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- PDB-5izp: Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position -

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Basic information

Entry
Database: PDB / ID: 5izp
TitleSolution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')
KeywordsDNA / Drew-Dickerson / dodecamer / non-canonical / modified DNA / oxidized DNA / DNA damage / DNA adduct / lesion
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsGruber, D.R. / Hoppins, J.J. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Yurkovskaya, A.V. / Zharkov, D.O. / Smirnov, S.L.
CitationJournal: Plos One / Year: 2016
Title: 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme.
Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / ...Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / Zharkov, D.O. / Smirnov, S.L.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / 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 / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,3592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2400 Å2
ΔGint1 kcal/mol
Surface area4440 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 18structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')


Mass: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
222isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
141isotropic12D DQF-COSY
151isotropic12D 1H-31P HETCOR

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 100% D2OD2O100% D2O
solution250 mM sodium chloride, 10 mM potassium phosphate, 1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3'), 90% H2O/10% D2OH2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
10 mMpotassium phosphatenatural abundance1
1 mMEDTAnatural abundance1
1 mMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance1
50 mMsodium chloridenatural abundance2
10 mMpotassium phosphatenatural abundance2
1 mMEDTAnatural abundance2
1 mMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*(8OG)P*CP*G)-3')natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mM298K6.8ambient 298 K
2120 mM278K6.8ambient 278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
NMRView9Johnson, One Moon Scientificchemical shift assignment
NMRView9Johnson, One Moon Scientificpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 18 / Conformers submitted total number: 15

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