[English] 日本語
![](img/lk-miru.gif)
- PDB-1kos: SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kos | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / TRNA / T STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / RNA FOLDING | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | ![]() Koshlap, K.M. / Guenther, R. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. | ![]() ![]() Title: A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain. Authors: Koshlap, K.M. / Guenther, R. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. #1: ![]() Title: Small Structural Ensembles for a 17-Nucleotide Mimic of the tRNA Tpsic-Loop Via Fitting Dipolar Relaxation Rates with the Quadratic Programming Algorithm Authors: Schmitz, U. / Donati, A. / James, T.L. / Ulyanov, N.B. / Yao, L. #2: ![]() Title: The Dynamic NMR Structure of the T Psi C-Loop: Implications for the Specificity of tRNA Methylation Authors: Yao, L.J. / James, T.L. / Kealey, J.T. / Santi, D.V. / Schmitz, U. #3: ![]() Title: Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer RNA. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles Authors: Westhof, E. / Sundaralingam, M. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 330.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 383.8 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: RNA chain | Mass: 5395.255 Da / Num. of mol.: 1 / Fragment: TPSIC DOMAIN OF TRNA / Mutation: +C49C / Source method: obtained synthetically Details: SEQUENCE FROM YEAST (SACCHAROMYCES CEREVISIAE) TRNA PHE |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||
NMR details | Text: EXPERIMENTS IN 100% D2O CONDUCTED AT 283, 288,293, AND 298 KELVIN; EXPERIMENTS IN 6% D2O/ 94% H2O CONDUCTED AT 274 AND 283 KELVIN. |
-
Sample preparation
Details | Contents: 100% D2O, 94% WATER/6% D2O |
---|---|
Sample conditions | pH: 6.0 / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX500 / Manufacturer: Bruker / Model: DRX500 / Field strength: 500 MHz |
---|
-
Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY STRUCTURES / Conformers calculated total number: 50 / Conformers submitted total number: 8 |