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- PDB-6gz7: Polyamide - DNA complex NMR structure -

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Basic information

Entry
Database: PDB / ID: 6gz7
TitlePolyamide - DNA complex NMR structure
ComponentsDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')
KeywordsUNKNOWN FUNCTION / Polyamide DNA complex
Function / homologyChem-FGW / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsAman, K.
CitationJournal: Chemistry / Year: 2019
Title: Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues.
Authors: Aman, K. / Padroni, G. / Parkinson, J.A. / Welte, T. / Burley, G.A.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / 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.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.4May 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

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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)9,1333
Polymers7,8812
Non-polymers1,2511
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1770 Å2
ΔGint-0 kcal/mol
Surface area4580 Å2
MethodPISA
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*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')


Mass: 3940.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FGW / dimethyl-[3-[3-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[(1-propan-2-ylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]butanoylamino]imidazol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]propanoylamino]propyl]azanium


Mass: 1251.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60H76N21O10 / 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
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H COSY
132isotropic12D 1H-13C HSQC
142isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.26 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 0.24 mM polyamide (PA9), 90% H2O/10% D2OPA-ODN1 complex90% H2O/10% D2O
solution21.26 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 0.24 mM polyamide (PA9), 99% D2OPA-ODN1 complex nowat99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.26 mMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance1
0.24 mMpolyamide (PA9)natural abundance1
1.26 mMDNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')natural abundance2
0.24 mMpolyamide (PA9)natural abundance2
Sample conditionsIonic strength units: Not defined / Label: PA-ODN1 complex conditions / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
Details: the structures are based on a total of 310 NOE distance restraints
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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