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- PDB-1k5e: Solution Structure of R-styrene Adduct in the Ras61 Sequence -

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Basic information

Entry
Database: PDB / ID: 1k5e
TitleSolution Structure of R-styrene Adduct in the Ras61 Sequence
Components
  • 5'-D(*CP*GP*GP*AP*CP*(ABR)P*AP*GP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'
KeywordsDNA / styrene / DNA adduct / solution structure of DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation
Model type detailsminimized average
AuthorsHennard, C. / Finneman, J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2001
Title: The nonmutagenic (R)- and (S)-beta-(N(6)-adenyl)styrene oxide adducts are oriented in the major groove and show little perturbation to DNA structure.
Authors: Hennard, C. / Finneman, J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 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_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
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(*CP*GP*GP*AP*CP*(ABR)P*AP*GP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,8282
Polymers6,8282
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 / 50back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3536.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was generated by an oligonucleotide synthesizer
#2: DNA chain 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was generated by an oligonucleotide synthesizer

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
NMR detailsText: NOESY at 100, 150 and 200 ms mixing time

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Sample preparation

DetailsContents: 130 OD260 of double stranded oligodeoxynucleotide are dissolved in 0.5 ml nmr buffer containing 99.996% D2O.
Solvent system: The buffer is 10mM sodium phosphate pH 6.9 containing 100mM NaCl and 0.05mM Na2EDTA.
Sample conditionsIonic strength: 10mM phosphate buffer / pH: 6.9 / Pressure: 1 atm / 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular simulationscollection
MARDIGRAS3James, TLrefinement
X-PLOR3.85Brungeriterative matrix relaxation
CORMA4Jamesdata analysis
RefinementMethod: simulated annealing, molecular dynamics, matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 50 / Conformers submitted total number: 1

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