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- PDB-2mo7: Solution NMR structure of DNA dodecamer with A:C mismatch -

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Basic information

Entry
Database: PDB / ID: 2mo7
TitleSolution NMR structure of DNA dodecamer with A:C mismatch
ComponentsDNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / dodecamer / mismatch
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsDonahue, P.S. / Szulik, M.W. / Stone, M.P.
CitationJournal: To be Published
Title: Characterization of 5-hydroxycytosine in DNA
Authors: Szulik, M. / Donahue, P. / Stone, M.
History
DepositionApr 18, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,2952
Polymers7,2952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area4740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 30back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA_(5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3647.393 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 100 mM DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 100 % D2O, 11 mM sodium azide, 0.5 mM EDTA, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')-11
10 mMsodium phosphate-21
100 mMsodium chloride-31
100 %D2O-41
11 mMsodium azide-51
0.5 mMEDTA-61
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 30 / Conformers submitted total number: 11

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