+Open data
-Basic information
Entry | Database: PDB / ID: 2jjn | ||||||
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Title | Structure of closed cytochrome P450 EryK | ||||||
Components | CYTOCHROME P450 113A1 | ||||||
Keywords | OXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / CYTOCHROME P450 / 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 / 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 | SACCHAROPOLYSPORA ERYTHRAEA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Savino, C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Vallone, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Investigating the Structural Plasticity of a Cytochrome P450: Three-Dimensional Structures of P450 Eryk and Binding to its Physiological Substrate. Authors: Savino, C. / Montemiglio, L.C. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Jemth, P. / Gianni, S. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jjn.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jjn.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jjn_validation.pdf.gz | 839.1 KB | Display | wwPDB validaton report |
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Full document | 2jjn_full_validation.pdf.gz | 857.2 KB | Display | |
Data in XML | 2jjn_validation.xml.gz | 25 KB | Display | |
Data in CIF | 2jjn_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/2jjn ftp://data.pdbj.org/pub/pdb/validation_reports/jj/2jjn | HTTPS FTP |
-Related structure data
Related structure data | 2jjoC 2wioC 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-SO4 / #4: 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: 1.9 Å3/Da / Density % sol: 34.9 % |
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Crystal grow | pH: 6.5 / Details: 2.0M AMMONIUM SULPHATE, 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: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 53926 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 19.1 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VRU 2vru Resolution: 1.59→56.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.803 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COORDINATES START FROM A.A. 17 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: 23.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→56.34 Å
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Refine LS restraints |
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