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- PDB-6alt: Solution structure of a DNA dodecamer with 5-methylcytosine at th... -

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Basic information

Entry
Database: PDB / ID: 6alt
TitleSolution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 9th position
ComponentsDNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3')
KeywordsDNA / Drew-Dickerson / non-canonical / modified DNA / epigenetics
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. / 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
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionSep 20, 2017ID: 5TMI
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
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

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Assembly

Deposited unit
A: DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3')
B: DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3')


Theoretical massNumber of molelcules
Total (without water)7,2232
Polymers7,2232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4190 Å2
ΔGint15 kcal/mol
Surface area4010 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 18structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3')


Mass: 3611.466 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
221isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
141isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3'), 100% D2O
Label: dd06 / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloridenatural abundance1
10 mMpotassium phosphatenatural abundance1
0.1 mMEDTAnatural abundance1
1 mMDNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3')natural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1120 mM100% D2O6.8ambient 298 K
2120 mM10% D2O6.8ambient 278 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, 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: 11

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