3A9C
| Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, RIBULOSE-1,5-DIPHOSPHATE, ... | Authors: | Nakamura, A, Fujihashi, M, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-10-22 | Release date: | 2010-11-03 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem., 287, 2012
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3ABF
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3A44
| Crystal structure of HypA in the dimeric form | Descriptor: | Hydrogenase nickel incorporation protein hypA, ZINC ION | Authors: | Watanabe, S, Arai, T, Matsumi, R, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-06-30 | Release date: | 2009-10-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.31 Å) | Cite: | Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J.Mol.Biol., 394, 2009
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3VM6
| Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate | Descriptor: | 1,5-di-O-phosphono-alpha-D-ribofuranose, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Nakamura, A, Fujihashi, M, Aono, R, Sato, T, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2011-12-08 | Release date: | 2012-04-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem., 287, 2012
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3VYT
| Crystal structure of the HypC-HypD-HypE complex (form I inward) | Descriptor: | CHLORIDE ION, Hydrogenase expression/formation protein HypC, Hydrogenase expression/formation protein HypD, ... | Authors: | Watanabe, S, Miki, K. | Deposit date: | 2012-10-02 | Release date: | 2012-11-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Structure, 20, 2012
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3VRC
| Crystal structure of cytochrome c' from Thermochromatium tepidum | Descriptor: | CADMIUM ION, CHLORIDE ION, Cytochrome c', ... | Authors: | Hirano, Y, Kimura, Y, Suzuki, H, Miki, K, Wang, Z.-Y. | Deposit date: | 2012-04-09 | Release date: | 2012-09-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | Structure Analysis and Comparative Characterization of the Cytochrome c' and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum Biochemistry, 51, 2012
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3VYS
| Crystal structure of the HypC-HypD-HypE complex (form I) | Descriptor: | Hydrogenase expression/formation protein HypC, Hydrogenase expression/formation protein HypD, Hydrogenase expression/formation protein HypE, ... | Authors: | Watanabe, S, Miki, K. | Deposit date: | 2012-10-02 | Release date: | 2012-11-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Structure, 20, 2012
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3VYR
| Crystal structure of the HypC-HypD complex | Descriptor: | CITRIC ACID, Hydrogenase expression/formation protein HypC, Hydrogenase expression/formation protein HypD, ... | Authors: | Watanabe, S, Miki, K. | Deposit date: | 2012-10-02 | Release date: | 2012-11-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Structure, 20, 2012
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3VRD
| Crystal structure of flavocytochrome c from Thermochromatium tepidum | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Flavocytochrome c flavin subunit, Flavocytochrome c heme subunit, ... | Authors: | Hirano, Y, Kimura, Y, Suzuki, H, Miki, K, Wang, Z.-Y. | Deposit date: | 2012-04-09 | Release date: | 2012-09-12 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structure Analysis and Comparative Characterization of the Cytochrome c' and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum Biochemistry, 51, 2012
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3VYU
| Crystal structure of the HypC-HypD-HypE complex (form II) | Descriptor: | Hydrogenase expression/formation protein HypC, Hydrogenase expression/formation protein HypD, Hydrogenase expression/formation protein HypE, ... | Authors: | Watanabe, S, Miki, K. | Deposit date: | 2012-10-02 | Release date: | 2012-11-28 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Structure, 20, 2012
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3WJX
| Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-amino-UMP | Descriptor: | 6-AMINOURIDINE 5'-MONOPHOSPHATE, GLYCEROL, Orotidine 5'-phosphate decarboxylase | Authors: | Fujihashi, M, Kuroda, S, Pai, E.F, Miki, K. | Deposit date: | 2013-10-17 | Release date: | 2013-12-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.23 Å) | Cite: | Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc., 135, 2013
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3WJW
| Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-methyl-UMP | Descriptor: | 6-methyluridine 5'-(dihydrogen phosphate), Orotidine 5'-phosphate decarboxylase | Authors: | Fujihashi, M, Kuroda, S, Pai, E.F, Miki, K. | Deposit date: | 2013-10-17 | Release date: | 2013-12-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.59 Å) | Cite: | Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc., 135, 2013
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3WMQ
| Crystal structure of the complex between SLL-2 and GalNAc. | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Kita, A, Jimbo, M, Sakai, R, Morimoto, Y, Miki, K. | Deposit date: | 2013-11-22 | Release date: | 2015-01-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystal structure of a symbiosis-related lectin from octocoral. Glycobiology, 25, 2015
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3WJY
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3WDM
| Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis | Descriptor: | 4-phosphopantoate--beta-alanine ligase, ADENOSINE | Authors: | Kishimoto, A, Kita, A, Ishibashi, T, Tomita, H, Yokooji, Y, Imanaka, T, Atomi, H, Miki, K. | Deposit date: | 2013-06-19 | Release date: | 2014-04-02 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Proteins, 82, 2014
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3WK2
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3WMP
| Crystal structure of SLL-2 | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Kita, A, Jimbo, M, Sakai, R, Morimoto, Y, Miki, K. | Deposit date: | 2013-11-22 | Release date: | 2015-01-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of a symbiosis-related lectin from octocoral. Glycobiology, 25, 2015
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3WK3
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3WDL
| Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP | Descriptor: | 4-phosphopantoate--beta-alanine ligase, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION | Authors: | Kishimoto, A, Kita, A, Ishibashi, T, Tomita, H, Yokooji, Y, Imanaka, T, Atomi, H, Miki, K. | Deposit date: | 2013-06-19 | Release date: | 2014-04-02 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Proteins, 82, 2014
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3WJQ
| Crystal structure of the HypE CN form | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, BENZAMIDINE, DI(HYDROXYETHYL)ETHER, ... | Authors: | Tominaga, T, Watanabe, S, Miki, K. | Deposit date: | 2013-10-14 | Release date: | 2013-12-18 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.645 Å) | Cite: | Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation Proc.Natl.Acad.Sci.USA, 110, 2013
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3WK0
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3WDK
| Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate | Descriptor: | 4-phosphopantoate--beta-alanine ligase, 5'-O-[(S)-hydroxy{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]oxy}phosphoryl]adenosine, CITRATE ANION | Authors: | Kishimoto, A, Kita, A, Ishibashi, T, Tomita, H, Yokooji, Y, Imanaka, T, Atomi, H, Miki, K. | Deposit date: | 2013-06-19 | Release date: | 2014-04-02 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Proteins, 82, 2014
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3WJP
| Crystal structure of the HypE CA form | Descriptor: | BENZAMIDINE, GLYCEROL, Hydrogenase expression/formation protein HypE, ... | Authors: | Tominaga, T, Watanabe, S, Miki, K. | Deposit date: | 2013-10-14 | Release date: | 2013-12-18 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.533 Å) | Cite: | Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation Proc.Natl.Acad.Sci.USA, 110, 2013
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3WK1
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3WJR
| crystal structure of HypE in complex with a nucleotide | Descriptor: | ADENOSINE MONOPHOSPHATE, BENZAMIDINE, DI(HYDROXYETHYL)ETHER, ... | Authors: | Tominaga, T, Watanabe, S, Miki, K. | Deposit date: | 2013-10-14 | Release date: | 2013-12-18 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.864 Å) | Cite: | Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation Proc.Natl.Acad.Sci.USA, 110, 2013
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