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Yorodumi- PDB-7kvt: Crystal structure of Squash RNA aptamer in complex with DFHBI-1T ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kvt | ||||||
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Title | Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions | ||||||
Components | Squash RNA aptamer bound to DFHBI-1T with iridium (III) ions | ||||||
Keywords | RNA / fluorogenic aptamer / adenine riboswitch | ||||||
Function / homology | Chem-2ZY / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å | ||||||
Authors | Truong, L. / Ferre-D'Amare, A.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Authors: Truong, L. / Kooshapur, H. / Dey, S.K. / Li, X. / Tjandra, N. / Jaffrey, S.R. / 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 | 7kvt.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kvt.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kvt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7kvt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7kvt_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 7kvt_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kvt ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kvt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 26986.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Chemical | ChemComp-2ZY / ( | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 40 mM Na cacodylate pH 7.0, 80 mM NaCl, 12 mM spermine hydrochloride, 36% (v/v) MPD, 40 mM NaI, and 1 mM iridium (III) hexammine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.105 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.105 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→46.5 Å / Num. obs: 7929 / % possible obs: 99.9 % / Redundancy: 24.7 % / Biso Wilson estimate: 81.37 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 69.6 |
Reflection shell | Resolution: 2.73→2.9 Å / Rmerge(I) obs: 3.114 / Num. unique obs: 1386 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.73→46.47 Å / SU ML: 0.408 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.374 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: 71.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→46.47 Å
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Refine LS restraints |
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LS refinement shell |
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