[English] 日本語
![](img/lk-miru.gif)
- PDB-7wzm: Crystal structure of Cytochrome P450 184A1 from streptomyces aver... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7wzm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis in complex with Oleic acid | ||||||
![]() | Putative cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / Streptomyces avermitilis / Oleic acid | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis in complex with Oleic acid Authors: Kim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7wzlS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53770.727 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: cyp21, SAVERM_5111 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-OLA / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
---|---|
Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop Details: 15% PEG3350, 0.2 M sodium chloride, 0.1M HEPES, pH 7.0, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 52789 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.949 / Net I/σ(I): 36.567 |
Reflection shell | Resolution: 1.68→1.71 Å / Num. unique obs: 52789 / CC1/2: 0.889 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7WZL Resolution: 1.68→45.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.796 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 69 Å2 / Biso mean: 14.682 Å2 / Biso min: 6.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→45.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.68→1.722 Å / Rfactor Rfree error: 0
|