+Open data
-Basic information
Entry | Database: PDB / ID: 6a7j | ||||||
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Title | Testerone bound CYP154C4 from Streptomyces sp. ATCC 11861 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / Streptomyces / steroid 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 violaceoruber (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å | ||||||
Authors | Lee, C.W. / Lee, J.H. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Characterization of two steroid hydroxylases from different Streptomyces spp. and their ligand-bound and -unbound crystal structures. Authors: Dangi, B. / Lee, C.W. / Kim, K.H. / Park, S.H. / Yu, E.J. / Jeong, C.S. / Park, H. / Lee, J.H. / Oh, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a7j.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a7j.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 6a7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a7j ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a7j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44828.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces violaceoruber (bacteria) / Gene: B1H20_20375 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0UEC8 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-TES / |
#4: 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: 3.69 Å3/Da / Density % sol: 66.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1 M sodium citrate tribasic and 0.1 M sodium cacodylate:HCl pH 6.5 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17614 / % possible obs: 96.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.419 / Num. unique obs: 872 |
-Processing
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Refinement | Resolution: 2.71→47.55 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.508 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.325 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.595 Å2
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Refinement step | Cycle: 1 / Resolution: 2.71→47.55 Å
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Refine LS restraints |
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