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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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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6LS8
 | | The monomeric structure of G80A/H81A/H82A myoglobin | | Descriptor: | Myoglobin, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagao, S, Suda, A, Kobayashi, H, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2020-01-17 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin.
Chem Asian J, 15, 2020
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6LTM
 | | The dimeric structure of G80A/H81A/H82A myoglobin | | Descriptor: | Myoglobin, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagao, S, Suda, A, Kobayashi, H, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2020-01-22 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin.
Chem Asian J, 15, 2020
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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: | 2023-11-08 | | 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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6LTL
 | | The dimeric structure of G80A myoglobin | | Descriptor: | Myoglobin, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nagao, S, Suda, A, Kobayashi, H, Shibata, N, Higuchi, Y, Hirota, S. | | Deposit date: | 2020-01-22 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin.
Chem Asian J, 15, 2020
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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: | 2020-02-26 | | 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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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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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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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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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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1BWV
 | | Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate | | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE) | | Authors: | Sugawara, H, Yamamoto, H, Shibata, N, Inoue, T, Miyake, C, Yokota, A, Kai, Y. | | Deposit date: | 1998-09-29 | | Release date: | 1999-09-27 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.
J.Biol.Chem., 274, 1999
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1BK0
 | | ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX) | | Descriptor: | FE (III) ION, ISOPENICILLIN N SYNTHASE, L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE, ... | | Authors: | Roach, P.L, Clifton, I.J, Hensgens, C.M.H, Shibata, N, Schofield, C.J, Hajdu, J, Baldwin, J.E. | | Deposit date: | 1998-07-14 | | Release date: | 1999-01-13 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.
Nature, 387, 1997
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1BLZ
 | | ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE-NO COMPLEX) | | Descriptor: | FE (III) ION, ISOPENICILLIN N SYNTHASE, L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE, ... | | Authors: | Roach, P.L, Clifton, I.J, Hensgens, C.M.H, Shibata, N, Schofield, C.J, Hajdu, J, Baldwin, J.E. | | Deposit date: | 1998-07-22 | | Release date: | 1999-01-13 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.
Nature, 387, 1997
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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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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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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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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: | 2024-05-29 | | 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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3AXG
 | | Structure of 6-aminohexanoate-oligomer hydrolase | | Descriptor: | Endotype 6-aminohexanoat-oligomer hydrolase, SODIUM ION | | Authors: | Negoro, S, Shibata, N, Tanaka, Y, Yasuhira, K, Shibata, H, Hashimoto, H, Lee, Y.H, Ohshima, S, Santa, R, Mochiji, K, Goto, Y, Ikegami, T, Nagai, K, Kato, D, Takeo, M, Higuchi, Y. | | Deposit date: | 2011-04-04 | | Release date: | 2011-12-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
J.Biol.Chem., 287, 2012
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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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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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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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