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- PDB-4wpz: Crystal structure of cytochrome P450 CYP107W1 from Streptomyces a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wpz | ||||||
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Title | Crystal structure of cytochrome P450 CYP107W1 from Streptomyces avermitilis | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / P450 / CYP / CYP107W1 / Streptomyces avermitilis / oligomycin | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
Model details | Biosynthesis of Oligomycin A | ||||||
![]() | Kang, L.W. / Kim, D.H. / Pham, T.V. / Han, S.H. | ||||||
![]() | ![]() Title: Functional characterization of CYP107W1 from Streptomyces avermitilis and biosynthesis of macrolide oligomycin A. Authors: Han, S. / Pham, T.V. / Kim, J.H. / Lim, Y.R. / Park, H.G. / Cha, G.S. / Yun, C.H. / Chun, Y.J. / Kang, L.W. / Kim, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 74 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.6 KB | Display | ![]() |
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Full document | ![]() | 805.9 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 43346.547 Da / Num. of mol.: 1 / Fragment: UNP residues 8-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: KBr, PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2013 / Details: mirror |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 31242 / % possible obs: 99.1 % / Redundancy: 6.7 % / Net I/σ(I): 40 |
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Processing
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Refinement | Resolution: 2.1→35.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.988 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 94.59 Å2 / Biso mean: 27.527 Å2 / Biso min: 11.48 Å2
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Refinement step | Cycle: final / Resolution: 2.1→35.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.154 Å / Total num. of bins used: 20
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