[English] 日本語
Yorodumi- PDB-2lbr: Conformation Effects of Base Modification on the Anticodon Stem-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lbr | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Conformation Effects of Base Modification on the Anticodon Stem-loop of Bacillus subtilis tRNATYR | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / Tyrosyl-tRNA | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | closest to the average, model 1 | Authors | Denmon, A.P. / Wang, J. / Nikonowicz, E.P. | Citation | Journal: J.Mol.Biol. / Year: 2011 | Title: Conformation Effects of Base Modification on the Anticodon Stem-Loop of Bacillus subtilis tRNA(Tyr). Authors: Denmon, A.P. / Wang, J. / Nikonowicz, E.P. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lbr.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lbr.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 2lbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/2lbr ftp://data.pdbj.org/pub/pdb/validation_reports/lb/2lbr | HTTPS FTP |
---|
-Related structure data
Related structure data | 2la9C 2lacC 2lbqC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 5512.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: molecule was made using T7 polymerase and primers |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 2.0 mM i6A,PSU-ASL, 10 mM potassium chloride, 0.02 mM EDTA, 10 mM potassium phosphate, 100% D2O Solvent system: 100% D2O | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||||||||
Sample conditions | pH: 6.3 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 8 |