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- PDB-2iro: The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2 -

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Entry
Database: PDB / ID: 2iro
TitleThe NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2
Components5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3'
KeywordsRNA / RNA INTERNAL LOOPS / SHEARED GA PAIRS / SHEARED GU PAIRS / NON CANONICAL PAIRS / THERMODYNAMICS
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, restrained molecular dynamics
AuthorsTolbert, B.S.
CitationJournal: 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
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3'
B: 5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3'


Theoretical massNumber of molelcules
Total (without water)5,7762
Polymers5,7762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: RNA chain 5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3'


Mass: 2887.767 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: natural abundance 13C-1H and 15N-1H HSQC

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Sample preparation

DetailsContents: 1 mM 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
Sample conditionspH: 5.18 / Temperature: 278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger et al.structure solution
NMRPipeDelaglio et al.processing
Sparky3Goddard et al.data analysis
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing, restrained molecular dynamics / Software ordinal: 1
Details: structures validated by chemical back calculation using the program Nuchemics
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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