+Open data
-Basic information
Entry | Database: PDB / ID: 8u5j | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Mango III variant aptamer bound to T01-07M-B | ||||||
Components | Mango III variant | ||||||
Keywords | RNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex | ||||||
Function / homology | : / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Passalacqua, L.F.M. / Ferre-D'Amare, A.R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of Mango III variant aptamer bound to T01-07M-B Authors: Passalacqua, L.F.M. / Ferre-D'Amare, A.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8u5j.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8u5j.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/8u5j ftp://data.pdbj.org/pub/pdb/validation_reports/u5/8u5j | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: RNA chain | Mass: 11688.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-K / | ||||||
#3: Chemical | #4: Chemical | ChemComp-W6F / | Mass: 763.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H51N6O6S2 / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.01 M magnesium sulphate heptahydrate, 0.05 M sodium cacodylate trihydrate pH 6.0, 1.8 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.87 Å / Num. obs: 13366 / % possible obs: 99.58 % / Redundancy: 17.5 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 1.7→1.761 Å / Num. unique obs: 1304 / CC1/2: 0.953 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5064 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: 35.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -18.0302315378 Å / Origin y: 17.2586091624 Å / Origin z: 5.68738769773 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |