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Yorodumi- PDB-7dvo: Structure of Reaction Intermediate of Cytochrome P450 NO Reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dvo | |||||||||
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Title | Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL | |||||||||
Components | NADP nitrous oxide-forming nitric oxide reductase | |||||||||
Keywords | OXIDOREDUCTASE / heme enzyme / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information nitric oxide reductase [NAD(P)+, nitrous oxide-forming] / nitric oxide reductase (NAD(P)H) activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Fusarium oxysporum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Model details | cytochrome P450nor | |||||||||
Authors | Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. ...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. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography. Authors: Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamada, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. / Gopalasingam, C. / Kousaka, R. / ...Authors: Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamada, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. / Gopalasingam, C. / Kousaka, R. / Yanagisawa, S. / Shoji, O. / Kumasaka, T. / Yamamoto, M. / Takano, Y. / Sugimoto, H. / Tosha, T. / Kubo, M. / Shiro, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dvo.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dvo.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/7dvo ftp://data.pdbj.org/pub/pdb/validation_reports/dv/7dvo | HTTPS FTP |
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-Related structure data
Related structure data | 5y5kS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1783177 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44420.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: CYP55A1, CYP55 / Plasmid: pRSET-C / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P23295, nitric oxide reductase [NAD(P)+, nitrous oxide-forming] #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8.5 Details: 38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23767 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2018 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23767 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 73309 / % possible obs: 100 % / Redundancy: 109.5 % / CC1/2: 0.987 / R split: 0.113 / Net I/σ(I): 6.76 |
Reflection shell | Resolution: 1.8→1.81 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 1828 / CC1/2: 0.6 / R split: 0.622 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y5K Resolution: 1.8→19.78 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.53 Å2 / Biso mean: 27.3508 Å2 / Biso min: 11.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→19.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %
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