+Open data
-Basic information
Entry | Database: PDB / ID: 2grb | ||||||||||||||||||
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Title | Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / RNA Quadruplex | Function / homology | : / STRONTIUM ION / RNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | Authors | Pan, B. / Shi, K. / Sundaralingam, M. | Citation | Journal: J.Mol.Biol. / Year: 2006 | Title: Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads. Authors: Pan, B. / Shi, K. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2grb.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2grb.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 2grb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/2grb ftp://data.pdbj.org/pub/pdb/validation_reports/gr/2grb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is one tetramer (e.g. chain A, B, C, D), half of the asymmetric unit. |
-Components
#1: RNA chain | Mass: 1916.099 Da / Num. of mol.: 8 / Source method: obtained synthetically #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-SR / | #4: 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: 1.82 Å3/Da / Density % sol: 32.38 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: KCl, CaCl2, MPD , pH 7.0, EVAPORATION, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9195,0.9200,0.8984 | ||||||||||||
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2003 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→30 Å / Num. obs: 23152 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.87 % | ||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.136 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.089 / 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: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.058 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.435 Å / Total num. of bins used: 20
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