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- PDB-2dd1: Three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCAAAGCCG -

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Basic information

Entry
Database: PDB / ID: 2dd1
TitleThree consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCAAAGCCG
Components
  • 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*CP*(P5P))-3'
  • 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3'
KeywordsRNA / Three consecutive sheared GA pairs / thermodynamics of molecular recognition / K-turn motif / A-minor motif / secondary structure of RNA
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsChen, G. / Kennedy, S.D. / Krugh, T.R. / Turner, D.H.
CitationJournal: Biochemistry / Year: 2006
Title: An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA
Authors: Chen, G. / Kennedy, S.D. / Qiao, J. / Krugh, T.R. / Turner, D.H.
History
DepositionJan 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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
Revision 1.4May 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: 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3'
B: 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*CP*(P5P))-3'


Theoretical massNumber of molelcules
Total (without water)6,4412
Polymers6,4412
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)24 / 40structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 3272.996 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*CP*(P5P))-3'


Mass: 3167.991 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 80mM NaCl, 10mM sodium phosphate, 0.5mM Na2EDTA, 2mM total duplex concentrations, pH 5.4, pD 6.8

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameClassification
Felixprocessing
Discoverrefinement
VNMRcollection
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 24

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