+Open data
-Basic information
Entry | Database: PDB / ID: 8u5k | ||||||
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Title | Structure of Mango II aptamer bound to T01-6A | ||||||
Components | Mango II | ||||||
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: 2.8 Å | ||||||
Authors | Passalacqua, L.F.M. / Ferre-D'Amare, A.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of Mango II 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u5k.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u5k.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 8u5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/8u5k ftp://data.pdbj.org/pub/pdb/validation_reports/u5/8u5k | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: 11936.274 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | Mass: 411.539 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H23N2OS / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: HEPES sodium, polyethylene glycol 400, and ammonium acetate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→69.73 Å / Num. obs: 9509 / % possible obs: 96.82 % / Redundancy: 6.1 % / Biso Wilson estimate: 64.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 5.51 |
Reflection shell | Resolution: 2.8→2.901 Å / Num. unique obs: 911 / CC1/2: 0.491 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→69.73 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1818 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: 66.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→69.73 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: 19.0983257456 Å / Origin y: 25.0057750675 Å / Origin z: -3.17061034553 Å
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Refinement TLS group | Selection details: all |