6A8V
| PhoQ sensor domain (D179R mutant): analysis of internal cavity | Descriptor: | Sensor protein PhoQ | Authors: | Yoshitani, K, Ishii, E, Taniguchi, K, Sugimoto, H, Shiro, Y, Mori, H, Akiyama, Y, Kato, A, Utsumi, R, Eguchi, Y. | Deposit date: | 2018-07-10 | Release date: | 2019-01-30 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control. Biosci. Biotechnol. Biochem., 83, 2019
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6A8U
| PhoQ sensor domain (wild type): analysis of internal cavity | Descriptor: | Sensor protein PhoQ | Authors: | Yoshitani, K, Ishii, E, Taniguchi, K, Sugimoto, H, Shiro, Y, Mori, H, Akiyama, Y, Kato, A, Utsumi, R, Eguchi, Y. | Deposit date: | 2018-07-10 | Release date: | 2019-01-30 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.848 Å) | Cite: | Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control. Biosci. Biotechnol. Biochem., 83, 2019
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3VOK
| X-ray Crystal Structure of Wild Type HrtR in the Apo Form with the Target DNA. | Descriptor: | 5'-D(*AP*TP*GP*AP*CP*AP*CP*TP*GP*TP*GP*TP*CP*AP*T)-3', Transcriptional regulator | Authors: | Sawai, H, Sugimoto, H, Shiro, Y, Aono, S. | Deposit date: | 2012-01-27 | Release date: | 2012-07-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for the Transcriptional Regulation of Heme Homeostasis in Lactococcus lactis. J.Biol.Chem., 287, 2012
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3VOX
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3VP5
| X-ray Crystal Structure of Wild Type HrtR in the Holo Form | Descriptor: | CACODYLATE ION, PROTOPORPHYRIN IX CONTAINING FE, Transcriptional regulator | Authors: | Sawai, H, Sugimoto, H, Shiro, Y, Aono, S. | Deposit date: | 2012-02-23 | Release date: | 2012-07-25 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structural Basis for the Transcriptional Regulation of Heme Homeostasis in Lactococcus lactis. J.Biol.Chem., 287, 2012
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3WVS
| Crystal Structure of Cytochrome P450revI | Descriptor: | (2E,4S,5S,6E,8E)-10-{(2R,3S,6S,8R,9S)-9-butyl-8-[(1E,3E)-4-carboxy-3-methylbuta-1,3-dien-1-yl]-3-methyl-1,7-dioxaspiro[5.5]undec-2-yl}-5-hydroxy-4,8-dimethyldeca-2,6,8-trienoic acid, GLYCEROL, L(+)-TARTARIC ACID, ... | Authors: | Nagano, S, Takahashi, S, Osada, H, Shiro, Y. | Deposit date: | 2014-06-06 | Release date: | 2014-10-01 | Last modified: | 2022-08-24 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Structure-function analyses of cytochrome P450revI involved in reveromycin A biosynthesis and evaluation of the biological activity of its substrate, reveromycin T. J.Biol.Chem., 289, 2014
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3A0R
| Crystal structure of histidine kinase ThkA (TM1359) in complex with response regulator protein TrrA (TM1360) | Descriptor: | MERCURY (II) ION, Response regulator, Sensor protein | Authors: | Yamada, S, Sugimoto, H, Kobayashi, M, Ohno, A, Nakamura, H, Shiro, Y. | Deposit date: | 2009-03-24 | Release date: | 2009-10-20 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (3.8 Å) | Cite: | Structure of PAS-linked histidine kinase and the response regulator complex Structure, 17, 2009
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5YL3
| Crystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5 | Descriptor: | Myoglobin, PORPHYCENE CONTAINING MN, SULFATE ION | Authors: | Oohora, K, Meichin, H, Kihira, Y, Sugimoto, H, Shiro, Y, Hayashi, T. | Deposit date: | 2017-10-17 | Release date: | 2017-12-27 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Manganese(V) Porphycene Complex Responsible for Inert C-H Bond Hydroxylation in a Myoglobin Matrix. J. Am. Chem. Soc., 139, 2017
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2Z6B
| Crystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III) protoporphyrin | Descriptor: | 1-ETHYL-PYRROLIDINE-2,5-DIONE, Baseplate structural protein Gp27, Tail-associated lysozyme | Authors: | Koshiyama, T, Yokoi, N, Ueno, T, Kanamaru, S, Nagano, S, Shiro, Y, Arisaka, F, Watanabe, Y. | Deposit date: | 2007-07-28 | Release date: | 2008-04-15 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (3.11 Å) | Cite: | Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor. Small, 4, 2008
