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- PDB-3slq: Crystal structure of the 2'- Deoxyguanosine riboswitch bound to g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3slq | ||||||
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Title | Crystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate | ||||||
![]() | RNA (68-MER) | ||||||
![]() | RNA / three-way junction / riboswitch / 2'-deoxy guanosine | ||||||
Function / homology | GUANOSINE-5'-MONOPHOSPHATE / SUCCINIC ACID / RNA / RNA (> 10)![]() | ||||||
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 | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 975.4 KB | Display | ![]() |
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Full document | ![]() | 985.5 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3skiC ![]() 3sklC ![]() 3skrC ![]() 3sktC ![]() 3skwC ![]() 3skzC ![]() 3slmC 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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2 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 22018.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcribed RNA #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-SIN / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.05 M Na-succinate, ~3.0 M (NH4)2SO4, 0.5 mM spermine and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 14173 / Num. obs: 13677 / % possible obs: 96.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5 / Num. unique all: 1343 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: Molrep / Resolution: 2.5→19.88 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 34.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.196 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.88 Å
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Refine LS restraints |
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LS refinement shell |
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