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- PDB-2kuz: 2-Aminopurine incorporation perturbs the dynamics and structure of DNA -

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Basic information

Entry
Database: PDB / ID: 2kuz
Title2-Aminopurine incorporation perturbs the dynamics and structure of DNA
Components
  • DNA (5'-D(*CP*GP*AP*CP*GP*TP*TP*TP*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*CP*AP*AP*AP*CP*GP*TP*CP*G)-3')
KeywordsDNA / 2-Aminopurine / fluorophore / structure perturbation
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsDallmann, A. / Dehmel, L. / Peters, T. / Muegge, C. / Griesinger, C.P. / Tuma, J. / Ernsting, N.P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: 2-aminopurine incorporation perturbs the dynamics and structure of DNA.
Authors: Dallmann, A. / Dehmel, L. / Peters, T. / Mugge, C. / Griesinger, C. / Tuma, J. / Ernsting, N.P.
History
DepositionMar 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,9442
Polymers7,9442
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)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*AP*CP*GP*TP*TP*TP*GP*CP*AP*GP*C)-3')


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HMQC
1232D 1H-13C HMQC
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1512D DQF-COSY
1622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride, 100% D2O100% D2O
23 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
33 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride, 20 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
3 mMDNAstrandI1
3 mMDNAstrandII1
10 mMsodium phosphate1
150 mMsodium chloride1
3 mMDNAstrandI2
3 mMDNAstrandII2
10 mMsodium phosphate2
150 mMsodium chloride2
3 mMDNAstrandI3
3 mMDNAstrandII3
10 mMsodium phosphate3
150 mMsodium chloride3
20 mg/mLPf1 phage3
Sample conditionspH: 7 / 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
CARA1.8.4Keller, R. et al.peak picking
CARA1.8.4Keller, R. et al.chemical shift assignment
X-PLOR NIH2.2Schwieters, C. et al.structure solution
X-PLOR NIH2.2Schwieters, C. et al.refinement
X-PLOR NIH2.2Schwieters, C. et al.geometry optimization
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
Gifa4Delsuc, M.A. et al.data analysis
3DNALu, X.J. et al.data analysis
PALESZweckstetter, M. et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Torsion angle dynamics, 50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end ...Details: Torsion angle dynamics, 50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end temperature) and a final minimization (3,000 steps).
NMR constraintsNOE constraints total: 340 / NOE intraresidue total count: 144 / NOE sequential total count: 196
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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