[English] 日本語
![](img/lk-miru.gif)
- PDB-7reh: Crystal structure of T252E CYP199A4 bound to 4-methoxybenzoic acid -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7reh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T252E CYP199A4 bound to 4-methoxybenzoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / peroxygenase / mutant | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Podgorski, M.N. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: An Altered Heme Environment in an Engineered Cytochrome P450 Enzyme Enables the Switch from Monooxygenase to Peroxygenase Activity Authors: Podgorski, M.N. / Harbort, J.S. / Lee, J.H.Z. / Nguyen, G.T. / Bruning, J.B. / Donald, W.A. / Bernhardt, P.V. / Harmer, J.R. / Bell, S.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uvbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44615.438 Da / Num. of mol.: 1 / Mutation: T252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HaA2 / Gene: RPB_3613 / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 477 molecules ![](data/chem/img/ANN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ANN / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | #6: Chemical | ChemComp-HEM / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.47 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75) 20-32% w/v PEG3350 PH range: 5.0-5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 8, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7108 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.545→43.24 Å / Num. obs: 48517 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 9.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.066 / Rrim(I) all: 0.179 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 5UVB Resolution: 1.545→29.218 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.19 Å2 / Biso mean: 12.5518 Å2 / Biso min: 1.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.545→29.218 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|