+
Open data
-
Basic information
Entry | Database: PDB / ID: 7olt | ||||||
---|---|---|---|---|---|---|---|
Title | Dioxygenase AsqJ in complex with 2 and Tris | ||||||
![]() | Iron/alpha-ketoglutarate-dependent dioxygenase asqJ | ||||||
![]() | OXIDOREDUCTASE / Quinolone Biosynthesis / Molecular Engineering / Epoxidation / Catalytic Mechanism | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Auman, D. / Mader, S.L. / Ecker, F. / Dorst, K. / Braeuer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I. | ||||||
![]() | ![]() Title: Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ. Authors: Auman, D. / Ecker, F. / Mader, S.L. / Dorst, K.M. / Brauer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 139 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7olkC ![]() 7ollC ![]() 7olmC ![]() 7oloC ![]() 7olpC ![]() 7olqC ![]() 7olrC ![]() 5dapS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33978.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: asqJ, AN9227 / Production host: ![]() ![]() References: UniProt: Q5AR53, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
---|
-Non-polymers , 7 types, 255 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/58J.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/58J.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-58J / | ||||||
#4: Chemical | ChemComp-TRS / | ||||||
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-K / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 100 mM TRIS/HCl, 1 M LiBr, 29% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 46712 / % possible obs: 98.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.5→1.6 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / Num. unique obs: 8208 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5DAP Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.623 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.067 / 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: 22.983 Å2 / Biso min: 13.9 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|