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- PDB-1bps: MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN ... -

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Basic information

Entry
Database: PDB / ID: 1bps
TitleMINOR CONFORMER OF A BENZO[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*(BAP)AP*CP*GP*AP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / BENZO[A]PYRENE DIOL EPOXIDE ADDUCT / DUPLEX DNA
Function / homology1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
AuthorsSchwartz, J.S. / Rice, J.S. / Luxon, B.A. / Sayer, J.M. / Xie, G. / Yeh, H.J.C. / Liu, X. / Jerina, D.M. / Gorenstein, D.G.
CitationJournal: Biochemistry / Year: 1997
Title: Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine.
Authors: Schwartz, J.L. / Rice, J.S. / Luxon, B.A. / Sayer, J.M. / Xie, G. / Yeh, H.J. / Liu, X. / Jerina, D.M. / Gorenstein, D.G.
History
DepositionAug 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_exptl / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_exptl.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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 1.4Dec 27, 2023Group: 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: DNA (5'-D(*GP*GP*TP*CP*(BAP)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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2780.836 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: (+)-(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 ...Details: (+)-(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.
Source: (synth.) synthetic construct (others)
#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: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA / Source: (synth.) synthetic construct (others)
#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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121ROESY
131TOCSY
1412D EXCHANGE-ONLY SPECTRA
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE- ...Text: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT ASSIGNMENT PROCESS.

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Sample preparation

Sample conditionsIonic strength: 76 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
MORASS2.2Luxonstructure calculation
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANstructure calculation
RefinementMethod: RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
Software ordinal: 1
Details: THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE ...Details: THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581] DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND. THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH THE OPPOSITE DG. MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ ET AL.,1997).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

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