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Yorodumi- PDB-2kqh: A G-rich sequence within the c-kit oncogene promoter forms a para... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kqh | |||||||||||||||||||||||
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Title | A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics | |||||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / c-kit2 / oncogene / promoter / G-quadruplex | Function / homology | : / DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, molecular dynamics | Model details | lowest energy, model 1 | Authors | Hsu, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kqh.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kqh.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 2kqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kqh_validation.pdf.gz | 307.5 KB | Display | wwPDB validaton report |
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Full document | 2kqh_full_validation.pdf.gz | 367.4 KB | Display | |
Data in XML | 2kqh_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 2kqh_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/2kqh ftp://data.pdbj.org/pub/pdb/validation_reports/kq/2kqh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6651.258 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: 10 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: Explicit water refinement including potassium ions within the G-tetrads. | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1 |