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Yorodumi- PDB-7wy2: Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wy2 | |||||||||||||||
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Title | Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 F87A Mutant Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine in complex with Styrene | |||||||||||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | |||||||||||||||
Keywords | OXIDOREDUCTASE / Monooxygenase | |||||||||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Priestia megaterium (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||||||||
Authors | Suzuki, K. / Stanfield, J.K. / Shisaka, Y. / Omura, K. / Kasai, C. / Sugimoto, H. / Shoji, O. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations. Authors: Suzuki, K. / Stanfield, J.K. / Omura, K. / Shisaka, Y. / Ariyasu, S. / Kasai, C. / Aiba, Y. / Sugimoto, H. / Shoji, O. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wy2.cif.gz | 431.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wy2.ent.gz | 352.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wy2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7wy2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7wy2_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 7wy2_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/7wy2 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/7wy2 | HTTPS FTP |
-Related structure data
Related structure data | 7wy1C 7wy3C 7wy4C 3wspS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52224.562 Da / Num. of mol.: 2 / Mutation: F87A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 6 types, 707 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: PEG8000, Magnesium Chloride, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→48.41 Å / Num. obs: 199079 / % possible obs: 100 % / Redundancy: 19.915 % / Biso Wilson estimate: 28.813 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.137 / Χ2: 0.821 / Net I/σ(I): 12.57 / Num. measured all: 3964720 / Scaling rejects: 6197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WSP Resolution: 1.45→48.41 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.489 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.12 Å2 / Biso mean: 24.787 Å2 / Biso min: 13.79 Å2
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Refinement step | Cycle: final / Resolution: 1.45→48.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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