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- PDB-2xbk: X-ray structure of the substrate-bound cytochrome P450 PimD - a p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xbk | ||||||
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Title | X-ray structure of the substrate-bound cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase | ||||||
![]() | PIMD PROTEIN | ||||||
![]() | OXIDOREDUCTASE / EPOXIDATION | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kells, P.M. / Ouellet, H. / Santos-Aberturas, J. / Aparicio, J.F. / Podust, L.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.2 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x9pSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44528.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-397 Source method: isolated from a genetically manipulated source Details: RESIDUES UPSTREAM OF SER 5 INCLUDING 6XHIS TAG ARE ENGINEERED Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-XBK / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | 4,5-DEEPOXYPIMARICIN: NON-EPOXIDATED PRECURSOR OF THE POLYENE ANTIBIOTIC PIMARICIN OR NATAMYCIN. ...4,5-DEEPOXYPIM |
Sequence details | 6XHIS TAG ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % / Description: NONE |
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Crystal grow | Temperature: 296 K / pH: 7 Details: 0.2 M SODIUM MALONATE, PH 7.0; 20% PEG 3330, T=23 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / 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: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→17.01 Å / Num. obs: 38650 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X9P Resolution: 1.95→67.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.439 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH THE SIDE CHAIN MISSING FROM THE ELECTRON DENSITY WERE MODELED AS ALANINE
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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: 30.816 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→67.88 Å
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Refine LS restraints |
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