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- PDB-2lxv: Dimeric pil-e g-quadruplex dna from neisseria gonorrhoeae, NMR 11... -

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Basic information

Entry
Database: PDB / ID: 2lxv
TitleDimeric pil-e g-quadruplex dna from neisseria gonorrhoeae, NMR 11 structures
Components5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP
KeywordsDNA / G-TETRAD / ALL-PARALLEL QUADRUPLEX / 5'-END STACKED DIMER / PILIN ANTIGE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics, matrix relaxation
Model detailslowest energy, model1
AuthorsKuryavyi, 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 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
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

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Assembly

Deposited unit
A: 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP
B: 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP


Theoretical massNumber of molelcules
Total (without water)10,2452
Polymers10,2452
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)11 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP


Mass: 5122.284 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-15N JRHMQC
1311H-15N HMBC
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1622D 1H-1H TOCSY
1722D DQF-COSY
1812D 1H-13C HSQC aromatic
1922D 1H-1H COSY
11021H-31P COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-3.5 mM 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP, 100 mM sodium chloride, 5 mM sodium phosphate, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
20.3-3.5 mM 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP, 100 % [U-100% 2H] D2O, 100 mM sodium chloride, 5 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP-10.3-3.51
100 mMsodium chloride-21
5 mMsodium phosphate-31
10 %D2O-41
90 %H2O-51
mM5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP-60.3-3.52
100 %D2O-7[U-100% 2H]2
100 mMsodium chloride-82
5 mMsodium phosphate-92
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, TJANDRA AND CLORE
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: 11

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