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- PDB-7euc: Parallel G-quadruplex structure -

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Basic information

Entry
Database: PDB / ID: 7euc
TitleParallel G-quadruplex structure
Components
  • DNA (5'-D(*TP*TP*GP*GP*GP*G)-3')
  • DNA (5'-D(P*GP*GP*GP*G)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / Four-layer / Parallel / L-serinol / Stable
Function / homologyO-PHOSPHOETHANOLAMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / molecular dynamics
AuthorsWinnerdy, F.R. / Devi, G. / Ang, J.C.Y. / Lim, K.W. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Acs Nano / Year: 2022
Title: Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold.
Authors: Devi, G. / Winnerdy, F.R. / Ang, J.C.Y. / Lim, K.W. / Phan, A.T.
History
DepositionMay 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*GP*GP*GP*G)-3')
B: DNA (5'-D(P*GP*GP*GP*G)-3')
C: DNA (5'-D(P*GP*GP*GP*G)-3')
D: DNA (5'-D(P*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,02710
Polymers6,0004
Non-polymers1,0276
Water00
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 DNA (5'-D(*TP*TP*GP*GP*GP*G)-3')


Mass: 1880.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*GP*GP*G)-3')


Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*GP*GP*T)-3')


Mass: 1576.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PSE / O-PHOSPHOETHANOLAMINE


Mass: 171.089 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H10NO5P
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
111isotropic1H2O NOESY
122isotropic1D2O NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM DNA (25-MER), 70 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2OH2O_sample90% H2O/10% D2O
solution21 mM DNA (25-MER), 70 mM potassium chloride, 20 mM potassium phosphate, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA (25-MER)natural abundance1
70 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
1 mMDNA (25-MER)natural abundance2
70 mMpotassium chloridenatural abundance2
20 mMpotassium phosphatenatural 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
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYLee, W., Tonelli, M., Markley, J.L.peak picking
NMRFAM-SPARKYLee, W., Tonelli, M., Markley, J.L.chemical shift assignment
NMRFAM-SPARKYLee, W., Tonelli, M., Markley, J.L.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing6
molecular dynamics7
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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