3AO0
 
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1EEX
 | | CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA | | Descriptor: | CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Shibata, N, Masuda, J, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-04 | | Release date: | 2001-02-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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1WLK
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1WLI
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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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6IQZ
 | | High resolution structure of bilirubin oxidase from Myrothecium verrucaria - wild type | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, COPPER (II) ION, ... | | Authors: | Shibata, N, Akter, M, Higuchi, Y. | | Deposit date: | 2018-11-09 | | Release date: | 2018-11-21 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.46 Å) | | Cite: | Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
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6IQY
 | | High resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, anaerobically prepared | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Bilirubin oxidase, ... | | Authors: | Shibata, N, Akter, M, Higuchi, Y. | | Deposit date: | 2018-11-09 | | Release date: | 2018-11-21 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
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6IQX
 | | High resolution structure of bilirubin oxidase from Myrothecium verrucaria - M467Q mutant, aerobically prepared | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Bilirubin oxidase, ... | | Authors: | Shibata, N, Akter, M, Higuchi, Y. | | Deposit date: | 2018-11-09 | | Release date: | 2018-11-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.432 Å) | | Cite: | Redox Potential-Dependent Formation of an Unusual His-Trp Bond in Bilirubin Oxidase.
Chemistry, 24, 2018
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2E8I
 | | Structure of 6-aminohexanoate-dimer hydrolase, D1 mutant | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 6-aminohexanoate-dimer hydrolase, GLYCEROL, ... | | Authors: | Shibata, N, Higuchi, Y, Negoro, S. | | Deposit date: | 2007-01-20 | | Release date: | 2008-01-15 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.
Febs J., 276, 2009
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3A20
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3A2Q
 | | Structure of 6-aminohexanoate cyclic dimer hydrolase complexed with substrate | | Descriptor: | 6-AMINOHEXANOIC ACID, 6-aminohexanoate-cyclic-dimer hydrolase, GLYCEROL | | Authors: | Shibata, N. | | Deposit date: | 2009-05-26 | | Release date: | 2009-11-03 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation
J.Biol.Chem., 285, 2010
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3A2P
 | | Structure of 6-aminohexanoate cyclic dimer hydrolase | | Descriptor: | 6-aminohexanoate-cyclic-dimer hydrolase, GLYCEROL | | Authors: | Shibata, N. | | Deposit date: | 2009-05-26 | | Release date: | 2009-11-03 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation
J.Biol.Chem., 285, 2010
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1QVC
 | | CRYSTAL STRUCTURE ANALYSIS OF SINGLE STRANDED DNA BINDING PROTEIN (SSB) FROM E.COLI | | Descriptor: | SINGLE STRANDED DNA BINDING PROTEIN MONOMER | | Authors: | Matsumoto, T, Morimoto, Y, Shibata, N, Shimamoto, N, Tsukihara, T, Yasuoka, N. | | Deposit date: | 1999-07-07 | | Release date: | 2000-06-05 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.2 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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4UBQ
 | | Crystal Structure of IMP-2 Metallo-beta-Lactamase from Acinetobacter spp. | | Descriptor: | ACETATE ION, Beta-lactamase, ZINC ION | | Authors: | Yamaguchi, Y, Matsueda, S, Matsunaga, K, Takashio, N, Toma-Fukai, S, Yamagata, Y, Shibata, N, Wachino, J, Shibayama, K, Arakawa, Y, Kurosaki, H. | | Deposit date: | 2014-08-13 | | Release date: | 2014-12-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of IMP-2 metallo-beta-lactamase from Acinetobacter spp.: comparison of active-site loop structures between IMP-1 and IMP-2.
