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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6IW3
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6JCK
| Complex structure of Axin-DIX and Dvl2-DIX | Descriptor: | Axin-1, Segment polarity protein dishevelled homolog DVL-2 | Authors: | Yamanishi, K, Shibata, N. | Deposit date: | 2019-01-29 | Release date: | 2020-01-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.09 Å) | Cite: | A direct heterotypic interaction between the DIX domains of Dishevelled and Axin mediates signaling to beta-catenin. Sci.Signal., 12, 2019
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6K7C
| Dimeric Shewanella violacea cytochrome c5 | Descriptor: | HEME C, NITRATE ION, Soluble cytochrome cA | Authors: | Yang, H, Yamanaka, M, Nagao, S, Yasuhara, K, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2019-06-07 | Release date: | 2019-09-04 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Protein surface charge effect on 3D domain swapping in cells for c-type cytochromes. Biochim Biophys Acta Proteins Proteom, 1867, 2019
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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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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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7DGN
| The Co-bound dimeric structure of K79H/G80A/H81A myoglobin | Descriptor: | COBALT (II) ION, Myoglobin, OXYGEN ATOM, ... | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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7DGJ
| The dimeric structure of K78H/G80A/H82A myoglobin | Descriptor: | Myoglobin, OXYGEN ATOM, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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7DGM
| The dimeric structure of K79H/G80A/H81A myoglobin | Descriptor: | Myoglobin, OXYGEN ATOM, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.62 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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7DGL
| The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin | Descriptor: | Myoglobin, NICKEL (II) ION, OXYGEN ATOM, ... | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.91 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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7DGO
| The Zn-bound dimeric structure of K79H/G80A/H81A myoglobin | Descriptor: | Myoglobin, OXYGEN ATOM, PROTOPORPHYRIN IX CONTAINING FE, ... | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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7DGK
| The Co-bound dimeric structure of K78H/G80A/H82A myoglobin | Descriptor: | COBALT (II) ION, Myoglobin, OXYGEN ATOM, ... | Authors: | Nagao, S, Idomoto, A, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2020-11-12 | Release date: | 2021-02-17 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem., 217, 2021
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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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1WRB
| Crystal structure of the N-terminal RecA-like domain of DjVLGB, a pranarian Vasa-like RNA helicase | Descriptor: | DjVLGB, SULFATE ION | Authors: | Kurimoto, K, Muto, Y, Obayashi, N, Terada, T, Shirouzu, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Kigawa, T, Okumura, H, Tanaka, A, Shibata, N, Kashikawa, M, Agata, K, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-10-14 | Release date: | 2005-04-12 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein J.Struct.Biol., 150, 2005
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1WYB
| Structure of 6-aminohexanoate-dimer hydrolase | Descriptor: | 6-aminohexanoate-dimer hydrolase | Authors: | Negoro, S, Ohki, T, Shibata, N, Mizuno, N, Wakitani, Y, Tsurukame, J, Matsumoto, K, Kawamoto, I, Takeo, M, Higuchi, Y. | Deposit date: | 2005-02-09 | Release date: | 2005-09-20 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structure of 6-aminohexanoate-dimer hydrolase To be Published
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5Y3C
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5Y3B
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1WYC
| Structure of 6-aminohexanoate-dimer hydrolase, DN mutant | Descriptor: | 6-aminohexanoate-dimer hydrolase | Authors: | Negoro, S, Ohki, T, Shibata, N, Mizuno, N, Wakitani, Y, Tsurukame, J, Matsumoto, K, Kawamoto, I, Takeo, M, Higuchi, Y. | Deposit date: | 2005-02-09 | Release date: | 2006-02-21 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase J.Mol.Biol., 370, 2007
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5Z25
| Trimeric Alpha-Helix-Inserted Circular Permutant of Cytochrome c555 | Descriptor: | Cytochrome c552, HEME C, TETRAETHYLENE GLYCOL | Authors: | Oda, A, Nagao, S, Yamanaka, M, Ueda, I, Shibata, N, Higuchi, Y, Hirota, S. | Deposit date: | 2017-12-28 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Construction of a Triangle-Shaped Trimer and a Tetrahedron Using an alpha-Helix-Inserted Circular Permutant of Cytochrome c555. Chem Asian J, 13, 2018
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1WUJ
| Three-Dimensional Structure Of The Ni-B State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F | Descriptor: | FE3-S4 CLUSTER, IRON/SULFUR CLUSTER, MAGNESIUM ION, ... | Authors: | Ogata, H, Hirota, S, Nakahara, A, Komori, H, Shibata, N, Kato, T, Kano, K, Higuchi, Y. | Deposit date: | 2004-12-07 | Release date: | 2005-12-07 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state Structure, 13, 2005
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1WUH
| Three-Dimensional Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, FE3-S4 CLUSTER, IRON/SULFUR CLUSTER, ... | Authors: | Ogata, H, Hirota, S, Nakahara, A, Komori, H, Shibata, N, Kato, T, Kano, K, Higuchi, Y. | Deposit date: | 2004-12-07 | Release date: | 2005-12-07 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (1.24 Å) | Cite: | Structural basis for the activation process of [NiFe] hydrogenase from D.vulgaris Miyazaki F To be Published
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1WUK
| High resolution Structure Of The Oxidized State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, FE3-S4 CLUSTER, IRON/SULFUR CLUSTER, ... | Authors: | Ogata, H, Hirota, S, Nakahara, A, Komori, H, Shibata, N, Kato, T, Kano, K, Higuchi, Y. | Deposit date: | 2004-12-07 | Release date: | 2005-12-07 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state Structure, 13, 2005
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1WUZ
| Structure of EC1 domain of CNR | Descriptor: | Pcdha4 protein | Authors: | Morishita, H, Umitsu, M, Yamaguchi, T, Murata, Y, Shibata, N, Udaka, K, Higuchi, Y, Akutsu, H, Yagi, T, Ikegami, T. | Deposit date: | 2004-12-09 | Release date: | 2005-12-13 | Last modified: | 2022-03-02 | Method: | SOLUTION NMR | Cite: | Structural diversity of the first cadherin domains revealed by the structure of CNR/Protocadherin alpha To be Published
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1WUL
| High Resolution Structure Of The Reduced State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, FE3-S4 CLUSTER, ... | Authors: | Ogata, H, Hirota, S, Nakahara, A, Komori, H, Shibata, N, Kato, T, Kano, K, Higuchi, Y. | Deposit date: | 2004-12-07 | Release date: | 2005-12-07 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state Structure, 13, 2005
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1WUI
| Ultra-High resolution Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, FE3-S4 CLUSTER, ... | Authors: | Ogata, H, Hirota, S, Nakahara, A, Komori, H, Shibata, N, Kato, T, Kano, K, Higuchi, Y. | Deposit date: | 2004-12-07 | Release date: | 2005-12-07 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (1.04 Å) | Cite: | Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state Structure, 13, 2005
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