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- PDB-2kyp: Monomeric Human CKIT-2 proto-oncogene promoter quadruplex DNA NMR... -

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Basic information

Entry
Database: PDB / ID: 2kyp
TitleMonomeric Human CKIT-2 proto-oncogene promoter quadruplex DNA NMR, 12 structures
Components5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*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 6, 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*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)6,6261
Polymers6,6261
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 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*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'


Mass: 6626.246 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
1111H-1H NOESY
1221H-1H TOCSY
1321H- 31P COSY
1421H-1H COSY
1511H-15N JRHMQC
1611H-15N HMBC
1722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-1.7 mM (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 0.2-0.5 mM [U-13C; U-15N]-Gua (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP *TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 90% H2O/10% D2O90% H2O/10% D2O
20.2-1.7 mM (5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-10.2-1.71
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-2[U-13C; U-15N]-Gua0.2-0.51
mM(5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3')-30.2-1.72
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-PLOR3.851Schwieters, Kuszewski, Tjandra and Clorerefinement
VNMR6.1Variancollection
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: 12

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