[English] 日本語
![](img/lk-miru.gif)
- PDB-6vp5: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vp5 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG | |||||||||
![]() | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | |||||||||
![]() | OXIDOREDUCTASE / 2-oxo-glutarate / iron / reactant complex | |||||||||
Function / homology | ![]() 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / ethylene biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Davis, K.M. / Copeland, R.A. / Boal, A.K. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. Authors: Copeland, R.A. / Davis, K.M. / Shoda, T.K.C. / Blaesi, E.J. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 310.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 243.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 294.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 297.2 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vp4C ![]() 5lsqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
4 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39592.645 Da / Num. of mol.: 4 / Mutation: D191E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: efe / Production host: ![]() ![]() References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) |
---|
-Non-polymers , 5 types, 1264 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-ARG / #5: Chemical | ChemComp-B3P / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane, 0.1-0.2 M sodium chloride, 24-30% PEG6000 PH range: 6.4-6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→49.52 Å / Num. obs: 105982 / % possible obs: 99.21 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.6 Å2 / Rpim(I) all: 0.04034 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 1.97→2.04 Å / Num. unique obs: 9842 / Rpim(I) all: 0.2801 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 5LSQ Resolution: 1.97→49.52 Å / SU ML: 0.1759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9225
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→49.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|