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Yorodumi- PDB-2jjp: Structure of cytochrome P450 EryK in complex with inhibitor ketoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jjp | ||||||
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Title | Structure of cytochrome P450 EryK in complex with inhibitor ketoconazole (KC) | ||||||
Components | CYTOCHROME P450 113A1 | ||||||
Keywords | OXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information 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 / monooxygenase activity / NADP binding / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | SACCHAROPOLYSPORA ERYTHRAEA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Savino, C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Vallone, B. | ||||||
Citation | Journal: Biochemistry / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jjp.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jjp.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/2jjp ftp://data.pdbj.org/pub/pdb/validation_reports/jj/2jjp | HTTPS FTP |
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-Related structure data
Related structure data | 2xfhC 2jjnS 2vru 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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1 |
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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.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL 23338 / Description: CDNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR 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 | ChemComp-KLN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 2.0M AMMONIUM SULHATE, 0.1M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 25326 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 12.7 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JJN Resolution: 2.1→56.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.695 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATE START FROM A.A. 15 BECAUSE THERE WAS NOT ELECTRON DENSITY FOR PREVIOUS RESIDUES
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→56.7 Å
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Refine LS restraints |
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