+Open data
-Basic information
Entry | Database: PDB / ID: 4zf6 | ||||||
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Title | Cytochrome P450 pentamutant from BM3 with bound PEG | ||||||
Components | Bifunctional P-450/NADPH-P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / Heme Oxidase Domain / Bacillus megaterium | ||||||
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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.773 Å | ||||||
Authors | Rogers, W.E. / Othman, T. / Heidary, D.K. / Huxford, T. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants. Authors: Geronimo, I. / Denning, C.A. / Rogers, W.E. / Othman, T. / Huxford, T. / Heidary, D.K. / Glazer, E.C. / Payne, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zf6.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zf6.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/4zf6 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/4zf6 | HTTPS FTP |
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-Related structure data
Related structure data | 4zf8C 4zfaC 4zfbC 3nplS 4zf9 4zfd 4zfe 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52571.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1-461 / Mutation: R47L, F81I, F87V, L188Q, E267V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 5 types, 66 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-1PE / | ||
#4: Chemical | ChemComp-EDO / | ||
#5: Chemical | ChemComp-NI / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 17.5mM NiCl2, 50mM PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→177.81 Å / Num. obs: 18183 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.77→2.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.4 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NPL Resolution: 2.773→59.269 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.13 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.773→59.269 Å
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Refine LS restraints |
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LS refinement shell |
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