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Yorodumi- PDB-5mns: Structural and functional characterization of OleP in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mns | ||||||
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Title | Structural and functional characterization of OleP in complex with 6DEB in sodium formate | ||||||
Components | Cytochrome P-450 | ||||||
Keywords | OXIDOREDUCTASE / P450 / cytochrome / 6DEB / epoxidase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Parisi, G. / Savino, C. / Montemiglio, L.C. / Vallone, B. | ||||||
Funding support | Italy, 1items
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Citation | Journal: FASEB J. / Year: 2019 Title: Substrate-induced conformational change in cytochrome P450 OleP. Authors: Parisi, G. / Montemiglio, L.C. / Giuffre, A. / Macone, A. / Scaglione, A. / Cerutti, G. / Exertier, C. / Savino, C. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mns.cif.gz | 474.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mns.ent.gz | 394.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mns_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 5mns_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 5mns_validation.xml.gz | 97.6 KB | Display | |
Data in CIF | 5mns_validation.cif.gz | 129 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/5mns ftp://data.pdbj.org/pub/pdb/validation_reports/mn/5mns | HTTPS FTP |
-Related structure data
Related structure data | 5mnvC 4xe3S 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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Unit cell |
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-Components
#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 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-DEB / #4: Water | ChemComp-HOH / | |
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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: 3.11 Å3/Da / Density % sol: 60.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4M HCOONa |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→120 Å / Num. obs: 98805 / % possible obs: 99.5 % / Redundancy: 6.09 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.63 |
Reflection shell | Resolution: 2.62→2.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XE3 Resolution: 2.62→120 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.925 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.312 / 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: 55.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→120 Å
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Refine LS restraints |
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