[English] 日本語
![](img/lk-miru.gif)
- PDB-2jyj: Re-refining the tetraloop-receptor RNA-RNA complex using NMR-deri... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2jyj | ||||||
---|---|---|---|---|---|---|---|
Title | Re-refining the tetraloop-receptor RNA-RNA complex using NMR-derived restraints and Xplor-nih (2.18) | ||||||
![]() | RNA (43-MER) | ||||||
![]() | RNA/RNA / RNA structure / RNA-RNA complex / tetraloop-receptor / GAAA-tetraloop / RNA global structure | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Zuo, X. / Wang, J. / Foster, T.R. / Schwieters, C.D. / Tiede, D.M. / Butcher, S.E. / Wang, Y. | ||||||
![]() | ![]() Title: RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. Authors: Davis, J.H. / Tonelli, M. / Scott, L.G. / Jaeger, L. / Williamson, J.R. / Butcher, S.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 525.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 447.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 323.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: RNA chain | Mass: 13873.258 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: 3D 1H-13C NOESY |
-
Sample preparation
Details | Contents: 8 mg/ml (w/v) Tetraloop-receptor RNA/RNA complex, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O |
---|---|
Sample | Conc.: 8 w/v Component: Tetraloop-receptor RNA:RNA complex RNA-RNA complex |
Sample conditions | Ionic strength: 20 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
---|
-
Processing
NMR software | Name: ![]() |
---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: This ensemble of the structures were re-refined with NMR-derived restraints. The original refinements have been published in JMB (2005, 351(2), pp351-82). We re-refined the structures of the ...Details: This ensemble of the structures were re-refined with NMR-derived restraints. The original refinements have been published in JMB (2005, 351(2), pp351-82). We re-refined the structures of the tetraloop-receptor RNA/RNA complex using the restraint files whose formats are consistent with Xplor-nih. No SAXS data was used in this refinement. |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |