[English] 日本語
![](img/lk-miru.gif)
- PDB-7tft: [T:Ag+/Hg2+:T--(pH11-pH7; 5s)] Metal-mediated DNA base pair in te... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7tft | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | [T:Ag+/Hg2+:T--(pH11-pH7; 5s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 5s | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | DNA / tensegrity triangle / self-assembling crystal / metal-mediated mismatch | |||||||||||||||||||||
Function / homology | SILVER ION / : / DNA / DNA (> 10)![]() | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Lu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs Authors: Lu, B. / Ohayon, Y.P. / Sha, R. / Woloszyn, K. / Rothschild, L. / Wind, S. / Hendrickson, W. / Mao, C. / Seeman, N.C. / Vecchioni, S. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7tfuC ![]() 7tfvC ![]() 7tfwC ![]() 7tfxC ![]() 7tfyC ![]() 7tfzC ![]() 7tg0C ![]() 7tg1C ![]() 7tg2C ![]() 7tg3C ![]() 7tg4C ![]() 7tg6C ![]() 7tg7C ![]() 7tg8C ![]() 7tg9C ![]() 7tgaC ![]() 7tgbC ![]() 7tgcC ![]() 7tgdC ![]() 8dxvC ![]() 8dxwC ![]() 8dxxC ![]() 8dxyC ![]() 8dxzC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
-DNA chain , 4 types, 4 molecules ABCD
#1: DNA chain | Mass: 6463.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 2066.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/HG.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/AG.gif)
#5: Chemical | ChemComp-HG / |
---|---|
#6: Chemical | ChemComp-AG / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 8.41 Å3/Da / Description: Rhombohedral |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tris, magnesium sulfate, silver nitrate, mercury chloride Temp details: 338-293 at 0.4/hr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00743 Å / Relative weight: 1 |
Reflection | Resolution: 4.42→64.78 Å / Num. obs: 3039 / % possible obs: 85.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 307 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 4.42→5 Å / Num. unique obs: 418 / CC1/2: 0.304 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 309.17 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.42→32.69 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 4.42→32.69 Å
|