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- PDB-1hs4: SOLUTION STRUCTURE OF RNA HAIRPIN LOOP UUAAAU AS PART OF HAIRPIN ... -

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Entry
Database: PDB / ID: 1hs4
TitleSOLUTION STRUCTURE OF RNA HAIRPIN LOOP UUAAAU AS PART OF HAIRPIN R(GCGUUAAAUCGCA)
Components5'-R(*GP*CP*GP*UP*UP*AP*AP*AP*UP*CP*GP*CP*A)-3'
KeywordsRNA / ribonucleic acid / hairpin loop / RNA structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, energy minimization
AuthorsZhang, H. / Culyba, M. / Volkman, H. / Krugh, T.R.
CitationJournal: To be Published
Title: Structural Characterization of Six-Nucleotide RNA Hairpin loops: r(UUAAUU), r(UUAAAU), r(UUAACU)
Authors: Zhang, H. / Culyba, M. / Volkman, H. / Krugh, T.R.
History
DepositionDec 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,1421
Polymers4,1421
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 / 30average structure of 30 conformers
Representative

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Components

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


Mass: 4141.526 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 1 mM RNA oligomer - H2O; 3 mM RNA oligomer - D2O
Sample conditionsIonic strength: 0.1 M NaCl, 0.01 M sodium phosphate / pH: 7 / Pressure: 1.0 atm / Temperature: 303 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discoverversion 2.98MSIstructure solution
Discoverversion 2.98MSIrefinement
RefinementMethod: restrained molecular dynamics, energy minimization / Software ordinal: 1
NMR ensembleConformer selection criteria: average structure of 30 conformers
Conformers calculated total number: 30 / Conformers submitted total number: 1

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