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- PDB-1osr: Structural study of dna duplex containaing a n-(2-deoxy-beta-eryt... -

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Basic information

Entry
Database: PDB / ID: 1osr
TitleStructural study of dna duplex containaing a n-(2-deoxy-beta-erytho-pentofuranosyl) formamide frameshift by nmr and restrained molecular dynamics
Components
  • 5'-D(*AP*GP*GP*AP*CP*CP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3'
KeywordsDNA / MODIFIED BASE / MUTAGENESIS / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR MODELING; SIMULATED ANNEALING; RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
AuthorsMaufrais, C. / Fazakerley, G.V. / Cadet, J. / Boulard, Y.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics.
Authors: Maufrais, C. / Fazakerley, G.V. / Cadet, J. / Boulard, Y.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*GP*GP*AP*CP*CP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)5,6962
Polymers5,6962
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)2 / -
RepresentativeModel #2those which were used to initiate molecular dynamic simulations

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Components

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


Mass: 2749.826 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3'


Mass: 2945.905 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
111NOESY
121COSY
131DQFCOSY
141TOCSY
151HSQC 1H-31P
NMR detailsText: THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. TWO REPRESENTATIVE STRUCTURES OF THE TWO ISOMER CIS AND TRANS FOR THE FORMAMIDE RESIDUE ARE PRESENTED.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA99.9% D2O
22 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA 6.5 AMBIENT 290 K
210 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA 5.5 AMBIENT 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
AmberKOLLMANrefinement
MORCADLEBRETrefinement
MOLMOL2.6Koradi, Wuthrichrefinement
XwinNMR2.5BRUKERprocessing
RefinementMethod: MOLECULAR MODELING; SIMULATED ANNEALING; RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
Software ordinal: 1
NMR representativeSelection criteria: those which were used to initiate molecular dynamic simulations
NMR ensembleConformers submitted total number: 2

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