4YSR
| Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.6 MGy | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, COPPER (II) ION, Nitrite reductase, ... | Authors: | Fukuda, Y, Tse, K.M, Suzuki, M, Diederichs, K, Hirata, K, Nakane, T, Sugahara, M, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Matsumura, H, Inoue, T, Iwata, S, Mizohata, E. | Deposit date: | 2015-03-17 | Release date: | 2016-02-24 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.34 Å) | Cite: | Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography J.Biochem., 159, 2016
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4YST
| Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 24.9 MGy | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, COPPER (II) ION, Nitrite reductase, ... | Authors: | Fukuda, Y, Tse, K.M, Suzuki, M, Diederichs, K, Hirata, K, Nakane, T, Sugahara, M, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Matsumura, H, Inoue, T, Iwata, S, Mizohata, E. | Deposit date: | 2015-03-17 | Release date: | 2016-02-24 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.34 Å) | Cite: | Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography J.Biochem., 159, 2016
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3WYQ
| Crystal structure of the low-immunogenic core streptavidin mutant LISA-314 (Y22S/Y83S/R84K/E101D/R103K/E116N) at 1.0 A resolution | Descriptor: | BIOTIN, GLYCEROL, SULFATE ION, ... | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | Deposit date: | 2014-09-05 | Release date: | 2014-12-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | Crystal structure of streptavidin mutant with low immunogenicity. J.Biosci.Bioeng., 119, 2015
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3WYP
| Crystal structure of wild-type core streptavidin in complex with D-biotin/biotin-D-sulfoxide at 1.3 A resolution | Descriptor: | BIOTIN, BIOTIN-D-SULFOXIDE, GLYCEROL, ... | Authors: | Kawato, T, Mizohata, E, Meshizuka, T, Doi, H, Kawamura, T, Matsumura, H, Yumura, K, Tsumoto, K, Kodama, T, Inoue, T, Sugiyama, A. | Deposit date: | 2014-09-05 | Release date: | 2014-12-24 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Crystal structure of streptavidin mutant with low immunogenicity. J.Biosci.Bioeng., 119, 2015
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3WZN
| Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin at 1.3 A resolution | Descriptor: | BIOTIN, SULFATE ION, Streptavidin | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | Deposit date: | 2014-10-01 | Release date: | 2015-02-18 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem., 157, 2015
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3WZP
| Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 A resolution | Descriptor: | 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, GLYCEROL, Streptavidin | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | Deposit date: | 2014-10-01 | Release date: | 2015-02-18 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem., 157, 2015
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3WZQ
| Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.7 A resolution | Descriptor: | 6-({5-[(2E,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, HEXAETHYLENE GLYCOL, Streptavidin | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | Deposit date: | 2014-10-01 | Release date: | 2015-02-18 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem., 157, 2015
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3WZO
| Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution | Descriptor: | 6-({5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid, CADMIUM ION, GLYCEROL, ... | Authors: | Kawato, T, Mizohata, E, Shimizu, Y, Meshizuka, T, Yamamoto, T, Takasu, N, Matsuoka, M, Matsumura, H, Tsumoto, K, Kodama, T, Kanai, M, Doi, H, Inoue, T, Sugiyama, A. | Deposit date: | 2014-10-01 | Release date: | 2015-02-18 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structure-based design of a streptavidin mutant specific for an artificial biotin analogue. J.Biochem., 157, 2015
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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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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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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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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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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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3VND
| Crystal structure of tryptophan synthase alpha-subunit from the psychrophile Shewanella frigidimarina K14-2 | Descriptor: | 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, SULFATE ION, Tryptophan synthase alpha chain | Authors: | Mitsuya, D, Tanaka, S, Matsumura, H, Takano, K, Urano, N, Ishida, M. | Deposit date: | 2012-01-12 | Release date: | 2013-01-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Strategy for cold adaptation of the tryptophan synthase alpha subunit from the psychrophile Shewanella frigidimarina K14-2: crystal structure and physicochemical properties J.Biochem., 155, 2014
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3VHI
| Crystal structure of monoZ-biotin-avidin complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-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 (1.76 Å) | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells Chem.Biol., 18, 2011
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3VI2
| Crystal Structure Analysis of Plasmodium falciparum OMP Decarboxylase in complex with inhibitor HMOA | Descriptor: | 4-(2-hydroxy-4-methoxyphenyl)-4-oxobutanoic acid, Orotidine 5'-phosphate decarboxylase, SODIUM ION | Authors: | Takashima, Y, Mizohata, E, Krungkrai, S.R, Matsumura, H, Krungkrai, J, Horii, T, Inoue, T. | Deposit date: | 2011-09-16 | Release date: | 2012-08-01 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase J.Biochem., 152, 2012
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3VHM
| Crystal structure of NPC-biotin-avidin complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-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: | 2011-08-29 | Release date: | 2011-12-28 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells Chem.Biol., 18, 2011
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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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