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- PDB-1kxs: NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYA... -

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Basic information

Entry
Database: PDB / ID: 1kxs
TitleNMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)
Components
  • 5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*AP*GP*TP*CP*(HEU)P*AP*AP*AP*AP*CP*G)-3'
KeywordsDNA / MODIFIED BASE / MUTAGENESIS / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNA SIMULATIONS
AuthorsBoulard, Y. / Fazakerley, G.V. / Sowers, L.C.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies.
Authors: Boulard, Y. / Fazakerley, G.V. / Sowers, L.C.
History
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,5902
Polymers8,5902
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)2 / 256Fit with NMR constraints and energy
Representative

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Components

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


Mass: 4327.857 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)-3'


Mass: 4261.775 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 NOESY
121DQF-COSY
131TOCSY
141DQ
151HSQC 1H-31P
NMR detailsText: THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. THE BEST REPRESENTATIVE STRUCTURES ARE PRESENTED, MODELS 1 AND 2.

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Sample preparation

DetailsContents: 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.5 MM
Sample conditionsIonic strength: 10 mM PHOSPHATE BUFFER, 5 NACL, 0.2 mM EDTA
pH: 6.7 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5data analysis
AmberKOLLMANrefinement
MORCAD, OCLLEBRETrefinement
MOLMOL2.6KORADIrefinement
RefinementMethod: RESTRAINED MOLECULAR DYNA SIMULATIONS / Software ordinal: 1
NMR ensembleConformer selection criteria: Fit with NMR constraints and energy
Conformers calculated total number: 256 / Conformers submitted total number: 2

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