+
Open data
-
Basic information
Entry | Database: PDB / ID: 8gzm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Cd2+-bound DNA aptamer T22C mutant | ||||||
![]() | 25-mer DNA | ||||||
![]() | DNA / DNA aptamer / Cd2+-binding / complex | ||||||
Function / homology | : / : / DNA / DNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gan, J.H. / Liu, H.H. / Gao, Y.Q. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structures and identification of novel Cd2+-specific DNA aptamer. Authors: Liu, H. / Gao, Y. / Mathivanan, J. / Armour-Garb, Z. / Shao, Z. / Zhang, Y. / Zhao, X. / Shao, Q. / Zhang, W. / Yang, J. / Cao, C. / Li, H. / Sheng, J. / Gan, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 38.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gzjSC ![]() 8gzkC ![]() 8gzlC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 7676.922 Da / Num. of mol.: 1 / Mutation: T22C / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.28 % / Description: Rod-like |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→30 Å / Num. obs: 4194 / % possible obs: 99.1 % / Redundancy: 22.4 % / Biso Wilson estimate: 50.03 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Χ2: 1.117 / Net I/σ(I): 14.2 / Num. measured all: 94083 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8GZJ Resolution: 2.55→22.67 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.08 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.88 Å2 / Biso mean: 54.2886 Å2 / Biso min: 20.24 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→22.67 Å
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→22.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -3.9855 Å / Origin y: 20.2266 Å / Origin z: -8.5624 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain A and resseq 1:25) |