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- PDB-7zem: Structure of a parallel G-quadruplex with a snapback loop -

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Basic information

Entry
Database: PDB / ID: 7zem
TitleStructure of a parallel G-quadruplex with a snapback loop
ComponentsDNA (5'-D(*(DT5)P*GP*GP*CP*TP*AP*GP*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3')
KeywordsDNA / G-quadruplex / parallel / snapback loop
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsJana, J. / Vianney, Y.M. / Schroeder, N. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)410497337 Germany
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Guiding the folding of G-quadruplexes through loop residue interactions.
Authors: Jana, J. / Vianney, Y.M. / Schroder, N. / Weisz, K.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 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: DNA (5'-D(*(DT5)P*GP*GP*CP*TP*AP*GP*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3')


Theoretical massNumber of molelcules
Total (without water)7,1541
Polymers7,1541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*(DT5)P*GP*GP*CP*TP*AP*GP*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3')


Mass: 7153.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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-13C HSQC aromatic
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution / Contents: 0.3 mM DNA, 90% H2O/10% D2O / Details: 30 C; 10 mM potassium phosphate buffer, pH 7.0. / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: DNA / Isotopic labeling: natural abundance
Sample conditionsDetails: 30 C; 10 mM potassium phosphate buffer, pH 7.0. / Ionic strength: 10 mM / Label: 1 / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIH3.0.3Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpin4.0.7Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNpeak picking
CcpNmr Analysis2.4.2CCPNdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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