[English] 日本語
![](img/lk-miru.gif)
- PDB-6c64: Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6c64 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Mango-II Fluorescent Aptamer Bound to TO3-Biotin | ||||||
![]() |
| ||||||
![]() | RNA / Fluorescent / Aptamer / G-quadruplex | ||||||
Function / homology | Chem-EKM / : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trachman, R.J. / Ferre-D'Amare, A.R. | ||||||
![]() | ![]() Title: Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness. Authors: Trachman 3rd., R.J. / Abdolahzadeh, A. / Andreoni, A. / Cojocaru, R. / Knutson, J.R. / Ryckelynck, M. / Unrau, P.J. / Ferre-D'Amare, A.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 884.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 889.2 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c63SC ![]() 6c65C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: RNA chain | Mass: 11936.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / Source: (synth.) synthetic construct (others) #2: RNA chain | | Mass: 10635.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was in vitro transcribed / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | ChemComp-K / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % / Description: cubic |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 2.45 M Ammonium Formate, 12.5% glycerol, 3% sorbitol PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3→46.52 Å / Num. obs: 7735 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 58.7167495741 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1268 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6C63 Resolution: 3.00014879601→46.5151662692 Å / SU ML: 0.359376037971 / Cross valid method: FREE R-VALUE / σ(F): 1.34562114754 / Phase error: 23.9164508394
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.3830391657 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.00014879601→46.5151662692 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|