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- PDB-1dxa: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA -

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Basic information

Entry
Database: PDB / ID: 1dxa
TitleBENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA
Components
  • DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3')
KeywordsDNA / DOUBLE HELIX / BENZO[A]PYRENE DIOL EPOXIDE ADDUCT / DUPLEX DNA / NON-WATSON-CRICK BASE PAIR
Function / homology1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA
Function and homology information
MethodSOLUTION NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS
AuthorsYeh, H.J.C. / Sayer, J.M. / Liu, X. / Altieri, A.S. / Byrd, R.A. / Lakshman, M.K. / Yagi, H. / Schurter, E.J. / Gorenstein, D.G. / Jerina, D.M.
CitationJournal: Biochemistry / Year: 1995
Title: NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy- ...Title: NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA
Authors: Yeh, H.J. / Sayer, J.M. / Liu, X. / Altieri, A.S. / Byrd, R.A. / Lakshman, M.K. / Yagi, H. / Schurter, E.J. / Gorenstein, D.G. / Jerina, D.M.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8023
Polymers5,4982
Non-polymers3041
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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


Mass: 2780.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')


Mass: 2716.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Keywords: DEOXYRIBONUCLEIC ACID
#3: Chemical ChemComp-BAP / 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE


Mass: 304.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16O3 / Details: chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ...Text: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE.

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

NMR softwareName: NMRCHITECT / Developer: BIOSYM / Classification: refinement
RefinementMethod: ENERGY MINIMIZATION, MOLECULAR DYNAMICS / Software ordinal: 1
Details: TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD ...Details: TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD (+)-DE2-[BAP] FRAGMENT. SOLUTION STRUCTURES FOR THE DUPLEX WERE GENERATED BY RESTRAINTED MOLECULAR DYNAMICS AND RESTRAINTED ENERGY MINIMIZATION USING A SET OF INTER-PROTON DISTANCE RESTRAINTS AND DIHEDRAL ANGLE RESTRAINTS WHICH WERE DERIVED FROM NMR EXPERIMENTS. SOME OF STRUCTURES WITH MINIMUM RESTRAINT VIOLATIONS WERE FURTHER REFINED BY THE ITERATIVE RELAXATION MATRIX ANALYSIS (IRMA) METHOD OVER 111 WELL-SEPARATED CROSS PEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 80, 120, 160 AND 200 MS. THE STRUCTURE PRESENTED HERE WAS ONE OF THE FIVE REFINED AND MINIMIZED STRUCTURES. THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS. THESE WERE; (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM NOE DATA; (2) BACKBONE DIHEDRAL ANGLE RESTRAINTS FOR A STANDARD B-DNA EXCEPT THOSE IMMEDIATELY ADJACENT TO THE MODIFIED RESIDUE; (3) DIHEDRAL ANGLE RESTRAINTS FOR ALL GLYCOSIDIC BONDS, EXCEPT MODIFIED DA RESIDUE IN THE CENTER; (4) HYDROGEN BOND RESTRAINTS (BOTH DISTANCE AND PLANARITY ) FOR ALL BASE-PAIRS EXCEPT CENTRAL DA-DG MISMATCH PAIR. THESE RESTRAINTS WERE JUSTIFIED BY THE FACT THAT THE MODIFIED DUPLEX DISPLAYED CHARACTERISTIC NMR SPECTRA OF A B-DNA EXCEPT NEAR LESION SITE, WHERE THE BAP MOIETY WAS INTERCALATED. THE MODIFIED DA RESIDUE DISPLAYED C3'-ENDO SUGAR RING AND A SYN GLYCOSIDIC BOND. IT ALSO FORMED A NON-WATSON-CRICK BASE PAIR WITH THE OPPOSITE DG.
NMR ensembleConformers submitted total number: 1

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