+Open data
-Basic information
Entry | Database: PDB / ID: 3lxh | ||||||
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Title | Crystal Structure of Cytochrome P450 CYP101D1 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 fold / Heme / Iron / Metal-binding / Monooxygenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yang, W. / Bell, S.G. / Wang, H. / Bartlam, M. / Wong, L.L. / Rao, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Molecular characterization of a class I P450 electron transfer system from Novosphingobium aromaticivorans DSM12444 Authors: Yang, W. / Bell, S.G. / Wang, H. / Zhou, W. / Hoskins, N. / Dale, A. / Bartlam, M. / Wong, L.L. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lxh.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lxh.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxh ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxh | HTTPS FTP |
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-Related structure data
Related structure data | 3lxdC 3lxfC 3lxiC 2cppS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47337.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Strain: DSM 12444 / Gene: Saro_0514 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GB12 #2: Chemical | #3: Chemical | ChemComp-DIO / | #4: Chemical | ChemComp-PO4 / #5: 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: 3.39 Å3/Da / Density % sol: 63.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris, pH 8.2, 12% 1,4-dioxane, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 67017 / Num. obs: 66042 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / Num. unique all: 6580 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CPP Resolution: 2.2→49.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.115 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.181 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.234 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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