[English] 日本語
![](img/lk-miru.gif)
- PDB-8jno: Crystal structure of cytochrome P450 IkaD from Streptomyces sp. Z... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8jno | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate 10-epi-deOH-HSAF | |||||||||
![]() | Cytochrome P450 | |||||||||
![]() | OXIDOREDUCTASE / hydroxylation / polycyclic tetramate macrolactam / cytochrome P450 | |||||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhang, Y.L. / Zhang, L.P. / Zhang, C.S. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: A Mechanistic Understanding of the Distinct Regio- and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates. Authors: Jiang, P. / Jin, H. / Zhang, G. / Zhang, W. / Liu, W. / Zhu, Y. / Zhang, C. / Zhang, L. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 320 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 259.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8jncC ![]() 8jnpC ![]() 8jnqC ![]() 8jooC ![]() 8juaC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 45887.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.35 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5-4 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2→12.91 Å / Num. obs: 70089 / % possible obs: 96.7 % / Redundancy: 9.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 1.1 / Net I/σ(I): 14 / Num. measured all: 657390 |
Reflection shell | Resolution: 2→2.04 Å / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.273 / Num. measured all: 21841 / Num. unique obs: 4645 / CC1/2: 0.931 / Rpim(I) all: 0.139 / Rrim(I) all: 0.307 / Χ2: 0.71 / Net I/σ(I) obs: 4.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→12.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|