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- PDB-7d5f: Left-handed G-quadruplex containing 3 bulges -

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Basic information

Entry
Database: PDB / ID: 7d5f
TitleLeft-handed G-quadruplex containing 3 bulges
Components3xBulge-LHG4motif
KeywordsDNA / Left-handed / G-quadruplex / Bulge / ZG4
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsWinnerdy, F.R. / Das, P. / Ngo, K.H. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Bulges in left-handed G-quadruplexes.
Authors: Das, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
History
DepositionSep 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3xBulge-LHG4motif


Theoretical massNumber of molelcules
Total (without water)8,5681
Polymers8,5681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 3xBulge-LHG4motif


Mass: 8568.456 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
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM 3Bulge, 70 mM potassium chloride, 20 mM potassium phosphate, 20 uM DSS, 90% H2O/10% D2O3Bulge_H2O90% H2O/10% D2O
solution21 mM 3Bulge, 70 mM potassium chloride, 20 mM potassium phosphate, 20 uM DSS, 100% D2O3Bulge_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM3Bulgenatural abundance1
70 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
20 uMDSSnatural abundance1
1 mM3Bulgenatural abundance2
70 mMpotassium chloridenatural abundance2
20 mMpotassium phosphatenatural abundance2
20 uMDSSnatural abundance2
Sample conditionsIonic strength: 100 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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing5
molecular dynamics6
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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