+Open data
-Basic information
Entry | Database: PDB / ID: 6zi2 | ||||||
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Title | OleP-oleandolide(DEO) in low salt crystallization conditions | ||||||
Components | Cytochrome P-450Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / 8.8a-deoxyoleandolide monooxygenase / 8.8a-deoxyoleandolide | ||||||
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 antibioticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å | ||||||
Authors | Savino, C. / Montemiglio, L.C. / Vallone, B. / Parisi, G. / Cecchetti, C. | ||||||
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 | 6zi2.cif.gz | 660.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zi2.ent.gz | 550.9 KB | Display | PDB format |
PDBx/mmJSON format | 6zi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/6zi2 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zi2 | HTTPS FTP |
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-Related structure data
Related structure data | 6zhzC 6zi3C 6zi7C 5mnvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 45012.070 Da / Num. of mol.: 9 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 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-QR8 / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M NaCl 0.1 M Tris HCl pH 7.4 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8723 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8723 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→39.92 Å / Num. obs: 115590 / % possible obs: 98.2 % / Redundancy: 3.56 % / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Net I/σ(I): 7.29 |
Reflection shell | Resolution: 2.87→3.05 Å / Rmerge(I) obs: 0.924 / Num. unique obs: 18262 / CC1/2: 0.688 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MNV Resolution: 2.93→39.89 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.822 / SU B: 31.65 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / 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: 50.368 Å2
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Refinement step | Cycle: 1 / Resolution: 2.93→39.89 Å
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Refine LS restraints |
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