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- PDB-6rio: Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3') -

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Basic information

Entry
Database: PDB / ID: 6rio
TitleImidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')
ComponentsDNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')
KeywordsDNA / Polyamide / Minor groove binder
Function / homologyChem-K4Z / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics / matrix relaxation
AuthorsPadroni, G. / Withers, J.M. / Taladriz-Sender, A. / Reichenbach, L.F. / Parkinson, J.A. / Burley, G.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/M000125/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R006857/1 United Kingdom
Leverhulme TrustRPG-2018-149 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components.
Authors: Padroni, G. / Withers, J.M. / Taladriz-Sender, A. / Reichenbach, L.F. / Parkinson, J.A. / Burley, G.A.
History
DepositionApr 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Mar 4, 2020Group: Data collection / Source and taxonomy
Category: chem_comp / pdbx_entity_src_syn / pdbx_nmr_spectrometer
Item: _chem_comp.type / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._chem_comp.type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')
B: DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4043
Polymers7,1652
Non-polymers1,2391
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2500 Å2
ΔGint3 kcal/mol
Surface area4380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2000structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')


Mass: 3582.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K4Z / 3-[3-[[4-[[4-[[4-[[4-[[(2~{R})-2-azaniumyl-4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]butanoyl]amino]-1-methyl-imidazol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]propanoylamino]propyl-dimethyl-azanium


Mass: 1239.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H74N22O10 / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-13C HSQC
122isotropic12D 1H-1H TOCSY
132isotropic12D DQF-COSY
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-31P COSY
162isotropic11D 31P
171isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate, 90% H2O/10% D2OH2O90% H2O/10% D2O
solution21.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate, 100% D2OD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMDNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')natural abundance1
1.3 mMPolyamidenatural abundance1
100 mMsodium phosphatenatural abundance1
1.3 mMDNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')natural abundance2
1.3 mMPolyamidenatural abundance2
100 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: Conditions 1 / pH: 7.45 / 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
MARDIGRASN. Ulyanovstructure calculation
TopSpinBruker Biospincollection
Refinement
MethodSoftware ordinal
molecular dynamics1
matrix relaxation2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2000 / Conformers submitted total number: 10

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