+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xjz | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of DNA1-Ag complex | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Ag / base pair | Function / homology | SILVER ION / SPERMINE / DNA | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Liu, H.H. / Gan, J.H. | Funding support | | ![]()
![]() ![]() Title: A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs Authors: Liu, H.H. / Shen, F.S. / Haruehanroengra, P. / Yao, Q.Q. / Cheng, Y.S. / Chen, Y.Q. / Yang, C. / Zhang, J. / Wu, B.X. / Luo, Q. / Cui, R.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H. History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 31.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 21.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 385.6 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 2412.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.19 % / Description: Needle |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% v/v MPD, 40mM Sodium cacodylate pH 7.0, 12mM Spermine tetra-HCl, 80mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→30 Å / Num. obs: 24202 / % possible obs: 99.4 % / Redundancy: 6.4 % / Net I/σ(I): 31 |
Reflection shell | Resolution: 0.98→1.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1694 / % possible all: 97.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.719 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 0.98→29.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|