[English] 日本語
![](img/lk-miru.gif)
- PDB-4jrt: Crystal structure of an A-form RNA duplex containing three GU bas... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jrt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an A-form RNA duplex containing three GU base pairs | ||||||
![]() |
| ||||||
![]() | RNA / A-form RNA / ribose-zipper motif / GU base pair | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E. | ||||||
![]() | ![]() Title: Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet Authors: Kondo, J. / Dock-Bregeon, A.C. / Willkomm, D.K. / Hartmann, R.K. / Westhof, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 23.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 14.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 382.4 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 353dS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: RNA chain | Mass: 3979.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription |
---|---|
#2: RNA chain | Mass: 3723.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription |
#3: Water | ChemComp-HOH / |
Nonpolymer details | HOH (A 111) AND HOH (A 112) ARE CLOSED TO SYMMETRY-RELATED RNA MOLECULE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % |
---|---|
Crystal grow | Temperature: 310 K / Method: vapor diffusion / pH: 7 Details: Sodium Cacodylate, Lithium acetate, PEG3350, pH 7.0, vapor diffusion, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jul 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20.7 Å / Num. obs: 2330 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 353D Resolution: 2.6→20.7 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 41.7378 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.1 Å2 / Biso mean: 76.1548 Å2 / Biso min: 41.68 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20.7 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|