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- PDB-6m6j: NMR solution structure of a DNA minidumbbell containing an abasic... -

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Basic information

Entry
Database: PDB / ID: 6m6j
TitleNMR solution structure of a DNA minidumbbell containing an abasic bulge between two CTTG repeats
ComponentsDNA (5'-D(*CP*TP*TP*GP*(3DR)P*CP*TP*TP*G)-3')
KeywordsDNA / Minidumbbell / Bulge / Abasic site
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)2,7739
Polymers2,5891
Non-polymers1848
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1310 Å2
ΔGint-78 kcal/mol
Surface area1570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest total 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: 2588.685 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 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.9 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi, 99.96% D2O
Label: CTTGXCTTG / Solvent system: 99.96% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 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
AmberDavid A. Case Thomas E. Cheatham III Tom Darden Holger Gohlke Ray Luo Kenneth M. Merz Jr. Alexey Onufriev Carlos Simmerling Bing Wang Robert J. Woodsstructure calculation
TopSpinBrukerchemical shift assignment
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest total energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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