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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4GA5
 | | Crystal structure of AMP phosphorylase C-terminal deletion mutant in the apo-form | | Descriptor: | Putative thymidine phosphorylase | | Authors: | Nishitani, Y, Aono, R, Nakamura, A, Sato, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2012-07-25 | | Release date: | 2013-05-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.25 Å) | | Cite: | Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization
J.Mol.Biol., 425, 2013
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4G9I
 | | Crystal structure of T.kodakarensis HypF | | Descriptor: | Hydrogenase maturation protein HypF, ZINC ION | | Authors: | Tominaga, T, Watanabe, S, Matsumi, R, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2012-07-24 | | Release date: | 2012-10-24 | | Method: | X-RAY DIFFRACTION (4.5 Å) | | Cite: | Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.
Acta Crystallogr.,Sect.F, 68, 2012
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4GA4
 | | Crystal structure of AMP phosphorylase N-terminal deletion mutant | | Descriptor: | PHOSPHATE ION, Putative thymidine phosphorylase | | Authors: | Nishitani, Y, Aono, R, Nakamura, A, Sato, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2012-07-25 | | Release date: | 2013-05-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.51 Å) | | Cite: | Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization
J.Mol.Biol., 425, 2013
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1GEH
 | | CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE) | | Descriptor: | RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, SULFATE ION | | Authors: | Kitano, K, Maeda, N, Fukui, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2000-11-13 | | Release date: | 2001-12-19 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal Structure of a Novel-Type Archaeal Rubisco with Pentagonal Symmetry
Structure, 9, 2001
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4GA6
 | | Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates | | Descriptor: | ADENOSINE MONOPHOSPHATE, Putative thymidine phosphorylase, SULFATE ION | | Authors: | Nishitani, Y, Aono, R, Nakamura, A, Sato, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2012-07-25 | | Release date: | 2013-05-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.21 Å) | | Cite: | Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization
J.Mol.Biol., 425, 2013
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3KDO
 | | Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-10-23 | | Release date: | 2010-10-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285, 2010
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3KDN
 | | Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-10-23 | | Release date: | 2010-10-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285, 2010
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8JVG
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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8JVC
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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8JVF
 | | Crystal structure of dephospho-coenzyme A kinase | | Descriptor: | GTP-dependent dephospho-CoA kinase, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION | | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | | Deposit date: | 2023-06-28 | | Release date: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.
Proteins, 92, 2024
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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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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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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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3A12
 | | Crystal structure of Type III Rubisco complexed with 2-CABP | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-03-25 | | Release date: | 2010-04-07 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile
J.Biol.Chem., 285, 2010
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3A13
 | | Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP and activated with Ca | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, CALCIUM ION, MAGNESIUM ION, ... | | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-03-25 | | Release date: | 2010-04-07 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Structure-based optimization of a Type III Rubisco from a hyperthermophile
To be Published
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6JBD
 | | Phosphotransferase-ATP complex related to CoA biosynthesis pathway | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CALCIUM ION, ... | | Authors: | Kita, A, Kishimoto, A, Shimosaka, T, Tomita, H, Yokooji, Y, Imanaka, T, Atomi, H, Miki, K. | | Deposit date: | 2019-01-25 | | Release date: | 2020-01-29 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of pantoate kinase from Thermococcus kodakarensis.
Proteins, 88, 2020
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6JBC
 | | Phosphotransferase related to CoA biosynthesis pathway | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, GLYCEROL, ... | | Authors: | Kita, A, Kishimoto, A, Shimosaka, T, Tomita, H, Yokooji, Y, Imanaka, T, Atomi, H, Miki, K. | | Deposit date: | 2019-01-25 | | Release date: | 2020-01-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of pantoate kinase from Thermococcus kodakarensis.
Proteins, 88, 2020
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3A11
 | | Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 | | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, Translation initiation factor eIF-2B, ... | | Authors: | Nakamura, A, Fujihashi, M, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2009-03-25 | | Release date: | 2010-03-31 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 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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2Z1C
 | | Crystal structure of HypC from Thermococcus kodakaraensis KOD1 | | Descriptor: | GLYCEROL, Hydrogenase expression/formation protein HypC, TETRAETHYLENE GLYCOL | | Authors: | Watanabe, S, Matsumi, R, Arai, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2007-05-08 | | Release date: | 2007-07-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
Mol.Cell, 27, 2007
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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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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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2Z1E
 | | Crystal structure of HypE from Thermococcus kodakaraensis (outward form) | | Descriptor: | Hydrogenase expression/formation protein HypE | | Authors: | Watanabe, S, Matsumi, R, Arai, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2007-05-08 | | Release date: | 2007-07-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
Mol.Cell, 27, 2007
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2Z1F
 | | Crystal structure of HypE from Thermococcus kodakaraensis (inward form) | | Descriptor: | Hydrogenase expression/formation protein HypE | | Authors: | Watanabe, S, Matsumi, R, Arai, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2007-05-08 | | Release date: | 2007-07-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
Mol.Cell, 27, 2007
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2Z1D
 | | Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis | | Descriptor: | Hydrogenase expression/formation protein hypD, IRON/SULFUR CLUSTER | | Authors: | Watanabe, S, Matsumi, R, Arai, T, Atomi, H, Imanaka, T, Miki, K. | | Deposit date: | 2007-05-08 | | Release date: | 2007-07-17 | | Last modified: | 2014-11-12 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
Mol.Cell, 27, 2007
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