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- PDB-2mwz: Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X... -

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Basic information

Entry
Database: PDB / ID: 2mwz
TitleXanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X O tetrad
ComponentsDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')
KeywordsDNA / xanthosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsCheong, V.V. / Heddi, B. / Lech, C.J. / Phan, A.T.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Xanthine and 8-oxoguanine in G-quadruplexes: formation of a GGXO tetrad.
Authors: Cheong, V.V. / Heddi, B. / Lech, C.J. / Phan, A.T.
History
DepositionDec 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jul 6, 2016Group: Structure summary
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 / pdbx_nmr_spectrometer / struct_conn
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 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: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,6091
Polymers7,6091
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)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*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')


Mass: 7608.868 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: An intramolecular human telomeric G-quadruplex with xanthine and 8-oxoguanine modifications within a G-tetrad
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC aromatic
1512D 1H-13C HSQC aliphatic
1612D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMDNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(XG)P*TP*TP*AP*GP*GP*GP*A)-3')-11
20 mMpotassium phosphate-21
70 mMpotassium chloride-31
Sample conditionsIonic strength: 90 / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNA chi-angle constraints total count: 12 / NOE constraints total: 591 / NOE intraresidue total count: 280 / NOE long range total count: 83 / NOE sequential total count: 164
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.131 Å / Maximum upper distance constraint violation: 0.191 Å
NMR ensemble rmsDistance rms dev: 0.023 Å / Distance rms dev error: 0.002 Å

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