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- PDB-3ski: Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ski | ||||||
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Title | Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine | ||||||
![]() | (RNA (68-MER)) x 2 | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | 2'-DEOXY-GUANOSINE / ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A. | ||||||
![]() | ![]() Title: Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch. Authors: Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / 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 | ![]() | 162.4 KB | Display | ![]() |
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PDB format | ![]() | 129.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sklC ![]() 3skrC ![]() 3sktC ![]() 3skwC ![]() 3skzC ![]() 3slmC ![]() 3slqC 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
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 22018.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed RNA |
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#2: RNA chain | Mass: 21858.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed RNA |
-Non-polymers , 5 types, 126 molecules ![](data/chem/img/GNG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-SIN / | ![]() #6: Chemical | ChemComp-SO4 / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.05 M Na-acetate or Na-succinate, pH 4.7-5.1, ~3.0 M ammonium sulfate, 0.5 mM spermine and 20 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→20 Å / Num. all: 17879 / Num. obs: 16645 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.278 / Num. unique all: 1049 / % possible all: 89.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.361 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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