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- PDB-2luj: Solution structure of a parallel-stranded oligoisoguanine DNA pen... -

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Basic information

Entry
Database: PDB / ID: 2luj
TitleSolution structure of a parallel-stranded oligoisoguanine DNA pentaplex formed by d(T(iG)4T) in the presence of Cs ions
ComponentsDNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')
KeywordsDNA / pentaplex / isoguanine / parallel-stranded
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKang, M. / Heuberger, B. / Chaput, J.C. / Switzer, C. / Feigon, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Solution Structure of a Parallel-Stranded Oligoisoguanine DNA Pentaplex Formed by d(T(iG)4T) in the Presence of Cs(+) Ions.
Authors: Kang, M. / Heuberger, B. / Chaput, J.C. / Switzer, C. / Feigon, J.
History
DepositionJun 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Nov 23, 2016Group: Non-polymer description
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')
B: DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')
C: DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')
D: DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')
E: DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')


Theoretical massNumber of molelcules
Total (without water)9,4015
Polymers9,4015
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)16 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain
DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')


Mass: 1880.251 Da / Num. of mol.: 5 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D 1H-1H TOCSY
1422D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3'), 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM DNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3'), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMDNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')-11
0.7 mMDNA (5'-D(*TP*(IGU)P*(IGU)P*(IGU)P*(IGU)P*T)-3')-22
Sample conditionsIonic strength: 50 / pH: 6.3 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
XwinNMRBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 30 / NA beta-angle constraints total count: 20 / NA chi-angle constraints total count: 20 / NA delta-angle constraints total count: 30 / NA epsilon-angle constraints total count: 30 / NA gamma-angle constraints total count: 20 / NA other-angle constraints total count: 260 / NA sugar pucker constraints total count: 20 / NOE constraints total: 1110 / NOE intraresidue total count: 670 / NOE long range total count: 170 / NOE sequential total count: 270
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 16

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