+Open data
-Basic information
Entry | Database: PDB / ID: 1p0x | ||||||
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Title | F393Y mutant heme domain of flavocytochrome P450 BM3 | ||||||
Components | Bifunctional P-450:NADPH-P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / fatty acid hydroxylase / monooxygenase | ||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ost, T.W.B. / Clark, J. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. / Daff, S. / Mowat, C.G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Oxygen Activation and Electron Transfer in Flavocytochrome P450 BM3 Authors: Ost, T.W.B. / Clark, J. / Mowat, C.G. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. / Daff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p0x.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p0x.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 1p0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p0x_validation.pdf.gz | 540.5 KB | Display | wwPDB validaton report |
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Full document | 1p0x_full_validation.pdf.gz | 555.3 KB | Display | |
Data in XML | 1p0x_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1p0x_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/1p0x ftp://data.pdbj.org/pub/pdb/validation_reports/p0/1p0x | HTTPS FTP |
-Related structure data
Related structure data | 1p0vC 1p0wC 2hpdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52185.461 Da / Num. of mol.: 2 / Fragment: Heme domain, residues 1-455 of SWS P14779 / Mutation: F393Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A21 / Plasmid: pCM126 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, PIPES, MAGNESIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 9, 2001 |
Radiation | Monochromator: 0.8 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 |
Reflection | Resolution: 2→17 Å / Num. all: 74261 / Num. obs: 67437 / % possible obs: 91 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.15 / Num. unique all: 6332 / % possible all: 85.8 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 17 Å / Num. measured all: 837703 |
Reflection shell | *PLUS Highest resolution: 2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2HPD Resolution: 2→17 Å / Cross valid method: thoughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.092 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 17 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.237 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d |