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- PDB-2mnx: Major groove orientation of the (2S)-N6-(2-hydroxy-3-buten-1-yl)-... -

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Basic information

Entry
Database: PDB / ID: 2mnx
TitleMajor groove orientation of the (2S)-N6-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene
Components
  • 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'
KeywordsDNA / B-form / 11-mer
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsKowal, E.A. / Kotapati, S. / Turo, M. / Tretyakova, N. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2014
Title: Major Groove Orientation of the (2S)-N(6)-(2-Hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA Adduct Induced by 1,2-Epoxy-3-butene.
Authors: Kowal, E.A. / Wickramaratne, S. / Kotapati, S. / Turo, M. / Tretyakova, N. / Stone, M.P.
History
DepositionApr 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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(*CP*GP*GP*AP*CP*(6HB)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)6,7772
Polymers6,7772
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)9 / 9back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'


Mass: 3486.353 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
2322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.51 mM 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate pH 7.0, 100% D2O100% D2O
20.51 mM 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate pH 7.0, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.51 mM5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'-11
0.51 mM5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'-21
100 mMsodium chloride-31
50 uMEDTA-41
10 mMsodium phosphate pH 7.0-51
0.51 mM5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3'-62
0.51 mM5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'-72
100 mMsodium chloride-82
50 uMEDTA-92
10 mMsodium phosphate pH 7.0-102
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.17ambient 288 K
20.17ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
CORMAJames, T. L.data analysis
MARDIGRASBrandan A. Borgias, T. L. Jamesconversion of intensities to distance restraints
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 18 / NA beta-angle constraints total count: 18 / NA delta-angle constraints total count: 18 / NA epsilon-angle constraints total count: 18 / NA gamma-angle constraints total count: 18 / NOE constraints total: 283 / NOE intraresidue total count: 125 / NOE sequential total count: 158
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 9 / Conformers submitted total number: 9

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