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Open data
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Basic information
Entry | Database: PDB / ID: 7kvu | ||||||
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Title | Crystal structure of Squash RNA aptamer in complex with DFHBI-1T | ||||||
![]() | Squash RNA aptamer | ||||||
![]() | RNA / fluorogenic aptamer / adenine riboswitch | ||||||
Function / homology | Chem-2ZY / : / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Truong, L. / Ferre-D'Amare, A.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.4 KB | Display | ![]() |
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PDB format | ![]() | 41.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 685.9 KB | Display | ![]() |
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Full document | ![]() | 686.8 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kvtSC ![]() 7kvvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-2ZY / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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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, and 40 mM NaI |
-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: Aug 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→46.46 Å / Num. obs: 8369 / % possible obs: 99.9 % / Redundancy: 24.7 % / Biso Wilson estimate: 81.37 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 71.7 |
Reflection shell | Resolution: 2.68→2.85 Å / Rmerge(I) obs: 4.494 / Num. unique obs: 1463 |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 7KVT Resolution: 2.68→46.46 Å / SU ML: 0.432 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.989 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: 75.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→46.46 Å
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Refine LS restraints |
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LS refinement shell |
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