4U72
 
 | | Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant) | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, 4-PHENYL-1H-IMIDAZOLE, Indoleamine 2,3-dioxygenase 1, ... | | Authors: | Sugimoto, H, Horitani, M, Kometani, E, Shiro, Y. | | Deposit date: | 2014-07-30 | | Release date: | 2015-09-02 | | Last modified: | 2020-01-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase
to be published
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4U74
 | | Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant) | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, 4-PHENYL-1H-IMIDAZOLE, Indoleamine 2,3-dioxygenase 1, ... | | Authors: | Sugimoto, H, Horitani, M, Kometani, E, Shiro, Y. | | Deposit date: | 2014-07-30 | | Release date: | 2015-09-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Conformation and Mobility of Active Site Loop is Critical for Substrate Binding and Inhibition in Human Indoleamine 2,3-Dioxygenase
to be published
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1JFC
 | | X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferrous CO state at atomic resolution | | Descriptor: | CARBON MONOXIDE, GLYCEROL, PROTOPORPHYRIN IX CONTAINING FE, ... | | Authors: | Shimizu, H, Adachi, S, Park, S.Y, Shiro, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-06-20 | | Release date: | 2001-12-20 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution.
Acta Crystallogr.,Sect.D, 58, 2002
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4YN8
 | | Crystal Structure of Response Regulator ChrA in Heme-Sensing Two Component System | | Descriptor: | MAGNESIUM ION, Response regulator ChrA, SULFATE ION | | Authors: | Doi, A, Nakamura, H, Shiro, Y, Sugimoto, H. | | Deposit date: | 2015-03-09 | | Release date: | 2015-08-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae.
Acta Crystallogr.,Sect.F, 71, 2015
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5GUX
 | | Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon | | Descriptor: | Antibody fab fragment heavy chain, Antibody fab fragment light chain, CALCIUM ION, ... | | Authors: | Ishii, S, Terasaka, E, Sugimoto, H, Shiro, Y, Tosha, T. | | Deposit date: | 2016-08-31 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Dynamics of nitric oxide controlled by protein complex in bacterial system.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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5GUW
 | | Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa | | Descriptor: | CALCIUM ION, CHLORIDE ION, FE (III) ION, ... | | Authors: | Terasaka, E, Sugimoto, H, Shiro, Y, Tosha, T. | | Deposit date: | 2016-08-31 | | Release date: | 2017-08-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Dynamics of nitric oxide controlled by protein complex in bacterial system
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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3CV9
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R73A/R84A mutant) in complex with 1alpha,25-dihydroxyvitamin D3 | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
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3CV8
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant) | | Descriptor: | Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
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6QQ5
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric oxide reductase subunit B, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
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6QQ6
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans | | Descriptor: | (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE, CALCIUM ION, DODECYL-BETA-D-MALTOSIDE, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
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1CMJ
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1CL6
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1CMN
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1D06
 | | STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, nitrogen fixation regulatory protein fixL | | Authors: | Miyatake, H, Mukai, M, Park, S.-Y, Adachi, S, Tamura, K, Nakamura, H, Nakamura, K, Tsuchiya, T, Iizuka, T, Shiro, Y. | | Deposit date: | 1999-09-09 | | Release date: | 2000-03-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies
J.MOL.BIOL., 301, 2000
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1WVP
 | | Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64) | | Descriptor: | Myoglobin, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION | | Authors: | Makino, M, Sugimoto, H, Kamiya, N, Shiro, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-12-23 | | Release date: | 2005-01-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.53 Å) | | Cite: | Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion
J.Am.Chem.Soc., 113, 1991
