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Yorodumi- PDB-3ekd: Crystal structure of the A264M heme domain of cytochrome P450 BM3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ekd | ||||||
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Title | Crystal structure of the A264M heme domain of cytochrome P450 BM3 | ||||||
Components | Cytochrome P450(BM-3) | ||||||
Keywords | OXIDOREDUCTASE / heme ligation / cytochrome P450 / Cytoplasm / Electron transport / FAD / Flavoprotein / FMN / Heme / Iron / Metal-binding / Monooxygenase / Multifunctional enzyme / NADP / Transport | ||||||
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: 2.5 Å | ||||||
Authors | Toogood, H.S. / Leys, D. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Novel haem co-ordination variants of flavocytochrome P450BM3. Authors: Girvan, H.M. / Toogood, H.S. / Littleford, R.E. / Seward, H.E. / Smith, W.E. / Ekanem, I.S. / Leys, D. / Cheesman, M.R. / Munro, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ekd.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ekd.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 3ekd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3ekd ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3ekd | HTTPS FTP |
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-Related structure data
Related structure data | 3ekbC 3ekfC 2ij3S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53699.215 Da / Num. of mol.: 2 / Fragment: heme domain / Mutation: A264M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | ChemComp-PAM / | #3: Chemical | #4: 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: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Magnesiumsulphate and PEG, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 40923 / Num. obs: 40923 / % possible obs: 99.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IJ3 Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.357 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.46 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.123 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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