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- PDB-2lvy: Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxym... -

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Basic information

Entry
Database: PDB / ID: 2lvy
TitleSolution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification
Components
  • RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3')
  • RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3')
KeywordsRNA / modification
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsBaraguey, C.
CitationJournal: Org.Biomol.Chem. / Year: 2013
Title: The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure.
Authors: Baraguey, C. / Lescrinier, E. / Lavergne, T. / Debart, F. / Herdewijn, P. / Vasseur, J.J.
History
DepositionJul 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3')
B: RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,8062
Polymers5,8062
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)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3')


Mass: 2919.889 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3')


Mass: 2885.794 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 DQF-COSY
1212D 1H-31P HETCOR
1312D 1H-1H NOESY
2422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM duplex, 100% D2O100% D2O
20.9 mM duplex, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.9 mMduplex-11
0.9 mMduplex-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
106.7ambient 293 K
206.7ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 14 / NA beta-angle constraints total count: 14 / NA chi-angle constraints total count: 16 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 14 / NA other-angle constraints total count: 14 / NA sugar pucker constraints total count: 32 / NOE constraints total: 292 / NOE intraresidue total count: 145
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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