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- PDB-5uz3: Solution Structure of a DNA Dodecamer with 5-methylcytosine at th... -

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Basic information

Entry
Database: PDB / ID: 5uz3
TitleSolution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 10th position
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3')
KeywordsDNA / Drew-Dickerson / non-canonical / modified DNA / methylated DNA / epigenetics / CpG site / 8-oxoguanine / 5-methylcytosine
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. / Endutkin, A.V. / Zharkov, D.O. / Smirnov, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1244641 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.
Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, ...Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, E.C. / Okon, M. / Bagryanskaya, E.G. / Zharkov, D.O. / Smirnov, S.L.
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)7,3872
Polymers7,3872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 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*(DMC)P*(8OG)P*CP*G)-3')


Mass: 3693.419 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
111isotropic22D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3'), 100% D2O
Label: met9oG10 / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
10 mMpotassium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
1 mMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(DMC)P*(8OG)P*CP*G)-3')natural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mMD2O6.8ambient 298 K
2120 mMH2O6.8ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 18 / Conformers submitted total number: 10

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