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- PDB-6zx6: Antiparallel basket-type G-quadruplex DNA structure formed in hum... -

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Basic information

Entry
Database: PDB / ID: 6zx6
TitleAntiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG
Componentsbcl2ex-oxoG19
KeywordsDNA / bcl2 / G-quadruplex / oxidative stress / 8-oxo-Guanine / promoter
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBielskute, S. / Plavec, J. / Podbevsek, P.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-1704 Slovenia
Slovenian Research AgencyP1-0242 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter.
Authors: Bielskute, S. / Plavec, J. / Podbevsek, P.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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: bcl2ex-oxoG19


Theoretical massNumber of molelcules
Total (without water)7,9771
Polymers7,9771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area510 Å2
ΔGint4 kcal/mol
Surface area4340 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain bcl2ex-oxoG19


Mass: 7977.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestN

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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 TOCSY
132isotropic22D 1H-13C HSQC aromatic
142isotropic22D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM NA bcl2ex-oxoG19, 90% H2O/10% D2Obcl2ex-oxoG1990% H2O/10% D2O
solution21.2 mM NA bcl2ex-oxoG19, 100% D2Obcl2ex-oxoG19_100%D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMbcl2ex-oxoG19NA1
1.2 mMbcl2ex-oxoG19NA2
Sample conditionsIonic strength: 90 mM / Label: Conditions_1 / pH: 7 / Pressure: 101 325 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian DD2VarianDD28001
Varian DD2VarianDD26002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 12

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