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- PDB-7nwd: Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate -

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Basic information

Entry
Database: PDB / ID: 7nwd
TitleThree-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate
Componentsc-kit2_py1
KeywordsDNA / c-kit2 / G-quadruplex / pyrene
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPeterkova, K. / Durnik, I. / Marek, R. / Plavec, J. / Podbevsek, P.
Funding supportEuropean Union, Slovenia, Czech Republic, 6items
OrganizationGrant numberCountry
European Commission765266European Union
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-1704 Slovenia
Ministry of Education, Youth and Sports of the Czech RepublicLQ1601 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018140 Czech Republic
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry.
Authors: Peterkova, K. / Durnik, I. / Marek, R. / Plavec, J. / Podbevsek, P.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: c-kit2_py1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8503
Polymers6,7721
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area4300 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain c-kit2_py1


Mass: 6771.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
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
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.0 mM c-kit2_py1, 5 mM potassium phosphate, 20 mM potassium chloride, 90% H2O/10% D2O
Label: c-kit2_py1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMc-kit2_py1natural abundance1
5 mMpotassium phosphatenatural abundance1
20 mMpotassium chloridenatural abundance1
Sample conditionsIonic strength: 25 mM / Label: H2O/D2O / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.7Bruker Biospincollection
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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