+Open data
-Basic information
Entry | Database: PDB / ID: 2irn | ||||||||||||||||||
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Title | The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2 | ||||||||||||||||||
Components | 5'-R(P*Keywords | RNA / RNA INERNAL LOOPS / SHEARED GA PAIRS / GU WOBBLE / THERMODYNAMICS | Function / homology | RNA | Function and homology information Method | SOLUTION NMR / simulated annealing, restrained molecular dynamics | Authors | Tolbert, B.S. | Citation | Journal: Biochemistry / Year: 2007 | Title: NMR Structures of (rGCUGAGGCU)(2) and (rGCGGAUGCU)(2): Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs(,). Authors: Tolbert, B.S. / Kennedy, S.D. / Schroeder, S.J. / Krugh, T.R. / Turner, D.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2irn.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2irn.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 2irn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/2irn ftp://data.pdbj.org/pub/pdb/validation_reports/ir/2irn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 2887.767 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: natural abundance 13C-1H HSQC, 15N-1H HSQC |
-Sample preparation
Details | Contents: 0.75 mM RNA duplex, 80 mM NaCl, 0.5 mM Na2EDTA, 10 mM sodium phosphate, pH 5.5, 90% H2O, 10%D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 5.5 / Temperature: 283 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, restrained molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 15 |