[English] 日本語
![](img/lk-miru.gif)
- PDB-3hxm: Structure of an argonaute complexed with guide DNA and target RNA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3hxm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches. | ||||||
![]() |
| ||||||
![]() | NUCLEIC ACID BINDING PROTEIN/DNA/RNA / argonaute / protein-DNA-RNA complex / NUCLEIC ACID BINDING PROTEIN-DNA-RNA 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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 149.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 502.8 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hjfC ![]() 3hk2C ![]() 3hm9C ![]() 3ho1C ![]() 3hvrC ![]() 3f73S ![]() 3hge C: citing same article ( 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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: DNA chain | Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 6248.750 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
---|---|
Crystal grow | Temperature: 308 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, temperature 308 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 27365 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1365 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3f73 Resolution: 3.1→30 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 42.776 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.59 Å2 / Biso mean: 72.548 Å2 / Biso min: 15.29 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|