[English] 日本語
Yorodumi- PDB-1kka: Solution Structure of the Unmodified Anticodon Stem-loop from E. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kka | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of the Unmodified Anticodon Stem-loop from E. coli tRNA(Phe) | ||||||
Components | anticodon stem-loop of tRNA(PHE) | ||||||
Keywords | RNA / RNA stem-loop / trinucleotide loop / hairpin | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | tRNA(Phe) | ||||||
Authors | Cabello-Villegas, J. / Winkler, M.E. / Nikonowicz, E.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe). Authors: Cabello-Villegas, J. / Winkler, M.E. / Nikonowicz, E.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kka.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kka.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kka ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kka | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 5466.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNA polymerase in vitro transcription |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: The structure was determined using 1H, 13C, 15N and 31P heteronuclear NMR spectroscopy. |
-Sample preparation
Details | Contents: 2mM ACSL-Phe, 15N, 13C Solvent system: 10 mM Potassium Phosphate, 10mM NaCl, 0.02mM EDTA. 90% H2O-10% D2O or 100% D2O. | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
| |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz |
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: 294 NOE distance constraints, 36 base pair constraints, 70 torsion angle constraints. Global fold without torsion angle constraints. Refinement with torsion angle constraints. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 8 |