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- PDB-1k4x: POTASSIUM FORM OF OXY-1.5 QUADRUPLEX DNA -

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Basic information

Entry
Database: PDB / ID: 1k4x
TitlePOTASSIUM FORM OF OXY-1.5 QUADRUPLEX DNA
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / QUADRUPLEX / POTASSIUM ION
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsSchultze, P. / Hud, N.V. / Smith, F.W. / Feigon, J.
Citation
Journal: Nucleic Acids Res. / Year: 1999
Title: The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4)).
Authors: Schultze, P. / Hud, N.V. / Smith, F.W. / Feigon, J.
#1: Journal: Nature / Year: 1992
Title: Quadruplex Structure of Oxytricha Telomeric DNA Oligonucleotides
Authors: Smith, F.W. / Feigon, J.
History
DepositionJun 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
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)8 / 20LEAST OVERALL ENERGY
RepresentativeModel #1

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Components

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


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE FROM OXYTRICHA NOVA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121P.COSY

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
AURELIAstructure solution
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: DETAILS GIVEN IN PUBLICATION
NMR ensembleConformer selection criteria: LEAST OVERALL ENERGY / Conformers calculated total number: 20 / Conformers submitted total number: 8

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