+Open data
-Basic information
Entry | Database: PDB / ID: 1fyo | ||||||
---|---|---|---|---|---|---|---|
Title | EUKARYOTIC DECODING REGION A-SITE RNA | ||||||
Components | FRAGMENT OF 18S RIBOSOMAL RNA | ||||||
Keywords | RNA / stem-internal loop-stem-tetraloop RNA / G-A base pair / bulged A | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Authors | Lynch, S.R. / Puglisi, J.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structure of a eukaryotic decoding region A-site RNA. Authors: Lynch, S.R. / Puglisi, J.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fyo.cif.gz | 410.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fyo.ent.gz | 361.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyo ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyo | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 8672.185 Da / Num. of mol.: 1 Fragment: 18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERS) Mutation: U1410A, A1490U / Source method: obtained synthetically Details: This sequence occurs naturally in Tetrahymena thermophila |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 3 mM decoding site RNA, 13C/15N, 10 mM phosphate pH 6.3, 90% H20/10% D20, 100% D20 Solvent system: 90% H2O/10% D20; 100% D2O |
---|---|
Sample conditions | Ionic strength: 10 mM / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: 682 NOEs, 129 dihedral constraints, 36 Hydrogen bonds | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 25 |