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- PDB-1r2l: A parallel stranded DNA duplex with an A-G mismatch base-pair -

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Basic information

Entry
Database: PDB / ID: 1r2l
TitleA parallel stranded DNA duplex with an A-G mismatch base-pair
Components
  • 5'-D(P*CP*CP*TP*AP*TP*GP*AP*AP*AP*TP*CP*C)-3'
  • DNA (5'-D(P*(DNR)P*(DNR)P*DAP*DTP*DAP*DAP*DTP*DTP*DTP*DAP*(DNR)P*(DNR))-3')
KeywordsDNA / ps-DNA / A:G mismatch / parallel DNA duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / From the structure 1JUU, the required T base was replaced by G using insightII.
Model type detailsminimized average
AuthorsVenkitakrishnan, R.P. / Bhaumik, S.R. / Chary, K.V.R. / govil, G. / Liu, K. / Howard, F.B. / Miles, T.H.
CitationJournal: RECENT TRENDS IN BIOPHYS.RES. / Year: 2004
Title: A parallel stranded DNA duplex with an A-G mismatch base-pair: (CCATAATTTACC:CCTATGAAATCC)
Authors: Venkitakrishnan, R.P. / Bhaumik, S.R. / Chary, K.V.R. / govil, G. / Liu, K. / Howard, F.B. / Miles, T.H.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*(DNR)P*(DNR)P*DAP*DTP*DAP*DAP*DTP*DTP*DTP*DAP*(DNR)P*(DNR))-3')
B: 5'-D(P*CP*CP*TP*AP*TP*GP*AP*AP*AP*TP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,1922
Polymers7,1922
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)1 / 1energy minimized using the NMR constraints
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA (5'-D(P*(DNR)P*(DNR)P*DAP*DTP*DAP*DAP*DTP*DTP*DTP*DAP*(DNR)P*(DNR))-3')


Mass: 3585.400 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the DNA duplex was synthesized with an applied biosystems model 380b DNA synthesizer using solid state phosphoramidate chemistry.
#2: DNA chain 5'-D(P*CP*CP*TP*AP*TP*GP*AP*AP*AP*TP*CP*C)-3'


Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ps-DNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D TOCSY
233jump return NOESY
144E-COSY
NMR detailsText: This structure was determined using 2D homonuclear techniques

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Sample preparation

DetailsContents: 5 mM concentration of each strand to form the duplex
Solvent system: 0.05 M deuterated sodium acetate buffer and 0.1 M NaCl pH 5.5 and 6.8
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl, 100% D2O 6.8 1 atm298 K
20.1 M NaCl, 10% D2O, 90% H2O 5.5 1 atm278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
Discover3.1MSIrefinement
InsightIIstructure solution
RefinementMethod: From the structure 1JUU, the required T base was replaced by G using insightII.
Software ordinal: 1
Details: THE RESULTING STRUCTURE WAS ENERGY MINIMIZED USING THE NMR CONSTRAINTS
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: energy minimized using the NMR constraints
Conformers calculated total number: 1 / Conformers submitted total number: 1

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