+Open data
-Basic information
Entry | Database: PDB / ID: 6zi3 | ||||||
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Title | Crystal structure of OleP-6DEB bound to L-rhamnose | ||||||
Components | Cytochrome P-450 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / 8.8a-deoxyoleandolide monooxygenase / 8.8a-deoxyoleandolide | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Streptomyces antibioticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å | ||||||
Authors | Montemiglio, L.C. / Savino, C. / Vallone, B. / Parisi, G. / Freda, I. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biomolecules / Year: 2020 Title: Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Authors: Parisi, G. / Freda, I. / Exertier, C. / Cecchetti, C. / Gugole, E. / Cerutti, G. / D'Auria, L. / Macone, A. / Vallone, B. / Savino, C. / Montemiglio, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zi3.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zi3.ent.gz | 897.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zi3_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 6zi3_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 6zi3_validation.xml.gz | 118 KB | Display | |
Data in CIF | 6zi3_validation.cif.gz | 162 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/6zi3 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zi3 | HTTPS FTP |
-Related structure data
Related structure data | 6zhzC 6zi2C 6zi7C 5mnsS 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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3 |
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6 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 13 molecules ABCDEF
#1: Protein | Mass: 45012.070 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819 #4: Sugar | ChemComp-RAM / |
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-Non-polymers , 7 types, 1390 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-DEB / #5: Chemical | #6: Chemical | ChemComp-FMT / #7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Details
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: 3.1 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4.2 M Sodium Formate (HCOONa) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 462663 / % possible obs: 97.7 % / Redundancy: 2.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.96→2.08 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 73872 / CC1/2: 0.362 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5MNS Resolution: 2.08→48.09 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.753 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.165 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.045 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→48.09 Å
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Refine LS restraints |
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