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- PDB-2kaz: Folding topology of a bimolecular DNA quadruplex containing a sta... -

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Basic information

Entry
Database: PDB / ID: 2kaz
TitleFolding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop
Components5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
KeywordsDNA / bimolecular DNA quadruplex / DNA hairpins / quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsBalkwill, G.D. / Garner, T.P. / Williams, H.E.L. / Searle, M.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop
Authors: Balkwill, G.D. / Garner, T.P. / Williams, H.E. / Searle, M.S.
History
DepositionNov 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
B: 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3044
Polymers8,2252
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 6000structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'


Mass: 4112.669 Da / Num. of mol.: 2 / 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 DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 2 mM DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'), 10 mM K+, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMDNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3')1
10 mMK1
10 %D2O1
Sample conditionsIonic strength: 10 / pH: 7.85 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
AMBER8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
AMBER8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TOPSPIN2.1Bruker Biospinprocessing
TOPSPIN2.1Bruker Biospincollection
Molmol2kKoradi, Billeter and Wuthrichdata analysis
CCPNMR1.16CCPNchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Molecular dynamics on selected model. Conformers selected from the last 200ps of rMD. 5 structures selected based on a cluster analysis to group structures by RMSD.
NMR constraintsNOE constraints total: 503 / NOE intraresidue total count: 248 / NOE long range total count: 47 / NOE medium range total count: 35 / NOE sequential total count: 173
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 6000 / Conformers submitted total number: 5

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