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- PDB-6kfj: NMR solution structure of the 1:1 complex of wtTel26 G-quadruplex... -

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Basic information

Entry
Database: PDB / ID: 6kfj
TitleNMR solution structure of the 1:1 complex of wtTel26 G-quadruplex and a tripodal cationic fluorescent probe NBTE
ComponentsG-quadruplex DNA wtTel26
KeywordsDNA / G-quadruplex DNA / probe / DNA-ligand complex
Function / homologyChem-D6F / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsLiu, W. / Liu, L.Y. / Mao, Z.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)21837006 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Quantitative Detection of G-Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination.
Authors: Liu, L.Y. / Liu, W. / Wang, K.N. / Zhu, B.C. / Xia, X.Y. / Ji, L.N. / Mao, Z.W.
History
DepositionJul 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: G-quadruplex DNA wtTel26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7642
Polymers8,2001
Non-polymers5641
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain G-quadruplex DNA wtTel26


Mass: 8200.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-D6F / 4,4',4''-(nitrilotris(benzene-4,1-diyl))tris(1-ethylpyridin-1-ium) iodide / 4-(1-ethylpyridin-1-ium-4-yl)-N,N-bis[4-(1-ethylpyridin-1-ium-4-yl)phenyl]aniline


Mass: 563.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H39N4
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D NOESY
121anisotropic12D TOCSY
131anisotropic12D COSY
241anisotropic22D NOESY
251anisotropic22D TOCSY
261anisotropic22D COSY

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Sample preparation

DetailsType: solution
Contents: 1 mM G-quadruplex DNA wtTel26, 1 mM NBTE, 100 mM patassium, 90% H2O/10% D2O
Label: 1-1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMG-quadruplex DNA wtTel26natural abundance1
1 mMNBTEnatural abundance1
100 mMpatassiumnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM25C71 atm298 K
2100 mM5C71 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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