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- PDB-6db8: Structural basis for promiscuous binding and activation of fluoro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6db8 | ||||||
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Title | Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer | ||||||
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![]() | RNA/IMMUNE SYSTEM / Fluorescent aptamer / Fab / DIR / RNA / RNA-IMMUNE SYSTEM complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-G4A / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shao, Y. / Shelke, S.A. / Laski, A. / Piccirilli, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Authors: Shelke, S.A. / Shao, Y. / Laski, A. / Koirala, D. / Weissman, B.P. / Fuller, J.R. / Tan, X. / Constantin, T.P. / Waggoner, A.S. / Bruchez, M.P. / Armitage, B.A. / Piccirilli, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.3 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 840.4 KB | Display | ![]() |
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Full document | ![]() | 844.5 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6db9C ![]() 4zkeS 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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Unit cell |
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Components
#1: Antibody | Mass: 24665.510 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: RNA chain | Mass: 19380.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Antibody | Mass: 23075.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
#4: Chemical | ChemComp-G4A / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, pH 5.6, 10 mM MgCl2, 1.8 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→80.27 Å / Num. obs: 63989 / % possible obs: 99.15 % / Redundancy: 12.9 % / Biso Wilson estimate: 41.9006599711 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3915 / CC1/2: 0.476 / Rpim(I) all: 0.685 / Rrim(I) all: 2.405 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZKE Resolution: 1.86541345549→37.59 Å / SU ML: 0.279977511605 / Cross valid method: FREE R-VALUE / σ(F): 1.33645911288 / Phase error: 28.7196515222
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.6096131687 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86541345549→37.59 Å
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Refine LS restraints |
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LS refinement shell |
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