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Open data
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Basic information
Entry | Database: PDB / ID: 8u5r | ||||||
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Title | Structure of Mango II variant aptamer bound to T01-6A | ||||||
![]() | Mango II variant | ||||||
![]() | RNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex | ||||||
Function / homology | : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Passalacqua, L.F.M. / Ferre-D'Amare, A.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Mango II variant aptamer bound to T01-6A Authors: Passalacqua, L.F.M. / Ferre-D'Amare, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.9 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.9 KB | Display | ![]() |
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Full document | ![]() | 412.7 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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3 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 11889.210 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Magnesium chloride hexahydrate, MOPS, Tacsimate, hexamine cobalt (III) chloride, and 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.6→45.8 Å / Num. obs: 11414 / % possible obs: 99.67 % / Redundancy: 12.3 % / Biso Wilson estimate: 43.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.83 |
Reflection shell | Resolution: 2.6→2.693 Å / Num. unique obs: 1114 / CC1/2: 0.823 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.3593509683 Å / Origin y: 25.2150076653 Å / Origin z: -2.93813679284 Å
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Refinement TLS group | Selection details: all |