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2ZQJ
| Substrate-Free Form of Cytochrome P450BSbeta | Descriptor: | Cytochrome P450 152A1, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Shoji, O, Fujishiro, T, Nagano, S, Hirose, T, Shiro, Y, Watanabe, Y. | Deposit date: | 2008-08-11 | Release date: | 2009-09-01 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis. J.Biol.Inorg.Chem., 2010
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2ZQX
| Cytochrome P450BSbeta cocrystallized with heptanoic acid | Descriptor: | Cytochrome P450 152A1, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Shoji, O, Fujishiro, T, Nagano, S, Hirose, T, Shiro, Y, Watanabe, Y. | Deposit date: | 2008-08-22 | Release date: | 2009-08-25 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.37 Å) | Cite: | Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis. J.Biol.Inorg.Chem., 2010
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3A1L
| Crystal Structure of 11,11'-Dichlorochromopyrrolic Acid Bound Cytochrome P450 StaP (CYP245A1) | Descriptor: | 3,4-bis(7-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylic acid, Cytochrome P450, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Makino, M, Sugimoto, H, Shiro, Y, Asamizu, S, Onaka, H, Nagano, S. | Deposit date: | 2009-04-09 | Release date: | 2009-05-12 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Theoretical and experimental studies of the conversion of chromopyrrolic acid to an antitumor derivative by cytochrome P450 StaP: the catalytic role of water molecules J.Am.Chem.Soc., 131, 2009
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3AGT
| Hemerythrin-like domain of DcrH (met) | Descriptor: | CHLORO DIIRON-OXO MOIETY, Hemerythrin-like domain protein DcrH | Authors: | Onoda, A, Okamoto, Y, Sugimoto, H, Mizohata, E, Inoue, T, Shiro, Y, Hayashi, T. | Deposit date: | 2010-04-06 | Release date: | 2011-04-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH to be published
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3AGU
| Hemerythrin-like domain of DcrH (semimet-R) | Descriptor: | CHLORO DIIRON-OXO MOIETY, Hemerythrin-like domain protein DcrH | Authors: | Onoda, A, Okamoto, Y, Sugimoto, H, Mizohata, E, Inoue, T, Shiro, Y, Hayashi, T. | Deposit date: | 2010-04-06 | Release date: | 2011-04-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.805 Å) | Cite: | Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH to be published
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3AWM
| Cytochrome P450SP alpha (CYP152B1) wild-type with palmitic acid | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, Fatty acid alpha-hydroxylase, PALMITIC ACID, ... | Authors: | Fujishiro, T, Shoji, O, Nagano, S, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2011-03-25 | Release date: | 2011-06-29 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position J.Biol.Chem., 286, 2011
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3AWP
| Cytochrome P450SP alpha (CYP152B1) mutant F288G | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, Fatty acid alpha-hydroxylase, PALMITIC ACID, ... | Authors: | Fujishiro, T, Shoji, O, Nagano, S, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2011-03-25 | Release date: | 2011-06-29 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position. J.Biol.Chem., 286, 2011
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3AWQ
| Cytochrome P450SP alpha (CYP152B1) mutant L78F | Descriptor: | Fatty acid alpha-hydroxylase, PALMITIC ACID, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Fujishiro, T, Shoji, O, Nagano, S, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2011-03-25 | Release date: | 2011-06-29 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position. J.Biol.Chem., 286, 2011
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5XA3
| Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine | Descriptor: | Bifunctional cytochrome P450/NADPH-P450 reductase, DIMETHYL SULFOXIDE, PHENYLALANINE, ... | Authors: | Shoji, O, Yanagisawa, S, Stanfield, J.K, Suzuki, K, Kasai, C, Cong, Z, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2017-03-10 | Release date: | 2018-02-21 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives. Angew. Chem. Int. Ed. Engl., 56, 2017
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5XSO
| Crystal structure of full-length FixJ from B. japonicum crystallized in space group C2221 | Descriptor: | FORMIC ACID, GLYCEROL, Response regulator FixJ | Authors: | Nishizono, Y, Hisano, T, Sawai, H, Shiro, Y, Nakamura, H, Wright, G.S.A, Saeki, A, Hikima, T, Yamamoto, M, Antonyuk, S.V, Hasnain, S.S. | Deposit date: | 2017-06-14 | Release date: | 2018-05-23 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.778 Å) | Cite: | Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system. Sci Signal, 11, 2018
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5XHJ
| Crystal Structure of P450BM3 with 5-Cyclohexylvaleroyl-L-Tryptophan | Descriptor: | 5-cyclohexylpentanoic acid, Bifunctional cytochrome P450/NADPH--P450 reductase, PROTOPORPHYRIN IX CONTAINING FE, ... | Authors: | Suzuki, K, Shoji, O, Stanfield, J.K, Kasai, C, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2017-04-21 | Release date: | 2017-12-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Control of stereoselectivity of benzylic hydroxylation catalysed by wild-type cytochrome P450BM3 using decoy molecules CATALYSIS SCIENCE AND TECHNOLOGY, 7, 2017
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5XT2
| Crystal structures of full-length FixJ from B. japonicum crystallized in space group P212121 | Descriptor: | FORMIC ACID, GLYCEROL, MAGNESIUM ION, ... | Authors: | Nishizono, Y, Hisano, T, Shiro, Y, Sawai, H, Wright, G.S.A, Saeki, A, Hikima, T, Nakamura, H, Yamamoto, M, Antonyuk, S.V, Hasnain, S.S. | Deposit date: | 2017-06-16 | Release date: | 2018-05-23 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.652 Å) | Cite: | Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system. Sci Signal, 11, 2018
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5Y89
| Periplasmic heme-binding protein BhuT in complex with one heme (holo-1) | Descriptor: | ACETATE ION, PROTOPORPHYRIN IX CONTAINING FE, Putative hemin transport system, ... | Authors: | Naoe, Y, Nakamura, N, Rahman, M.M, Shiro, Y, Sugimoto, H. | Deposit date: | 2017-08-20 | Release date: | 2017-10-11 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems Proteins, 85, 2017
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5Y8B
| Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in apo form | Descriptor: | MAGNESIUM ION, Periplasmic binding protein | Authors: | Rahman, M.M, Naoe, Y, Nakamura, N, Doi, A, Shiro, Y, Sugimoto, H. | Deposit date: | 2017-08-20 | Release date: | 2017-10-11 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems Proteins, 85, 2017
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5Y8A
| Periplasmic heme-binding protein BhuT in complex with two hemes (holo-2 form) | Descriptor: | CALCIUM ION, PROTOPORPHYRIN IX CONTAINING FE, Putative hemin transport system, ... | Authors: | Nakamura, N, Naoe, Y, Rahman, M.M, Shiro, Y, Sugimoto, H. | Deposit date: | 2017-08-20 | Release date: | 2017-10-11 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.001 Å) | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems Proteins, 85, 2017
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5YHJ
| Cytochrome P450EX alpha (CYP152N1) wild-type with myristic acid | Descriptor: | Cytochrome P450, MYRISTIC ACID, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Onoda, H, Shoji, O, Suzuki, K, Sugimoto, H, Shiro, Y, Watanabe, Y. | Deposit date: | 2017-09-28 | Release date: | 2017-12-06 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Alpha-Oxidative Decarboxylation of Fatty Acids Catalysed by Cytochrome P450 Peroxygenases Yielding Shorter-Alkyl-Chain Fatty Acids Catalysis Science And Technology, 2017
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