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Open data
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Basic information
Entry | Database: PDB / ID: 4qlm | ||||||
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Title | ydao riboswitch binding to c-di-AMP | ||||||
![]() | RNA (108-MER) | ||||||
![]() | RNA / second message molecule / c-di-AMP binding | ||||||
Function / homology | Chem-2BA / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, A.M. / Patel, D.J. | ||||||
![]() | ![]() Title: c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Authors: Ren, A. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.5 KB | Display | ![]() |
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PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | AUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
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Components
#1: RNA chain | Mass: 40514.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ydao Riboswitch Source: (gene. exp.) ![]() Strain: MB4 / Description: in vitro translation | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.39 % |
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Crystal grow | Temperature: 293 K Details: 0.1 M Na-Bicine, pH 8.7-9.2 and 2.6-3.2 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 8.7-9.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.721→50 Å / Num. obs: 13840 / % possible obs: 99.7 % / Observed criterion σ(I): 1.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.721→45.64 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: 6.8744 Å / Origin y: 30.0921 Å / Origin z: -16.4253 Å
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Refinement TLS group | Selection details: all |