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Yorodumi- PDB-3slm: Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3slm | ||||||
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Title | Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine-5'-monophosphate | ||||||
Components | RNA (68-MER) | ||||||
Keywords | RNA / three-way junction / riboswitch / 2'-deoxy guanosine | ||||||
Function / homology | 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / SUCCINIC ACID / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molrep / Resolution: 2.7 Å | ||||||
Authors | Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.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 | 3slm.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3slm.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 3slm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3slm ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3slm | HTTPS FTP |
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-Related structure data
Related structure data | 3skiC 3sklC 3skrC 3sktC 3skwC 3skzC 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
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 22018.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcribed |
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-Non-polymers , 5 types, 29 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-SIN / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % |
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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 ammonium sulfate, 0.5 mM spermine and 20 mM magnesium chloride , pH 5.1, 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: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 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: 2.7→20 Å / Num. all: 11084 / Num. obs: 11084 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1100 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Molrep / Resolution: 2.7→19.543 Å / SU ML: 0.77 / σ(F): 1.34 / Phase error: 28.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.757 Å2 / ksol: 0.283 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.543 Å
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Refine LS restraints |
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LS refinement shell |
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