[English] 日本語
![](img/lk-miru.gif)
- PDB-5gq9: Crystal structure of Thermus thermophilus Argonaute in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gq9 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | DNA BINDING PROTEIN/DNA / Argonaute / Complex / Guide DNA / DNA BINDING PROTEIN-DNA complex | ||||||||||||||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Zhao, H. / Sheng, G. / Wang, Y. | ||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||
![]() | ![]() Title: Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target Authors: Zhao, H. / Sheng, G. / Wang, Y. | ||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 302 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 238.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502.4 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 65.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ncbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 76728.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Some residues are missing due to disorder in the coordinate. Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0026 / Production host: ![]() ![]() #2: DNA chain | Mass: 6573.254 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The last five nucleotides are missing due to disorder. Source: (synth.) ![]() ![]() #3: DNA chain | Mass: 4787.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Chemical | ChemComp-MG / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.96 % |
---|---|
Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium acetate, 0.1M Bis-tris Propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97848 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 58404 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rsym value: 0.066 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.45 / % possible all: 99.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4NCB Resolution: 2.7→39.13 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.21
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→39.13 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|