULFATE ION | | Authors: | Inoue, T, Suzuki, S, Nisho, N, Yamaguchi, K, Kataoka, K, Tobari, J, Yong, X, Hamanaka, S, Matsumura, H, Kai, Y. | | Deposit date: | 2003-03-19 | | Release date: | 2004-03-30 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J
J.Mol.Biol., 333, 2003
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1WSF
 | | Co-crystal structure of E.coli RNase HI active site mutant (D134A*) with Mn2+ | | Descriptor: | MANGANESE (II) ION, Ribonuclease HI | | Authors: | Tsunaka, Y, Takano, K, Matsumura, H, Yamagata, Y, Kanaya, S. | | Deposit date: | 2004-11-05 | | Release date: | 2005-02-08 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Identification of Single Mn(2+) Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography
J.Mol.Biol., 345, 2005
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1WS8
 | | Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini) | | Descriptor: | COPPER (II) ION, GLYCEROL, mavicyanin | | Authors: | Xie, Y, Inoue, T, Miyamoto, Y, Matsumura, H, Kunishige, K, Yamaguchi, K, Nojini, M, Suzuki, S, Kai, Y. | | Deposit date: | 2004-11-02 | | Release date: | 2004-11-23 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural reorganization of the copper binding site involving Thr15 of mavicyanin from Cucurbita pepo medullosa (zucchini) upon reduction.
J.Biochem.(Tokyo), 137, 2005
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1WSE
 | | Co-crystal structure of E.coli RNase HI active site mutant (E48A*) with Mn2+ | | Descriptor: | MANGANESE (II) ION, Ribonuclease HI | | Authors: | Tsunaka, Y, Takano, K, Matsumura, H, Yamagata, Y, Kanaya, S. | | Deposit date: | 2004-11-05 | | Release date: | 2005-02-08 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Identification of Single Mn(2+) Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography
J.Mol.Biol., 345, 2005
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1WS7
 | | Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini) | | Descriptor: | COPPER (I) ION, Mavicyanin | | Authors: | Xie, Y, Inoue, T, Miyamoto, Y, Matsumura, H, Kataoka, K, Yamaguchi, K, Nojini, M, Suzuki, S, Kai, Y. | | Deposit date: | 2004-11-02 | | Release date: | 2004-11-23 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural reorganization of the copper binding site involving Thr15 of mavicyanin from Cucurbita pepo medullosa (zucchini) upon reduction.
J.Biochem.(Tokyo), 137, 2005
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1WSG
 | | Co-crystal structure of E.coli RNase HI active site mutant (E48A/D134N*) with Mn2+ | | Descriptor: | MANGANESE (II) ION, Ribonuclease HI | | Authors: | Tsunaka, Y, Takano, K, Matsumura, H, Yamagata, Y, Kanaya, S. | | Deposit date: | 2004-11-05 | | Release date: | 2005-02-08 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Identification of Single Mn(2+) Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography
J.Mol.Biol., 345, 2005
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1X0R
 | | Thioredoxin Peroxidase from Aeropyrum pernix K1 | | Descriptor: | 1,2-ETHANEDIOL, Probable peroxiredoxin | | Authors: | Nakamura, T, Yamamoto, T, Inoue, T, Matsumura, H, Kobayashi, A, Hagihara, Y, Uegaki, K, Ataka, M, Kai, Y, Ishikawa, K. | | Deposit date: | 2005-03-28 | | Release date: | 2005-12-20 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1
Proteins, 62, 2006
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3AG6
 | | Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus in complex with pantoyl adenylate | | Descriptor: | ACETIC ACID, PANTOYL ADENYLATE, Pantothenate synthetase, ... | | Authors: | Satoh, A, Konishi, S, Tamura, H, Stickland, H.G, Whitney, H.M, Smith, A.G, Matsumura, H, Inoue, T. | | Deposit date: | 2010-03-19 | | Release date: | 2010-07-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus.
Biochemistry, 49, 2010
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2ZXC
 | | Ceramidase complexed with C2 | | Descriptor: | DIMETHYL SULFOXIDE, FORMIC ACID, MAGNESIUM ION, ... | | Authors: | Okano, H, Inoue, T, Okino, N, Kakuta, Y, Matsumura, H, Ito, M. | | Deposit date: | 2008-12-22 | | Release date: | 2009-02-03 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase.
J.Biol.Chem., 284, 2009
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1YC9
 | | The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 resolution | | Descriptor: | MERCURY (II) ION, multidrug resistance protein, octyl beta-D-glucopyranoside | | Authors: | Federici, L, Du, D, Walas, F, Matsumura, H, Fernandez-Recio, J, McKeegan, K.S, Borges-Walmsley, M.I, Luisi, B.F, Walmsley, A.R. | | Deposit date: | 2004-12-22 | | Release date: | 2005-03-01 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The crystal structure of the outer membrane protein VCEC from the bacterial pathogen vibrio cholerae at 1.8 A resolution
J.Biol.Chem., 280, 2005
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3AGV
 | | Crystal structure of a human IgG-aptamer complex | | Descriptor: | 5'-R(*GP*GP*AP*GP*GP*(UFT)P*GP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*GP*AP*AP*A*GP*GP*AP*AP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*A)-3', CALCIUM ION, Ig gamma-1 chain C region, ... | | Authors: | Nomura, Y, Sugiyama, S, Sakamoto, T, Miyakawa, S, Adachi, H, Takano, K, Murakami, S, Inoue, T, Mori, Y, Nakamura, Y, Matsumura, H. | | Deposit date: | 2010-04-08 | | Release date: | 2010-11-10 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex
Nucleic Acids Res., 38, 2010
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3AG5
 | | Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus | | Descriptor: | Pantothenate synthetase | | Authors: | Satoh, A, Konishi, S, Tamura, H, Stickland, H.G, Whitney, H.M, Smith, A.G, Matsumura, H, Inoue, T. | | Deposit date: | 2010-03-19 | | Release date: | 2010-07-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus.
Biochemistry, 49, 2010
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1IR2
 | | Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP) | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, GLYCEROL, Large subunit of Rubisco, ... | | Authors: | Mizohata, E, Matsumura, H, Okano, Y, Kumei, M, Takuma, H, Onodera, J, Kato, K, Shibata, N, Inoue, T, Yokota, A, Kai, Y. | | Deposit date: | 2001-09-03 | | Release date: | 2002-03-20 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316, 2002
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1IR1
 | | Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, Large subunit of Rubisco, MAGNESIUM ION, ... | | Authors: | Mizohata, E, Matsumura, H, Okano, Y, Kumei, M, Takuma, H, Onodera, J, Kato, K, Shibata, N, Inoue, T, Yokota, A, Kai, Y. | | Deposit date: | 2001-08-31 | | Release date: | 2002-03-13 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316, 2002
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1IWA
 | | RUBISCO FROM GALDIERIA PARTITA | | Descriptor: | SULFATE ION, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit | | Authors: | Okano, Y, Mizohata, E, Xie, Y, Matsumura, H, Sugawara, H, Inoue, T, Yokota, A, Kai, Y. | | Deposit date: | 2002-04-30 | | Release date: | 2003-04-30 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | X-Ray Structure of Galdieria Rubisco Complexed with one sulfate ion per active site
FEBS LETT., 527, 2002
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3VGW
 | | Crystal structure of monoAc-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-21 | | Release date: | 2011-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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3VHH
 | | Crystal structure of DiMe-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-25 | | Release date: | 2011-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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