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Yorodumi- PDB-2wio: Structure of the histidine tagged, open cytochrome P450 Eryk from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wio | ||||||
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Title | Structure of the histidine tagged, open cytochrome P450 Eryk from S. erythraea | ||||||
Components | ERYTHROMYCIN B/D C-12 HYDROXYLASE | ||||||
Keywords | OXIDOREDUCTASE / SUBSTRATE SPECIFICITY / ANTIBIOTIC BIOSYNTHESIS / METAL-BINDING / CYTOCHROME P450 / IRON / HEME / ERYTHROMICYN / MONOOXYGENASE | ||||||
Function / homology | Function and homology information erythromycin 12-hydroxylase / 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 / macrolide biosynthetic process / 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: 2 Å | ||||||
Authors | Savino, C. / Montemiglio, L.C. / Sciara, G. / Miele, A.E. / Kedrew, S.G. / Gianni, S. / 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 | 2wio.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wio.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wio_validation.pdf.gz | 811.3 KB | Display | wwPDB validaton report |
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Full document | 2wio_full_validation.pdf.gz | 818.9 KB | Display | |
Data in XML | 2wio_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 2wio_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/2wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/2wio | HTTPS FTP |
-Related structure data
Related structure data | 2jjnC 2jjoC 1oxaS 2vru C: citing same article (ref.) S: Starting model for refinement |
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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: 47518.375 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Description: CDNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (STAR) References: UniProt: P48635, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Sequence details | MGSSHHHHHH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.4 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 25% PEG3350, 0.2M NACL, 0.1M TRIS PH 8.0 |
-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: MARRESEARCH / Detector: CCD / Date: Feb 17, 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: 2→29 Å / Num. obs: 22549 / % possible obs: 82.2 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 / % possible all: 85.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OXA Resolution: 2→89.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.007 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PDB STARTS FROM A.A. 19 SINCE THERE WAS NO INTERPRETABLE 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: 25.901 Å2
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Refinement step | Cycle: LAST / Resolution: 2→89.8 Å
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Refine LS restraints |
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