+
Open data
-
Basic information
Entry | Database: PDB / ID: 2kd4 | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution structure and thermodynamics of 2',5' RNA intercalation | ||||||||||||||||||||
![]() | 5'-R(*![]() RNA / proflavine / intercalation / 2' / 5' RNA / nearest-neighbor exclusion | Function / homology | PROFLAVIN / RNA | ![]() Method | SOLUTION NMR / simulated annealing | Model details | lowest energy, model 1 | ![]() Horowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V. | ![]() ![]() Title: Solution structure and thermodynamics of 2',5' RNA intercalation. Authors: Horowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 19.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 13.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 329.7 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: RNA chain | Mass: 2556.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 2',5' RNA #2: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details | Contents: 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O Solvent system: 99.9% D2O | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||||||||
Sample conditions |
|
-NMR measurement
NMR spectrometer |
|
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: 300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed | ||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 14 / NA other-angle constraints total count: 14 / NOE constraints total: 378 / NOE intraresidue total count: 258 / NOE medium range total count: 378 / NOE sequential total count: 258 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 1 |