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- PDB-6jce: NMR solution and X-ray crystal structures of a DNA containing bot... -

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Basic information

Entry
Database: PDB / ID: 6jce
TitleNMR solution and X-ray crystal structures of a DNA containing both right-and left-handed parallel-stranded G-quadruplexes
Components29-mer DNA
KeywordsDNA / Left-handed / Z-G4 / G-quadruplex / hybrid
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsWinnerdy, F.R. / Bakalar, B. / Maity, A. / Vandana, J.J. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore)NRF-NRFI2017-09 Singapore
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes.
Authors: Winnerdy, F.R. / Bakalar, B. / Maity, A. / Vandana, J.J. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 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: 29-mer DNA


Theoretical massNumber of molelcules
Total (without water)9,2021
Polymers9,2021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4790 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 29-mer DNA


Mass: 9201.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TBA-TT-Block2 / 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
111isotropic22D 1H-1H NOESY
221isotropic22D 1H-1H NOESY
231isotropic12D 1H-13C HSQC aliphatic
241isotropic12D 1H-13C HSQC aromatic
251isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM TBA-TT-Block2, 70 mM potassium chloride, 20 mM potassium phosphate, 20 uM DSS, 90% H2O/10% D2O
Label: TBA-2T-Block2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMTBA-TT-Block2natural abundance1
70 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
20 uMDSSnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
190 mMH2O71 atm298 K
290 mMD2O71 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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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
RefinementMethod: simulated annealing / Software ordinal: 5
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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