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Yorodumi- PDB-3skl: Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3skl | ||||||
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Title | Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'-deoxyguanosine, iridium hexammine soak | ||||||
Components | RNA (66-MER) | ||||||
Keywords | RNA / three way junction / riboswitch / deoxyguanosine | ||||||
Function / homology | 2'-DEOXY-GUANOSINE / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3skl.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3skl.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3skl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3skl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3skl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3skl_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3skl_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/3skl ftp://data.pdbj.org/pub/pdb/validation_reports/sk/3skl | HTTPS FTP |
-Related structure data
Related structure data | 3skiC 3skrC 3sktC 3skwC 3skzC 3slmC 3slqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 21368.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: dG riboswitch #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-IRI / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M potassium chloride and 0.0-2.0 mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1052 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1052 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 8590 / Num. obs: 8487 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Num. unique all: 764 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
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