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- PDB-7wex: The crystal structure of substrate-free CYP107X1 from Streptomyce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wex | ||||||
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Title | The crystal structure of substrate-free CYP107X1 from Streptomyces avermitilis | ||||||
![]() | Cytochrome P450 hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / substrate-free | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Xu, L.-H. / Lin, S. / Gao, L. | ||||||
Funding support | 1items
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![]() | ![]() Title: The 16 alpha-Hydroxylation of Progesterone by Cytochrome P450 107X1 from Streptomyces avermitilis. Authors: Lin, S. / Ma, B. / Gao, Q. / Yang, J. / Lai, G. / Lin, R. / Yang, B. / Han, B.N. / Xu, L.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.4 KB | Display | ![]() |
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PDB format | ![]() | 70.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2whwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components
#1: Protein | Mass: 44695.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: cyp23, SAVERM_6249 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate (pH 6.5) and 20% w/v polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 25483 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.985 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.99→2.02 Å / Num. unique obs: 25483 / CC1/2: 0.841 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WHW Resolution: 1.99→41.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.558 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.18 / 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: 93.9 Å2 / Biso mean: 33.872 Å2 / Biso min: 15.63 Å2
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Refinement step | Cycle: final / Resolution: 1.99→41.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Rfactor Rfree error: 0
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