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- PDB-7d0y: NMR solution structures of the DNA minidumbbell formed by two CmC... -

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Entry
Database: PDB / ID: 7d0y
TitleNMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5
ComponentsDNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3')
KeywordsDNA / minidumbbell / methylation / CCTG / 5-methylcytosine / pH 5
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsWan, L. / Guo, P. / Lam, S.L.
CitationJournal: Chemistry / Year: 2021
Title: 5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells.
Authors: Wan, L. / Yi, J. / Lam, S.L. / Lee, H.K. / Guo, P.
History
DepositionSep 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 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(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4426
Polymers2,3271
Non-polymers1155
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2080 Å2
ΔGint-45 kcal/mol
Surface area1100 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3')


Mass: 2326.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
Compound detailsDCZ (A 1), 5CM (A 2) have extra atom H3 as N3-site protonated.
Has ligand of interestY

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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
151isotropic22D 1H-1H COSY
161isotropic22D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaCl, 99.96% D2O
Label: CmCTG2, pH 5, D2O / Solvent system: 99.96% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDNANA1
0.02 mMDSSNA1
10 mMNaClNA1
Sample conditionsIonic strength: 10 mM / Label: pH 5 / pH: 5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: restrained molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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