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- PDB-1xv6: The solution structure of 2',5'-linked 3'-O-(2-methoxyethyl)-RNA ... -

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Basic information

Entry
Database: PDB / ID: 1xv6
TitleThe solution structure of 2',5'-linked 3'-O-(2-methoxyethyl)-RNA hairpin
Components5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2'
KeywordsRNA / hairpin / (2' / 5')-RNA / 3'-O-(2-methoxyethyl) ribose
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsPlevnik, M. / Gdaniec, Z. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex
Authors: Plevnik, M. / Gdaniec, Z. / Plavec, J.
History
DepositionOct 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2'


Theoretical massNumber of molelcules
Total (without water)4,6081
Polymers4,6081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30all calculated structures submitted
RepresentativeModel #18closest to the average

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Components

#1: RNA chain 5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2' / 2'-MOE RNA


Mass: 4608.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis, phosphoramidite chemistry

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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: Structure was determined using standard 2D homo- and heteronuclear techniques.

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Sample preparation

DetailsContents: 0.9mM hairpin, 100% D2O, 50mM NaCl / Solvent system: 100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 7.4 / Pressure: ambient / 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: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
Felix2000Accelerysprocessing
Amber6Kollman et al.refinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: structures were refined by NMR restrained molecular dynamics in two stages using a generalized born (GB) implicit solvation model. The resulting structures were subjected to energy ...Details: structures were refined by NMR restrained molecular dynamics in two stages using a generalized born (GB) implicit solvation model. The resulting structures were subjected to energy minimization. 2',5' phosphodiester linkages between residues, O3* of each ribose modified by methoxyethyl.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

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