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Open data
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Basic information
Entry | Database: PDB / ID: 4zfb | ||||||
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Title | Cytochrome P450 pentamutant from BM3 bound to Palmitic Acid | ||||||
![]() | Bifunctional P-450/NADPH-P450 reductase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / Heme Oxidase Domain / Bacillus megaterium | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rogers, W.E. / Othman, T. / Heidary, D.K. / Huxford, T. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 82.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 928.7 KB | Display | ![]() |
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Full document | ![]() | 932.7 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zf6C ![]() 4zf8C ![]() 4zfaC ![]() 3nplS ![]() 4zf9 ![]() 4zfd ![]() 4zfe C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53500.973 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.) ![]() ![]() ![]() References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 5 types, 63 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-PLM / | ||
#4: Chemical | ChemComp-EDO / | ||
#5: Chemical | ChemComp-NI / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NPL Resolution: 2.84→117.929 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82 / 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: 2.84→117.929 Å
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Refine LS restraints |
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LS refinement shell |
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