[English] 日本語
![](img/lk-miru.gif)
- PDB-5gn2: Crystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gn2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens | ||||||
![]() | Blr0248 protein | ||||||
![]() | HYDROLASE / Uracil DNA glycosylase (UDG) / Bradyrhizobium diazoefficiens / nitrogen fixing symbion | ||||||
Function / homology | Uracil-DNA glycosylase-like domain superfamily / Blr0248 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Patil, V.V. / Chembazhi, U.V. / Varshney, U. / Woo, E. | ||||||
![]() | ![]() Title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity Authors: Chembazhi, U.V. / Patil, V.V. / Sah, S. / Reeve, W. / Tiwari, R.P. / Woo, E. / Varshney, U. #1: Journal: NUCLEIC ACIDS RES. / Year: 2015 Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily Authors: Sang, P.B. / Srinath, T. / Patil, A.G. / Woo, E. / Varshney, U. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 221.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 185.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 484 KB | Display | |
Data in XML | ![]() | 45.6 KB | Display | |
Data in CIF | ![]() | 65.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29725.795 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USDA 110 / Gene: blr0248 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.03 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20% PEG3350, 200 mM sodium citrate, 100 mM sodium citrate/citric acid |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.952→30.524 Å / Num. obs: 117654 / % possible obs: 98.71 % / Redundancy: 4 % / Net I/σ(I): 13.34 |
-
Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.952→30.524 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.99 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.952→30.524 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|