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- PDB-2lfa: Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine -

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Basic information

Entry
Database: PDB / ID: 2lfa
TitleOligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine
Components
  • DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*(2LF)P*TP*GP*TP*TP*TP*GP*T)-3')
KeywordsDNA / (5'S)-8 / 5'-cyclo-2'-deoxyguanosine / cyclopurine / cyclo-dG
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsHuang, H. / Das, R.S. / Basu, A. / Stone, M.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA.
Authors: Huang, H. / Das, R.S. / Basu, A.K. / Stone, M.P.
History
DepositionJun 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: 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: DNA (5'-D(*GP*TP*GP*CP*(2LF)P*TP*GP*TP*TP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3232
Polymers7,3232
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 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*CP*(2LF)P*TP*GP*TP*TP*TP*GP*T)-3')


Mass: 3713.394 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')


Mass: 3609.398 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 1H-1H NOESY
1212D 1H-1H COSY

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Sample preparation

DetailsContents: 1.0 mM DNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3'), 1.0 mM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMDNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3')-11
1.0 mMDNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')-21
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: Amber / Version: 10
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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