[English] 日本語
![](img/lk-miru.gif)
- PDB-3hvr: Crystal structure of T. thermophilus Argonaute complexed with DNA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3hvr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt RNA target strand with two Mg2+ at the cleavage site | ||||||
![]() |
| ||||||
![]() | NUCLEIC ACID BINDING PROTEIN/DNA/RNA / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Li, H. / Sheng, G. / Patel, D.J. | ||||||
![]() | ![]() Title: Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Authors: Wang, Y. / Juranek, S. / Li, H. / Sheng, G. / Wardle, G.S. / Tuschl, T. / Patel, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 287.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 220.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3hjfC ![]() 3hk2SC ![]() 3hm9C ![]() 3ho1C ![]() 3hxmC ![]() 3hge C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 76728.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: RNA chain | Mass: 5942.584 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-MG / #5: Chemical | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.4 % |
---|---|
Crystal grow![]() | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80 mM MgCl2, 1.0 M Na tartrate, 50 mM Tris.HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 308 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→50 Å / Num. obs: 34970 / % possible obs: 95.2 % / Observed criterion σ(F): -1 / Redundancy: 4.9 % / Biso Wilson estimate: 95.75 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3220 / % possible all: 88.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3HK2 Resolution: 3.211→37.68 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU ML: 0.51 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0.13 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.32 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 293.57 Å2 / Biso mean: 97.522 Å2 / Biso min: 20 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.211→37.68 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
|