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- PDB-6m6k: NMR solution structure of a DNA minidumbbell containing an abasic... -

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Basic information

Entry
Database: PDB / ID: 6m6k
TitleNMR solution structure of a DNA minidumbbell containing an abasic bulge between two CCTG repeats
ComponentsDNA (5'-D(*CP*TP*TP*GP*(3DR)P*CP*TP*TP*G)-3')
KeywordsDNA / Minidumbbell / abasic site / bulge / CC mispair
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsWan, L. / Lam, S.L. / Guo, P.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Rational design of a reversible Mg2+/EDTA-controlled molecular switch based on a DNA minidumbbell.
Authors: Wan, L. / Lam, S.L. / Lee, H.K. / Guo, P.
History
DepositionMar 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 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(*CP*TP*TP*GP*(3DR)P*CP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7439
Polymers2,5591
Non-polymers1848
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1150 Å2
ΔGint-69 kcal/mol
Surface area1540 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(*CP*TP*TP*GP*(3DR)P*CP*TP*TP*G)-3')


Mass: 2558.663 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.: 8 / Source method: obtained synthetically / Formula: Na
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 NOESY
121isotropic12D DQF-COSY
131isotropic22D TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi, 99.96% D2O
Label: CCTGXCCTG / Solvent system: 99.96% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDNANA1
0.02 mMDSSNA1
10 mMNaPiNA1
Sample conditionsIonic strength: 10 mM / Ionic strength err: 0.1 / Label: condition_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 273 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TopSpinBrukerchemical shift assignment
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
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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