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- PDB-1ntq: 5'(dCCUCCUU)3':3'(rAGGAGGAAA)5' -

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Basic information

Entry
Database: PDB / ID: 1ntq
Title5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'
Components
  • 5'-D(*CP*CP*UP*CP*CP*UP*U)-3'
  • 5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3'
KeywordsDNA/RNA / DNA / RNA / hybrid / propynyl / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
Model type detailsminimized average
AuthorsZnosko, B.M. / Barnes III, T.W. / Krugh, T.R. / Turner, D.H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2003
Title: NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines
Authors: Znosko, B.M. / Barnes III, T.W. / Krugh, T.R. / Turner, D.H.
#1: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines
Authors: Barnes III, T.W. / Turner, D.H.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,9642
Polymers4,9642
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 / -
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*UP*CP*CP*UP*U)-3'


Mass: 1982.270 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

Details
Solution-IDContentsSolvent system
1~1mM hybrid, 80 mM NaCl, 10 mM phosphate buffer, 0.5 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
2~2.5 mM hybrid, 80 mM NaCl, 10 mM phosphate, 0.5 mM EDTA, 99.996% D2O99.996% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
180 mM NaCl 7ambient 273 K
280 mM NaCl 7ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
VNMR5.2Variancollection
Felix2000MSIdata analysis
Discover95MSIstructure solution
Discover95MSIrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: The structure is based on a total of 140 interproton distance restraints, 18 hydrogen bond restraints, and 104 dihedral angle restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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