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- PDB-7b4z: Synthetic DNA duplex dodecamer -

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Basic information

Entry
Database: PDB / ID: 7b4z
TitleSynthetic DNA duplex dodecamer
Components
  • DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')
  • DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')
KeywordsDNA / duplex
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsLomzov, A.A. / Shernuykov, A.V. / Sviridov, E.A. / Shevelev, G.Y. / Bagryanskaya, E.G. / Pyshnyi, D.V.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation18-14-00357 Russian Federation
Ministry of Education and Science of the Russian FederationA-0309-2016-0004 Russian Federation
CitationJournal: J Phys Chem B / Year: 2016
Title: Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels.
Authors: Lomzov, A.A. / Sviridov, E.A. / Shernuykov, A.V. / Shevelev, G.Y. / Pyshnyi, D.V. / Bagryanskaya, E.G.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area3940 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')


Mass: 3086.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
231isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA, 100% D2OD2O100% D2O
solution21.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA, 90% H2O/10% D2OH2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMDNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')NA-H1
1.1 mMDNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')NA-H1
10 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
200 mMEDTAnatural abundance1
1.1 mMDNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3')NA-H2
1.1 mMDNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3')NA-H2
10 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
200 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthIonic strength errLabelpHPressure (kPa)Temperature (K)
1510 M1515.3C7.2 1 atm288.4 K
2510 M1533.3C7.2 1 atm306.5 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
CcpNmr Analysis2.3.1Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Lauechemical shift assignment
CcpNmr Analysis2.3.1Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Lauepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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