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- PDB-2l8c: NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG... -

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Entry
Database: PDB / ID: 2l8c
TitleNMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1 - UU pair with zero hydrogen bond pairs
ComponentsRNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')
KeywordsRNA / UU mismatch
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 1
AuthorsParkesh, R. / Fountain, M.A. / Disney, M.D.
CitationJournal: Biochemistry / Year: 2011
Title: NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)(2) Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
Authors: Parkesh, R. / Fountain, M. / Disney, M.D.
History
DepositionJan 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2023Group: Data collection / Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')
B: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,7262
Polymers5,7262
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)1 / 25structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

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


Mass: 2862.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3'), 100% D2O
Solvent system: 100% D2O
SampleConc.: 1.5 mM / Component: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')-1
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddarddata analysis
Sparky3.111Goddardpeak picking
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 25 / Conformers submitted total number: 1

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