+Open data
-Basic information
Entry | Database: PDB / ID: 8u5z | ||||||
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Title | Structure of Mango II variant aptamer bound to T01-7M-B | ||||||
Components | Mango II 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: 2.5 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 variant aptamer bound to T01-7M-B 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 | 8u5z.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u5z.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u5z_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8u5z_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8u5z_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 8u5z_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/8u5z ftp://data.pdbj.org/pub/pdb/validation_reports/u5/8u5z | HTTPS FTP |
-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: 11889.210 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-NA / | #4: Chemical | Mass: 763.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H51N6O6S2 / Feature type: SUBJECT OF INVESTIGATION #5: 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: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Magnesium chloride hexahydrate, MOPS, TacsimateTM, hexamine cobalt (III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 2.5→45.27 Å / Num. obs: 12754 / % possible obs: 97.99 % / Redundancy: 12.5 % / Biso Wilson estimate: 45.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.51 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 1213 / CC1/2: 0.903 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.27 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4926 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: 46.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.27 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: -16.4864640461 Å / Origin y: 25.2521957482 Å / Origin z: -3.03685615613 Å
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Refinement TLS group | Selection details: all |