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- PDB-6i4n: Dodecamer DNA containing the synthetic base pair P-Z in complex w... -

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Basic information

Entry
Database: PDB / ID: 6i4n
TitleDodecamer DNA containing the synthetic base pair P-Z in complex with a pyrrole-imidazole polyamide
ComponentsDNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')
KeywordsDNA / synthetic base pair / Z / P / pyrrole-imidazole polyamide
Function / homologyChem-K4Z / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsPadroni, G. / Parkison, J. / Burley, G.A.
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
DepositionNov 10, 2018Deposition 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 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _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*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6523
Polymers7,4132
Non-polymers1,2391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1840 Å2
ΔGint1 kcal/mol
Surface area4630 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000structures with acceptable covalent geometry
RepresentativeModel #1most represented cluster

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Components

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


Mass: 3706.414 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: isolated from a genetically manipulated source
Formula: C58H74N22O10

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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
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-13C HSQC
151isotropic131P -1H COSY
162isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3'), 100% D2OD2O100% D2O
solution21.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3'), 90% H2O/10% D2OH2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMDNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')natural abundance1
1.3 mMDNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3')natural abundance2
Sample conditionsIonic strength: 100 mM / Label: D2O / 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
MARDIGRASBorgias ABstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing1
molecular dynamics2
NMR representativeSelection criteria: most represented cluster
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 5000 / Conformers submitted total number: 10

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