[English] 日本語
![](img/lk-miru.gif)
- PDB-3v9d: Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3v9d | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Tetra-decanucleotide / A-DNA duplex / Crystal packing / A-type double helix | Function / homology | : / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Mandal, P.K. / Venkadesh, S. / Gautham, N. | ![]() ![]() Title: Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 26.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 16.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 389.1 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 4282.768 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MN / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM MnCl2, 10mM spermine, equilibrated against 50 % methyl pentane diol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2011 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.34 Å / Num. all: 2606 / Num. obs: 2599 / % possible obs: 99.7 % / Redundancy: 4.64 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.69 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.5 / Num. unique all: 253 / Rsym value: 0.272 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: A-DNA duplex Fiber model (tetra-decanucleotide) built using Insight-II Resolution: 2.5→29.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU ML: 0.252 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.252 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Molecular replacement was carried out using AMoRe [Navaza, 1994] of the CCP4 suite. The A-DNA duplex gave the best correlation coefficient (83%)
| |||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3799 Å2
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.34 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.501→2.565 Å / Total num. of bins used: 20
|