[English] 日本語
![](img/lk-miru.gif)
- PDB-1naj: High resolution NMR Structure Of DNA Dodecamer Determined In Aque... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1naj | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | High resolution NMR Structure Of DNA Dodecamer Determined In Aqueous Dilute Liquid Crystalline Phase | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Dickerson Dodecamer | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS | ![]() Wu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V. / Bax, A. | ![]() ![]() Title: Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and (31)P chemical shift anisotropy. Authors: Wu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V.B. / Bax, A. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 89.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 307 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 327.4 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 40mM / pH: 7 / Pressure: 1 atm / Temperature: 308 K | |||||||||
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 |
|
-
Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON DIPOLAR COUPLINGS, 300 quantitative proton-proton dipolar restraints, 22 31P-1H dipolar couplings, and 22 31P chemical shift anisotropy restraints. THE COORDINATE OF THE ALIGNMENT TENSOR IS DEFINED BY molecule 500 and 501. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 5 |