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- PDB-2xfh: Structure of cytochrome P450 EryK cocrystallized with inhibitor c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xfh | |||||||||
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Title | Structure of cytochrome P450 EryK cocrystallized with inhibitor clotrimazole. | |||||||||
![]() | ERYTHROMYCIN B/D C-12 HYDROXYLASE | |||||||||
![]() | OXIDOREDUCTASE / MONOXYGENASE / ERYTHROMYCIN A BIOSYNTHESIS | |||||||||
Function / homology | ![]() erythromycin 12-hydroxylase / macrolide biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / NADP binding / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Savino, C. / Montemiglio, L.C. / Gianni, S. / Vallone, B. | |||||||||
![]() | ![]() Title: Azole Drugs Trap Cytochrome P450 Eryk in Alternative Conformational States. Authors: Montemiglio, L.C. / Gianni, S. / Vallone, B. / Savino, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jjpC ![]() 2vrv C: citing same article ( S: Starting model for refinement |
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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: 45347.031 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P48635, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 42.1 % / Description: NONE |
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Crystal grow | Details: 25% PEG 3350, 0.1M HEPES PH 7.0, 0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX / Detector: CCD / Date: Jan 21, 2010 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 36185 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.16 / % possible all: 84.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VRV ![]() 2vrv Resolution: 1.9→42.76 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.711 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE FIRST 17 N-TERMINAL RESIDUES ARE MISSING IN THE PDB FILE DUE TO INSUFFICIENT ELECTRON DENSITY
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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: 26.637 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.76 Å
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Refine LS restraints |
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