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- PDB-2jjo: Structure of cytochrome P450 EryK in complex with its natural sub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jjo | ||||||
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Title | Structure of cytochrome P450 EryK in complex with its natural substrate erD | ||||||
![]() | CYTOCHROME P450 113A1 | ||||||
![]() | OXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / ANTIBIOTIC BIOSYNTHESIS / TIE-ROD MECHANISM OF ACTION / SUBSTRATE SPECIFICITY | ||||||
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. / Sciara, G. / Miele, A.E. / Kendrew, S.G. / Vallone, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 76.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jjnSC ![]() 2wioC ![]() 2vru 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 | ChemComp-EY5 / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.6 % |
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Crystal grow | pH: 8.5 Details: 25% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 23, 2007 |
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: 27953 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 10.9 / % possible all: 80.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JJN Resolution: 1.99→95.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.99 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→95.78 Å
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Refine LS restraints |
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