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- PDB-2mgn: Solution structure of a G-quadruplex bound to the bisquinolinium ... -

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Basic information

Entry
Database: PDB / ID: 2mgn
TitleSolution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3
Components5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'
KeywordsDNA / ligand / c-MYC promoter
Function / homologyChem-PQ3 / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsChung, W.J. / Heddi, B. / Hamon, F. / Teulade-Fichou, M.P. / Phan, A.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3.
Authors: Chung, W.J. / Heddi, B. / Hamon, F. / Teulade-Fichou, M.P. / Phan, A.T.
History
DepositionNov 1, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Non-polymer description
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 15, 2024Group: Data collection / Database references / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.formula / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2432
Polymers7,6921
Non-polymers5511
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'


Mass: 7691.935 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PQ3 / N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide / Phen-DC3


Mass: 550.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H26N6O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-1H NOESY
2232D 1H-1H NOESY
2332D 1H-1H TOCSY
1422D 1H-13C HSQC
1522D 13C-filtered HSQC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-2.0 mM DNA, 0.2-2.0 mM PQ3, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3, 100% D2O100% D2O
30.2-2.0 mM DNA, 0.2-2.0 mM PQ3, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA-10.2-21
mMPQ3-20.2-21
1 mMDNA-32
1 mMPQ3-4[U-100% 13C]-CH32
mMDNA-50.2-23
mMPQ3-60.2-23
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
1907298 K
2457298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX7002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1
Details: Extracted distances from structure of free DNA (PDB entry 2A5P) were used during calculation
NMR constraintsNA chi-angle constraints total count: 24 / NOE constraints total: 111
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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