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- PDB-1xav: Major G-quadruplex structure formed in human c-MYC promoter, a mo... -

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Basic information

Entry
Database: PDB / ID: 1xav
TitleMajor G-quadruplex structure formed in human c-MYC promoter, a monomeric parallel-stranded quadruplex
Components5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'
KeywordsDNA / c-MYC promoter DNA / parallel stranded guanine-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsAmbrus, A. / Chen, D. / Dai, J. / Jones, R.A. / Yang, D.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure of the biologically relevant G-Quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization.
Authors: Ambrus, A. / Chen, D. / Dai, J. / Jones, R.A. / Yang, D.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Other / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0873
Polymers7,0091
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'


Mass: 7008.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by solid phase DNA synthesizer
#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 NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY
NMR detailsText: Constraints for structure calculations were collected from standard homonuclear NMR experiments. Site-specific imino-assignments were obtained from 1D HMQC with presaturation. 2D NOESY in water ...Text: Constraints for structure calculations were collected from standard homonuclear NMR experiments. Site-specific imino-assignments were obtained from 1D HMQC with presaturation. 2D NOESY in water used jump-and-return solvent suppression. The average RMSD is 0.880531.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-3mM DNA oligonucleotides, 25mM potassium-phosphate,70mM potassium-chloride,pH7.0 buffer, 10% D2O/90% H2O10% D2O/90% H2O
20.2-3mM DNA oligonucleotides, 25mM potassium-phosphate,70mM potassium-chloride,pH7.0 buffer, 99.96% D2O99.96% D2O
Sample conditionsIonic strength: 25mM potassium-phosphate,70mM potassium-chloride
pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3.5collection
Sparky3.1Goddard,T.D., Kneller,D.G.data analysis
Insight II2000Lrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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