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- PDB-6k3x: G-quadruplex complex with linear dinucleotide d(AG) -

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Basic information

Entry
Database: PDB / ID: 6k3x
TitleG-quadruplex complex with linear dinucleotide d(AG)
Components
  • DNA (5'-D(*AP*G)-3')
  • DNA (5'-D(*TP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / complex / dinucleotide / vacancy
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsWinnerdy, F.R. / Heddi, B. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Solution Structures of a G-Quadruplex Bound to Linear- and Cyclic-Dinucleotides.
Authors: Winnerdy, F.R. / Das, P. / Heddi, B. / Phan, A.T.
History
DepositionMay 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 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(*TP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,9992
Polymers5,9992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area600 Å2
ΔGint1 kcal/mol
Surface area3500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') / delta1


Mass: 5401.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*G)-3')


Mass: 597.455 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
112isotropic12D 1H-1H TOCSY
122isotropic12D 1H-1H NOESY
161isotropic12D 1H-1H NOESY
132isotropic12D 1H-13C HSQC aliphatic
142isotropic12D 1H-13C HSQC aromatic
151isotropic12D JRHMBC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM delta1, 1.2 mM d(AG), 10 mM potassium phosphate, 10 mM potassium chloride, 90% H2O/10% D2Odelta1-d(AG) complex in H2O solvent, Potassium Phosphate buffer.delta1-d(AG)-H2O90% H2O/10% D2O
solution21 mM delta1, 1.2 mM d(AG), 10 mM potassium phosphate, 10 mM potassium chloride, 100% D2OLyophilized sample diluted in D2O solvent, Potassium Phosphate buffer.delta1-d(AG)-D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMdelta1natural abundance1
1.2 mMd(AG)natural abundance1
10 mMpotassium phosphatenatural abundance1
10 mMpotassium chloridenatural abundance1
1 mMdelta1natural abundance2
1.2 mMd(AG)natural abundance2
10 mMpotassium phosphatenatural abundance2
10 mMpotassium chloridenatural abundance2
Sample conditionsDetails: 10 mM KPi, 10 mM KCl, pH 7 / Ionic strength: 20 mM / Label: condition_1 / pH: 7 / 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
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing4
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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