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Open data
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Basic information
Entry | Database: PDB / ID: 4qk9 | ||||||
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Title | Thermovirga lienii c-di-AMP riboswitch | ||||||
![]() | C-di-AMP riboswitch | ||||||
![]() | RNA / c-di-AMP riboswitch | ||||||
Function / homology | Chem-2BA / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, A. / Serganov, A. | ||||||
![]() | ![]() Title: Structural insights into recognition of c-di-AMP by the ydaO riboswitch. Authors: Gao, A. / Serganov, 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 | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qk8SC ![]() 4qkaC 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: RNA chain | Mass: 40379.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription | ||
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#2: Chemical | #3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 0.5mM Spermine, 20mM Magnesium acetrate, 100mM Sodium achloride, 0.05M Sodium cacodylate pH6.5, 20%MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 14, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→30 Å / Num. all: 9193 / Num. obs: 9173 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.05→3.11 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4QK8 Resolution: 3.05→29.47 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 21.79 / Stereochemistry target values: ML
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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: 3.05→29.47 Å
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Refine LS restraints |
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LS refinement shell |
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