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- PDB-2k41: NMR structure of uridine bulged RNA duplex -

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Basic information

Entry
Database: PDB / ID: 2k41
TitleNMR structure of uridine bulged RNA duplex
Components
  • RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_
  • RNA_(5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3')_
KeywordsRNA / duplex / uridine bulge
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPopenda, L. / Bielecki, L. / Gdaniec, Z. / Adamiak, R.W.
CitationJournal: ARKIVOC / Year: 2008
Title: Structure and dynamics of adenosine bulged RNA duplex reveals formation of the dinucleotide platform in the C:G-A triple
Authors: Popenda, L. / Bielecki, L. / Gdaniec, Z. / Adamiak, R.W.
History
DepositionMay 26, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA_(5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3')_
B: RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_


Theoretical massNumber of molelcules
Total (without water)5,3892
Polymers5,3892
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)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 2864.727 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_


Mass: 2524.593 Da / Num. of mol.: 1 / 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 1H-1H NOESY
1212D DQF-COSY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC
1512D 1H-31P HSQC
2622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3'), 100% D2O100% D2O
21 mM RNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3')1
1 mMRNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')1
1 mMRNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3')2
1 mMRNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1606.8ambient 298 K
2606.8ambient 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CurvesLavery and Sklenardata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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