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- PDB-2kqh: A G-rich sequence within the c-kit oncogene promoter forms a para... -

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Basic information

Entry
Database: PDB / ID: 2kqh
TitleA G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics
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 / c-kit2 / oncogene / promoter / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsHsu, S.-T.D. / Varnai, P. / Bugaut, A. / Reszka, A.P. / Neidle, S. / Balasubramanian, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics
Authors: Hsu, S.-T.D. / Varnai, P. / Bugaut, A. / Reszka, A.P. / Neidle, S. / Balasubramanian, S.
#1: Journal: Biochemistry / Year: 2006
Title: A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene
Authors: Fernando, H. / Reszka, A.P. / Huppert, J. / Ladame, S. / Rankin, S. / Venkitaraman, A.R. / Neidle, S. / Balasubramanian, S.
History
DepositionNov 5, 2009Deposition site: BMRB / Processing site: PDBJ
SupersessionNov 24, 2009ID: 2KJ2
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 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 / struct_site
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_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7293
Polymers6,6511
Non-polymers782
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 least restraint violations
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.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
200 uMDNA (5'-D(*(DC5)P*DGP*DGP*DGP*DCP*DGP*DGP*DGP*DCP*DAP*DCP*DGP*DAP*DGP*DGP*DGP*DAP*DGP*DGP*DGP*(DT3))-3')-11
10 mMpotassium phosphate-21
Sample conditionsIonic strength: 10 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Explicit water refinement including potassium ions within the G-tetrads.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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