+Open data
-Basic information
Entry | Database: PDB / ID: 3aba | ||||||
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Title | Crystal structure of CYP105P1 in complex with filipin I | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE/ANTIBIOTIC / P450 / oxidoreductase / heme / monooxygenase / macrolide / filipin / Iron / Metal-binding / OXIDOREDUCTASE-ANTIBIOTIC complex | ||||||
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 Similarity search - Function | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis Authors: Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H. #1: Journal: J.Bacteriol. / Year: 2009 Title: Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state Authors: Xu, L.H. / Fushinobu, S. / Ikeda, H. / Wakagi, T. / Shoun, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aba.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aba.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3aba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3aba ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3aba | HTTPS FTP |
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-Related structure data
Related structure data | 3abbC 3e5jS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44429.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: pteC, SAV413, SAV_413 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus (DE3) References: UniProt: Q93H81, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-FLI / ( | ||
#4: Chemical | #5: 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: 3.55 Å3/Da / Density % sol: 65.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: (NH4)2SO4, Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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 315r / Detector: CCD / Date: Dec 24, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 59975 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E5J Resolution: 1.8→39.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.688 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.114 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.525 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2373 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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