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- PDB-6jcd: G-quadruplex peripheral knot -

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Basic information

Entry
Database: PDB / ID: 6jcd
TitleG-quadruplex peripheral knot
Components24-mer DNA
KeywordsDNA / G-quadruplex / diagonal loop / knot / triad
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsWinnerdy, F.R. / Truong, T.H.A. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore)NRF-NRFI2017-09 Singapore
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: An Unprecedented Knot-like G-Quadruplex Peripheral Motif.
Authors: Truong, T.H.A. / Winnerdy, F.R. / Phan, A.T.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 24-mer DNA


Theoretical massNumber of molelcules
Total (without water)7,5561
Polymers7,5561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4270 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 24-mer DNA


Mass: 7555.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AT21S / 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
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
231isotropic12D 1H-1H TOCSY
241isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM AT21S, 70 mM potassium chloride, 20 mM potassium phosphate, 20 uM DSS, 90% H2O/10% D2O
Label: AT21S / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAT21Snatural abundance1
70 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
20 uMDSSnatural abundance1
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
170 mM KCl, 20 mM KPO4, 10%D2O and 20 uM DSS90 mMH2O7 1 atm298 K
270 mM KCl, 20 mM KPO4, 100%D2O and 20 uM DSS90 mMD2O7 1 atm298 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
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing5
molecular dynamics4
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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