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Basic information

Entry
Database: PDB / ID: 6asf
TitleNMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA- Sequence
Components
  • DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3')
  • DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')
KeywordsDNA / Mixed base pair sequence / Minor groove / single GC base pair recognition
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsHarika, N.K. / Germann, M.W. / Boykin, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM111749 United States
CitationJournal: Chemistry / Year: 2017
Title: First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.
Authors: Harika, N.K. / Germann, M.W. / Wilson, W.D.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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 1.2May 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*CP*AP*AP*GP*AP*TP*AP*G)-3')
B: DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,4712
Polymers5,4712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: AAGATA DNA hairpin was used for NMR calculations with loop region CTCT. For molecular dynamic (MD) calculations the hairpin loop was not used and calculations were done on a double strand ...Evidence: AAGATA DNA hairpin was used for NMR calculations with loop region CTCT. For molecular dynamic (MD) calculations the hairpin loop was not used and calculations were done on a double strand DNA. Hairpin loop does not interfere in the complex formation.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area3630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 11all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2748.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3')


Mass: 2721.796 Da / Num. of mol.: 1 / 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 100MS
121isotropic22D 1H-1H NOESY 100MS
131isotropic12D 1H-1H NOESY 50MS
141isotropic22D 1H-1H NOESY 50MS
151isotropic12D 1H-1H NOESY 150MS
161isotropic12D 1H-1H NOESY 300MS
171isotropic12D 1H-1H CONSTANT TIME NOESY
181isotropic11D 31P
191isotropic11H, 31P-correlated 2D spectra (HPCOR)
1101isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.54 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS, 100% D2O
Label: 1H_sample / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.54 mMDNA hairpinnatural abundance1
10 mMTris-d11 buffernatural abundance1
10 mMsodium chloridenatural abundance1
0.14 mMEDTAnatural abundance1
0.4 mMDSSnatural abundance1
Sample conditionsIonic strength: 0.5 mM / Label: conditions_1 / pH: 6.3 pH* / Pressure: AMBIENT / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
SparkyGoddard,T.D.; Kneller,D.G.chemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddard,T.D.; Kneller,D.G.chemical shift assignment
SparkyGoddard,T.D.; Kneller,D.G.peak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 11 / Conformers submitted total number: 11

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