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- PDB-2l7d: Ribonucleotide Perturbation of DNA Structure: Solution Structure ... -

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Basic information

Entry
Database: PDB / ID: 2l7d
TitleRibonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2
Components5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / RNA / Ribonucleotide substituted DNA
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E.
CitationJournal: Biochemistry / Year: 2012
Title: Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide.
Authors: DeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E.
History
DepositionDec 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 13, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,3592
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA/RNA hybrid 5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'


Mass: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: rG4 substituted Drew Dickerson dodecamer

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H COSY
1522D 1H-1H NOESY
1612D 1H-31P COSY
1712D 1H-31P J-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM rG4 substituted Drew Dickerson dodecamer, 50.0 mM sodium chloride, 50.0 mM sodium phosphate, 0.5 mM EDTA, 100% D2O100% D2O
22.0 mM rG4 substituted Drew Dickerson dodecamer, 50.0 mM sodium chloride, 50.0 mM sodium phosphate, 0.5 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.0 mMrG4 substituted Drew Dickerson dodecamer-11
50.0 mMsodium chloride-21
50.0 mMsodium phosphate-31
0.5 mMEDTA-41
2.0 mMrG4 substituted Drew Dickerson dodecamer-52
50.0 mMsodium chloride-62
50.0 mMsodium phosphate-72
0.5 mMEDTA-82
2.0 mMrG4 substituted Drew Dickerson dodecamer-93
50.0 mMsodium chloride-103
50.0 mMsodium phosphate-113
0.5 mMEDTA-123
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRJ2.1BVariancollection
NMRPipe2010.190.16.149Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8.0.b64Johnson, One Moon Scientificchemical shift assignment
NMRView8.0.b64Johnson, One Moon Scientificdata analysis
NMRView8.0.b64Johnson, One Moon Scientificpeak picking
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 212 / Hydrogen bond constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 5
NMR ensemble rmsDistance rms dev: 0.096 Å / Distance rms dev error: 0.02 Å

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