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5GJ3
 | | Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2) | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, Periplasmic binding protein, ZINC ION | | Authors: | Rahman, M.M, Naoe, Y, Nakamura, N, Shiro, Y, Sugimoto, H. | | Deposit date: | 2016-06-26 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85, 2017
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5GIZ
 | | Periplasmic heme-binding protein BhuT in apo form | | Descriptor: | CHLORIDE ION, Putative hemin transport system, substrate-binding protein, ... | | Authors: | Nakamura, N, Naoe, Y, Rahman, M.M, Shiro, Y, Sugimoto, H. | | Deposit date: | 2016-06-26 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85, 2017
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1X3U
 | | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot | | Descriptor: | Transcriptional regulatory protein fixJ | | Authors: | Kurashima-Ito, K, Kasai, Y, Hosono, K, Tamura, K, Oue, S, Isogai, M, Ito, Y, Nakamura, H, Shiro, Y. | | Deposit date: | 2005-05-10 | | Release date: | 2006-05-02 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter
Biochemistry, 44, 2005
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6K9S
 | | Structure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan | | Descriptor: | (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid, Bifunctional cytochrome P450/NADPH--P450 reductase, CARBON MONOXIDE, ... | | Authors: | Stanfield, J.K, Omura, K, Kasai, C, Sugimoto, H, Shiro, Y, Watanabe, Y, Shoji, O. | | Deposit date: | 2019-06-17 | | Release date: | 2020-03-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6K24
 | | Structure of the Rhodium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan | | Descriptor: | (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid, Bifunctional cytochrome P450/NADPH--P450 reductase, DIMETHYL SULFOXIDE, ... | | Authors: | Stanfield, J.K, Matsumoto, A, Kasai, C, Sugimoto, H, Shiro, Y, Watanabe, Y, Shoji, O. | | Deposit date: | 2019-05-13 | | Release date: | 2020-03-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6JZS
 | | Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan in complex with Pyridine | | Descriptor: | (2S)-2-[[(1R,4aR,4bR,10aR)-1,4a-dimethyl-7-propan-2-yl-2,3,4,4b,5,6,10,10a-octahydrophenanthren-1-yl]carbonylamino]-3-( 1H-indol-3-yl)propanoic acid, Bifunctional cytochrome P450/NADPH--P450 reductase, GLYCEROL, ... | | Authors: | Stanfield, J.K, Omura, K, Matsumoto, A, Kasai, C, Sugimoto, H, Shiro, Y, Watanabe, Y, Shoji, O. | | Deposit date: | 2019-05-03 | | Release date: | 2020-03-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain.
Angew.Chem.Int.Ed.Engl., 59, 2020
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1WN1
 | | Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3 | | Descriptor: | COBALT (II) ION, dipeptidase | | Authors: | Jeyakanthan, J, Taka, J, Kitaguchi, Y, Shiro, Y, Yokoyama, S, Yutani, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-07-26 | | Release date: | 2005-08-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Crystal Structure of Dipeptiase from Pyrococcus Horikoshii OT3
To be Published
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3O0R
 | | Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment | | Descriptor: | CALCIUM ION, FE (III) ION, HEME C, ... | | Authors: | Hino, T, Matsumoto, Y, Nagano, S, Sugimoto, H, Fukumori, Y, Murata, T, Iwata, S, Shiro, Y. | | Deposit date: | 2010-07-20 | | Release date: | 2010-12-29 | | Last modified: | 2013-10-16 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of biological N2O generation by bacterial nitric oxide reductase
Science, 330, 2010
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6JLG
 | | Crystal Structure of HasAp with Co-9,10,19,20-Tetraphenylporphycene | | Descriptor: | GLYCEROL, Heme acquisition protein HasA, PHOSPHATE ION, ... | | Authors: | Sakakibara, E, Shisaka, Y, Onoda, H, Sugimoto, H, Shiro, Y, Watanabe, Y, Shoji, O. | | Deposit date: | 2019-03-05 | | Release date: | 2020-03-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Highly malleable haem-binding site of the haemoprotein HasA permits stable accommodation of bulky tetraphenylporphycenes.
Rsc Adv, 9, 2019
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7DVO
 | | Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Nomura, T, Kimura, T, Kanematsu, Y, Yamashita, K, Hirata, K, Ueno, G, Murakami, H, Hisano, T, Yamagiwa, R, Takeda, H, Gopalasingam, C, Yuki, K, Kousaka, R, Yanagasawa, S, Shoji, O, Kumasaka, T, Takano, Y, Ago, H, Yamamoto, M, Sugimoto, H, Tosha, T, Kubo, M, Shiro, Y. | | Deposit date: | 2021-01-14 | | Release date: | 2021-05-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.
Proc.Natl.Acad.Sci.USA, 118, 2021
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