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- PDB-2kh4: Aflatoxin Formamidopyrimidine alpha anomer in single strand DNA -

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Basic information

Entry
Database: PDB / ID: 2kh4
TitleAflatoxin Formamidopyrimidine alpha anomer in single strand DNA
Components5'-D(*CP*TP*(FAG)P*A)-3'
KeywordsDNA / Aflatoxin / Formamidopyrimidine / alpha anomer
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsBrown, K.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structural perturbations induced by the alpha-anomer of the aflatoxin B(1) formamidopyrimidine adduct in duplex and single-strand DNA
Authors: Brown, K.L. / Voehler, M.W. / Magee, S.M. / Harris, C.M. / Harris, T.M. / Stone, M.P.
History
DepositionMar 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*TP*(FAG)P*A)-3'


Theoretical massNumber of molelcules
Total (without water)1,5371
Polymers1,5371
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)8 / 8back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*CP*TP*(FAG)P*A)-3'


Mass: 1537.118 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
1322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM (5'-D(*DCP*DTP*(FAG)P*DA)-3')-1, 100% D2O100% D2O
20.4 mM (5'-D(*DCP*DTP*(FAG)P*DA)-3')-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.4 mM5'-D(*DCP*DTP*(FAG)P*DA)-3'-11
0.4 mM5'-D(*DCP*DTP*(FAG)P*DA)-3'-22
Sample conditionsIonic strength: 0.1 / pH: 8.7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker Advance / Manufacturer: Bruker / Model: Advance / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospinprocessing
MARDIGRASBorgias, B.A. & James, T.L.restraint generation
CORMAJames T.L.structure validation
CurvesLavery, R. and Sklenar, Hdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 8 / Conformers submitted total number: 8

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