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- PDB-2kyo: Dimeric human ckit-2 proto-oncogene promoter quadruplex DNA NMR, ... -

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Basic information

Entry
Database: PDB / ID: 2kyo
TitleDimeric human ckit-2 proto-oncogene promoter quadruplex DNA NMR, 10 structures
Components5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'
KeywordsDNA / G-tetrad / all-parallel quadruplex / intergenic recombination
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKuryavyi, V. / Phan, A.T. / Patel, D.J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Solution structures of all parallel-stranded monomeric and dimeric G-quadruplex scaffolds of the human c-kit2 promoter.
Authors: Kuryavyi, V. / Phan, A.T. / Patel, D.J.
History
DepositionJun 5, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'
B: 5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)13,3032
Polymers13,3032
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 5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'


Mass: 6651.258 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-1H TOCSY
1311H- 31P COSY
1411H-1H COSY
1521H-15N JRHMQC
1621H-15N HMBC
1712D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-5.0 mM (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 0.2-0.3 mM [U-13C; U-15N]-Gua (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100% D2O100% D2O
20.2-5.0 mM (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 0.2-0.3 mM [U-100% 13C; U-100% 15N] (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-10.2-5.01
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-2[U-13C; U-15N]-Gua0.2-0.31
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-30.2-5.02
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *GP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-4[U-100% 13C; U-100% 15N]0.2-0.32
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, Schwieters, Kuszewski, Tjandra and Clorerefinement
VNMR6.1CVariancollection
Felix2007Accelrys Software Inc.chemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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