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- PDB-5odf: NtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamid... -

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Basic information

Entry
Database: PDB / ID: 5odf
TitleNtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies
ComponentsDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
KeywordsDNA BINDING PROTEIN / DNA / Minor groove binders / Hairpin polyamides
Function / homologyNtMe polyamide / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPadroni, G. / Parkinson, J. / Burley, G.A.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides.
Authors: Padroni, G. / Parkinson, J.A. / Fox, K.R. / Burley, G.A.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 8, 2019Group: Data collection
Category: chem_comp / pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _chem_comp.type / _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4053
Polymers7,1652
Non-polymers1,2401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Tm analysis and Circular Dichroism
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1880 Å2
ΔGint-0 kcal/mol
Surface area4740 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10na
RepresentativeModel #1na

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Components

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


Mass: 3582.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CWN / NtMe polyamide


Mass: 1240.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H71N20O10S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
122isotropic12D DQF-COSY
132isotropic12D 1H-1H TOCSY
142isotropic12D 1H-13C HSQC
152isotropic11H-31P COSY
162isotropic12D 1H-1H NOESY
171isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.3 nM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 90% H2O/10% D2ONtMe PA_H2O90% H2O/10% D2O
solution21.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 100% D2ONtMe PA_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 nMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance1
1.3 mMPA6natural abundance1
1.3 mMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance2
1.3 mMPA6natural abundance2
Sample conditionsIonic strength: 100 Phosphate mM / Label: NtMe PA / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
MARDIGRASN. Ulyanovstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: na
NMR ensembleConformer selection criteria: na / Conformers calculated total number: 10 / Conformers submitted total number: 10

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