[English] 日本語
![](img/lk-miru.gif)
- PDB-6k1d: Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6k1d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP | ||||||
![]() | Exonuclease 3'-5' domain-containing protein 2 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, J. / Lee, C. | ||||||
![]() | ![]() Title: The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination. Authors: Park, J. / Lee, S.Y. / Jeong, H. / Kang, M.G. / Van Haute, L. / Minczuk, M. / Seo, J.K. / Jun, Y. / Myung, K. / Rhee, H.W. / Lee, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 166.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6k17SC ![]() 6k18C ![]() 6k19C ![]() 6k1aC ![]() 6k1bC ![]() 6k1cC ![]() 6k1eC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24396.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG 8000, 2-(N-morpholino)ethanesulfonic acid, Calcium acetate, Dithiothreitol, Manganese Chloride, Guanosine monophosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3→50 Å / Num. obs: 9290 / % possible obs: 95.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 465 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 6K17 Resolution: 3→49.348 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.13
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.348 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|