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- PDB-2l8q: Solution Structure of a control DNA Duplex -

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Basic information

Entry
Database: PDB / ID: 2l8q
TitleSolution Structure of a control DNA Duplex
Components
  • DNA (5'-D(*CP*GP*CP*AP*TP*GP*CP*TP*AP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*TP*AP*GP*CP*AP*TP*GP*CP*G)-3')
KeywordsDNA / poxvirus / HPMPC
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsJulien, O. / Beadle, J.R. / Magee, W.C. / Chatterjee, S. / Hostetler, K.Y. / Evans, D.H. / Sykes, B.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir.
Authors: Julien, O. / Beadle, J.R. / Magee, W.C. / Chatterjee, S. / Hostetler, K.Y. / Evans, D.H. / Sykes, B.D.
History
DepositionJan 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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)10 / 50lowest RMSD to average structure
RepresentativeModel #1closest to the average

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Components

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


Mass: 3623.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*GP*CP*AP*TP*GP*CP*G)-3')


Mass: 3703.416 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-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1412D DQF-COSY
1512D 1H-13C HSQC

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Sample preparation

DetailsContents: 2 mM control DNA duplex, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 2 mM / Component: Cidofovir DNA duplex-1
Sample conditionsIonic strength: 70 / pH: 7.0-7.2 / 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
NMRPipe4.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8.0.b30Johnson, One Moon Scientificchemical shift assignment
MARDIGRAST.L. Jamesnoe calibration
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
CORMAT.L. Jamesstructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using ...Details: The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using the pairwise generalized Born model was as follows: the temperature of the system was kept constant at 600 K during the first 5 ps, cooled down slowly to 100 K between 5-18 ps, and cooled down to 0 K for the last 7 ps. The protocol was repeated 50 times to obtain an NMR ensemble with the 10 lowest RMSD structures. The structure with the lowest RMSD of the ensemble was put back into MARDIGRAS for a second and third cycle of NOE calibration and structure calculations.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest RMSD to average structure
Conformers calculated total number: 50 / Conformers submitted total number: 10

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