[English] 日本語
![](img/lk-miru.gif)
- PDB-7bxs: 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bxs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine binding form | |||||||||
![]() | 2-amino-3-ketobutyrate coenzyme A ligase | |||||||||
![]() | LIGASE / TRANSFERASE / 2-amino-3-ketobutyrate CoA ligase / Cupriavidus necator | |||||||||
Function / homology | ![]() glycine C-acetyltransferase / glycine C-acetyltransferase activity / L-threonine catabolic process to glycine / biosynthetic process / ligase activity / pyridoxal phosphate binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Motoyama, T. / Nakano, S. / Hasebe, F. / Miyoshi, N. / Ito, S. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Authors: Motoyama, T. / Nakano, S. / Hasebe, F. / Miyata, R. / Kumazawa, S. / Miyoshi, N. / Ito, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 207.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7bxpC ![]() 7bxqC ![]() 7bxrC ![]() 1fc4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44791.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG3350, 3% w/v Dextran sulfate sodium salt (Mr 5000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.73 Å / Num. obs: 26198 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.67 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 3804 / CC1/2: 0.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1FC4 Resolution: 2.5→47.73 Å / SU ML: 0.3352 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.2866 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|