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Yorodumi- PDB-2x9p: X-ray structure of the substrate-free cytochrome P450 PimD - a po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9p | ||||||
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Title | X-ray structure of the substrate-free cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase | ||||||
Components | PIMD PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / EPOXIDATION | ||||||
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 NATALENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kells, P.M. / Ouellet, H. / Santos-Aberturas, J. / Aparicio, J.F. / Podust, L.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2010 Title: Structure of Cytochrome P450 Pimd Suggests Epoxidation of the Polyene Macrolide Pimaricin Occurs Via a Hydroperoxoferric Intermediate. Authors: Kells, P.M. / Ouellet, H. / Santos-Aberturas, J. / Aparicio, J.F. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9p.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9p.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 2x9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9p ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9p | HTTPS FTP |
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-Related structure data
Related structure data | 2xbkC 2zbzS 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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Unit cell |
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-Components
#1: Protein | Mass: 44528.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES NATALENSIS (bacteria) / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q9EW92 | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS346 SULFATE ION (SO4): PART OF ...PROTOPORPH | Sequence details | RESIDUES UPSTREAM OF SER 5 INCLUDING 6XHIS TAG ARE ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Temperature: 296 K / pH: 8.5 Details: 1.75 M AMMONIUM SULFATE, 2% PEG400, 0.1 M TRIS-HCL, PH 8.5; T=23 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→16.98 Å / Num. obs: 34176 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZBZ Resolution: 2.1→90.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.629 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 82-89 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.299 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→90.17 Å
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Refine LS restraints |
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