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- PDB-1k29: Solution Structure of a DNA Duplex Containing M1G Opposite a 2 Ba... -

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Basic information

Entry
Database: PDB / ID: 1k29
TitleSolution Structure of a DNA Duplex Containing M1G Opposite a 2 Base Pair Deletion
Components
  • 5'-D(*AP*TP*CP*GP*CP*(M1G)P*CP*GP*GP*CP*AP*TP*G)-3'
  • 5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3'
KeywordsDNA / two base deletion / DNA adduct / malondialdehyde
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / matrix relaxation, simulated annealing, distance restraints, dihedral angle restraints
Model type detailsminimized average
AuthorsSchnetz-Boutaud, N.C. / Saleh, S. / Marnett, L.J. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2001
Title: The exocyclic 1,N2-deoxyguanosine pyrimidopurinone M1G is a chemically stable DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene.
Authors: Schnetz-Boutaud, N.C. / Saleh, S. / Marnett, L.J. / Stone, M.P.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 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(*AP*TP*CP*GP*CP*(M1G)P*CP*GP*GP*CP*AP*TP*G)-3'
B: 5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3632
Polymers7,3632
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)1 / 20the submitted structure is an average of 10 different structures that were back calculated and the data agreed with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*AP*TP*CP*GP*CP*(M1G)P*CP*GP*GP*CP*AP*TP*G)-3'


Mass: 4028.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE occurs naturally in THE SALMONELLA TYPHIMURIUM HIS3052 GENE
#2: DNA chain 5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3'


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE occurs naturally in THE SALMONELLA TYPHIMURIUM HIS3052 GENE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121E-COSY
231P-COSY
342NOESY
NMR detailsText: This structure was determined using standard 2D homo- and hetero- nuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM DNA, 10mM phosphate buffer, 0.1M NaCl, 50 uM EDTA , pH 799.96% D2o
22mM DNA, 10mM phosphate buffer, 0.1M NaCl, 50 uM EDTA , pH 790% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1M NaCl 7 ambient 293 K
20.1M NaCl 7 ambient 303 K
30.1M NaCl 7 ambient 278 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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Instrumentcollection
Felix2000accelrysdata analysis
MARDIGRAS3T. L. Jamesiterative matrix relaxation
X-PLOR3.85Brungerstructure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: matrix relaxation, simulated annealing, distance restraints, dihedral angle restraints
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: the submitted structure is an average of 10 different structures that were back calculated and the data agreed with experimental NOESY spectrum
Conformers calculated total number: 20 / Conformers submitted total number: 1

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