+Open data
-Basic information
Entry | Database: PDB / ID: 6l69 | ||||||
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Title | Crystal structure of CYP154C2 from Streptomyces avermitilis | ||||||
Components | Cytochrome P450 hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / substrate-free / hydroxylase | ||||||
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: 1.5 Å | ||||||
Authors | Xu, L.H. / Fushinobu, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Regio- and stereoselective hydroxylation of testosterone by a novel cytochrome P450 154C2 from Streptomyces avermitilis. Authors: Wang, Q. / Ma, B. / Fushinobu, S. / Zhang, C. / Xu, L.H. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Overview of refinement procedures within REFMAC5: utilizing data from different sources. Authors: Kovalevskiy, O. / Nicholls, R.A. / Long, F. / Carlon, A. / Murshudov, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l69.cif.gz | 223.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l69.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 6l69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/6l69 ftp://data.pdbj.org/pub/pdb/validation_reports/l6/6l69 | HTTPS FTP |
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-Related structure data
Related structure data | 1gwiS 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: 45272.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: cyp19, SAVERM_3882 / Production host: unidentified plasmid (others) / References: UniProt: Q82GL5 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 6.5), 28% PEGMME 2000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 112411 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 9.27 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 16190 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GWI Resolution: 1.5→33.89 Å / SU ML: 0.1292 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.9099 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→33.89 Å
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Refine LS restraints |
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LS refinement shell |
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