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- PDB-2lxq: Monomeric PilE G-Quadruplex DNA from Neisseria Gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 2lxq
TitleMonomeric PilE G-Quadruplex DNA from Neisseria Gonorrhoeae
ComponentsDNA (5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*T)-3')
KeywordsDNA / G-TETRAD / ALL-PARALLEL QUADRUPLEX / 5'-END STACKED / PILIN Av
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics, matrix relaxation
Model detailslowest energy, model1
AuthorsKuryavyi, V.V. / Patel, D.J.
CitationJournal: Structure / Year: 2012
Title: RecA-Binding pilE G4 Sequence Essential for Pilin Antigenic Variation Forms Monomeric and 5' End-Stacked Dimeric Parallel G-Quadruplexes.
Authors: Kuryavyi, V. / Cahoon, L.A. / Seifert, H.S. / Patel, D.J.
History
DepositionAug 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,9991
Polymers6,9991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*T)-3')


Mass: 6999.496 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1421H-15N JRHMQC
1521H-15N HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-6.0 mM 5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3', 0.8 mM [U-13C; U-15N] 5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3', 100 mM potassium chloride, 5 mM potassium phosphate, 90 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM 5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3', 100 mM potassium chloride, 5 mM potassium phosphate, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3'-10.8-6.01
0.8 mM5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3'-2[U-13C; U-15N]1
100 mMpotassium chloride-31
5 mMpotassium phosphate-41
90 %D2O-51
0.8 mM5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP *T)-3'-62
100 mMpotassium chloride-72
5 mMpotassium phosphate-82
10 %D2O-92
90 %H2O-102
Sample conditionsIonic strength: 0.105 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: BRUNGER, SCHWIETERS, KUSZEWSKI, TJ / Classification: refinement
RefinementMethod: torsion angle dynamics, molecular dynamics, matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 12

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