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- PDB-2koc: NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop -

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Basic information

Entry
Database: PDB / ID: 2koc
TitleNMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop
ComponentsRNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3')
KeywordsRNA / UUCG tetraloop / 14-mer hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsNozinovic, S. / Fuertig, B. / Jonker, H.R.A. / Richter, C. / Schwalbe, H.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA
Authors: Nozinovic, S. / Furtig, B. / Jonker, H.R.A. / Richter, C. / Schwalbe, H.
History
DepositionSep 17, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4551
Polymers4,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4454.683 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: High-Resolution NMR Structure of a RNA model system: the 14mer cUUCGg tetraloop hairpin RNA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
2412D 1H-1H NOESY
1513D 1H-13C-31P HCP
1612D 1H-15N IPAP HSQC
1712D 1H-15N IPAP HSQC
1812D 1H-13C IPAP HSQC
1912D 1H-13C IPAP HSQC
11013D HCC-TOCSY-CCH-E.COSY
11113D 1H-13C HC(C)H-TOCSY
11212D 1H-13C G-(H)CCH
11312D 1H-13C CT-TROSY
11413D 1H-13C-31P G-HCP

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Sample preparation

DetailsContents: 0.7mM [U-100% 13C; U-100% 15N] 14-MER RNA-1, 20mM potassium phosphate-2, 0.4mM EDTA-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mM14-MER RNA-1[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphate-21
0.4 mMEDTA-31
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.4ambient atm298 K
2206.4ambient atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.113Goddarddata analysis
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 259 / Hydrogen bond constraints total count: 32
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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