Biol.Pharm.Bull., 38, 2015
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1EGV
 | | CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. | | Descriptor: | CO-(ADENIN-9-YL-PENTYL)-COBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Masuda, J, Shibata, N, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-17 | | Release date: | 2001-02-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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1EGM
 | | CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. | | Descriptor: | CYANOCOBALAMIN, POTASSIUM ION, PROPANEDIOL DEHYDRATASE, ... | | Authors: | Masuda, J, Shibata, N, Toraya, T, Morimoto, Y, Yasuoka, N. | | Deposit date: | 2000-02-15 | | Release date: | 2000-09-20 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
Structure Fold.Des., 8, 2000
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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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7V5P
 | | The dimeric structure of G80A/H81A myoglobin | | Descriptor: | Myoglobin, OXYGEN ATOM, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Xie, C, Nagao, S, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2021-08-17 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.16 Å) | | Cite: | Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.
Rsc Adv, 11, 2021
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1FLM
 | | DIMER OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F) | | Descriptor: | FLAVIN MONONUCLEOTIDE, PROTEIN (FMN-BINDING PROTEIN) | | Authors: | Suto, K, Kawagoe, K, Shibata, N, Morimoto, K, Higuchi, Y, Kitamura, M, Nakaya, T, Yasuoka, N. | | Deposit date: | 1999-03-10 | | Release date: | 2000-03-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | How do the x-ray structure and the NMR structure of FMN-binding protein differ?
Acta Crystallogr.,Sect.D, 56, 2000
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5AWE
 | | Crystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-beta-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains | | Descriptor: | Putative acetoin utilization protein, acetoin dehydrogenase | | Authors: | Nakabayashi, M, Shibata, N, Kanagawa, M, Nakagawa, N, Kuramitsu, S, Higuchi, Y. | | Deposit date: | 2015-07-03 | | Release date: | 2016-05-18 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal structure of a hypothetical protein, TTHA0829 from Thermus thermophilus HB8, composed of cystathionine-beta-synthase (CBS) and aspartate-kinase chorismate-mutase tyrA (ACT) domains.
Extremophiles, 20, 2016
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5B7E
 | | Structure of perdeuterated CueO | | Descriptor: | Blue copper oxidase CueO, COPPER (II) ION, CU-O-CU LINKAGE, ... | | Authors: | Akter, M, Higuchi, Y, Shibata, N. | | Deposit date: | 2016-06-07 | | Release date: | 2016-10-19 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.42 Å) | | Cite: | Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Acta Crystallogr.,Sect.F, 72, 2016
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5B7F
 | | Structure of CueO - the signal peptide was truncated by HRV3C protease | | Descriptor: | 1,2-ETHANEDIOL, Blue copper oxidase CueO, CALCIUM ION, ... | | Authors: | Akter, M, Higuchi, Y, Shibata, N. | | Deposit date: | 2016-06-07 | | Release date: | 2016-10-19 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Acta Crystallogr.,Sect.F, 72, 2016
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5B7M
 | | Structure of perdeuterated CueO - the signal peptide was truncated by HRV3C protease | | Descriptor: | Blue copper oxidase CueO, COPPER (II) ION | | Authors: | Akter, M, Higuchi, Y, Shibata, N. | | Deposit date: | 2016-06-07 | | Release date: | 2016-10-19 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Acta Crystallogr.,Sect.F, 72, 2016
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5GYR
 | | Tetrameric Allochromatium vinosum cytochrome c' | | Descriptor: | Cytochrome c', HEME C | | Authors: | Yamanaka, M, Hoshizumi, M, Nagao, S, Nakayama, R, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2016-09-23 | | Release date: | 2017-02-08 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers
Protein Sci., 26, 2017
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6L1V
 | | Domain-swapped Alcaligenes xylosoxidans azurin dimer | | Descriptor: | Azurin-1, COPPER (II) ION | | Authors: | Cahyono, R.N, Yamanaka, M, Nagao, S, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2019-09-30 | | Release date: | 2020-02-05 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | 3D domain swapping of azurin from Alcaligenes xylosoxidans.
Metallomics, 12, 2020
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