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Yorodumi- PDB-3kx3: Crystal structure of Bacillus megaterium BM3 heme domain mutant L86E -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kx3 | ||||||
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Title | Crystal structure of Bacillus megaterium BM3 heme domain mutant L86E | ||||||
Components | Bifunctional P-450/NADPH-P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / L86E mutant / Heme domain / 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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.803 Å | ||||||
Authors | Girvan, H.M. / Levy, C.W. / Leys, D. / Munro, A.W. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Glutamate-haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3. Authors: Girvan, H.M. / Levy, C.W. / Williams, P. / Fisher, K. / Cheesman, M.R. / Rigby, S.E. / Leys, D. / 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 | 3kx3.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kx3.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kx3 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kx3 | HTTPS FTP |
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-Related 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: 53655.055 Da / Num. of mol.: 2 / Fragment: heme domain (UNP residues 2-471) / Mutation: L86E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Plasmid: TG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100mM cacodylic acid, pH 6.0, 16% PEG 3350, 140mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0698 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0698 Å / Relative weight: 1 |
Reflection | Resolution: 1.803→40 Å / Num. obs: 100096 / % possible obs: 89.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8026→1.8231 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.6 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.803→39.41 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 17.63 / 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 / Bsol: 58.922 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.803→39.41 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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