data_4240 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Minor conformer of a benzo[a]pyrene diol epoxide adduct of DA in duplex DNA ; _BMRB_accession_number 4240 _BMRB_flat_file_name bmr4240.str _Entry_type new _Submission_date 1998-10-08 _Accession_date 1998-10-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schwartz J. S. . 2 Rice J. S. . 3 Luxon B. A. . 4 Sayer J. M. . 5 Xie G. . . 6 Yeh H. J.C. . 7 Liu X. . . 8 Jerina D. M. . 9 Gorenstein D. G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-05-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_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 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 97470529 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schwartz J. S. . 2 Rice J. S. . 3 Luxon B. A. . 4 Sayer J. M. . 5 Xie G. . . 6 Yeh H. J.C. . 7 Liu X. . . 8 Jerina D. M. . 9 Gorenstein D. G. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 36 _Journal_issue 37 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11069 _Page_last 11076 _Year 1997 _Details . loop_ _Keyword 'Deoxyribonucleic acid' 'benzo[a]pyrene diol epoxide adduct' 'Duplex DNA' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full . _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code 97470529 _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_2 _Saveframe_category citation _Citation_full . _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code 96027474 _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_3 _Saveframe_category citation _Citation_full 'Meadows, R., Post, C. B., Luxon B. A., & Gorenstein, D. G. (1996) MORASS' _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_4 _Saveframe_category citation _Citation_full ; Pearlman, D. A., Case, D. A., Caldwell, J. C., Ross, W. L., Cheatham, T. E., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K., & Kollman, P. A. (1995) AMBER 4.1 ; _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ save_ref_5 _Saveframe_category citation _Citation_full 'Yeh, H. J. C. et al. (1995) Biochemistry 34, 1364-1375.' _Citation_title 'NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 7827084 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schurter 'E J' J. . 2 Yeh 'H J' J. . 3 Sayer 'J M' M. . 4 Lakshman 'M K' K. . 5 Yagi H . . 6 Jerina 'D M' M. . 7 Gorenstein 'D G' G. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 34 _Journal_issue 4 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 1364 _Page_last 1375 _Year 1995 _Details ; A nonanucleotide in which (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy- 7,8,9,10-tetrahydrobenzo[a]pyrene (7-hydroxy group and epoxide oxygen are trans) is covalently bonded to the exocyclic N6-amino group of deoxyadenosine through trans addition at C10 of the epoxide (10R adduct) has been synthesized. The modified oligonucleotide d(GGTCA*CGAG) was incorporated into the duplex d(GGTCA*CGAG).d(CTCGGGACC), containing a dG mismatch opposite the modified base (dA*). Proton assignments for the solution structure of the duplex containing the 10R adduct were made using 2D TOCSY and NOESY NMR spectra. The complete hybrid relaxation matrix program, MORASS2.0, was used to generate NOESY distance constraints for iterative refinement using distance-restrained molecular dynamics calculations with AMBER4.0. The iteratively refined structure showed the hydrocarbon intercalated from the major groove immediately below the dC4-dG15 base pair and oriented toward the 5'-end of the modified strand. The modified dA is in an anti configuration, with the dG of the GA mismatch turned out into the major groove. Chemical shifts of the hydrocarbon protons and unusual chemical shifts of sugar protons were accounted for by this orientation of the adduct. The information available currently provides the foundation for the rational explanation of observed benzo[a]pyrene (BaP) structures and predictions for other BaP dG and dA adducts. ; save_ ################################## # Molecular system description # ################################## save_DNA _Saveframe_category molecular_system _Mol_system_name 'Duplex DNA (5'-D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3') (DOT)(5'-D(CP*TP*CP*GP*GP*GP*AP*CP*C)-3')' _Abbreviation_common DNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA Strand A' $strand_A 'DNA Strand B' $strand_B stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_strand_A _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(GP*GP*TP*CP*AP*CP*GP*AP*G)-3' _Abbreviation_common DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GGTCXCGAG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DT 4 DC 5 ABP 6 DC 7 DG 8 DA 9 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_strand_B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common (5'-D(CP*TP*CP*GP*GP*GP*AP*CP*C)-3' _Abbreviation_common DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 9 _Mol_residue_sequence CTCGGGACC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 10 DC 2 11 DT 3 12 DC 4 13 DG 5 14 DG 6 15 DG 7 16 DA 8 17 DC 9 18 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_ABP _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common ABP _Abbreviation_common ABP _Name_IUPAC (7R,8S,9R,10S)-N6-[10-(7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosine _BMRB_code . _PDB_code . _Standard_residue_derivative deoxyadenosine loop_ _Mol_label _Residue_seq_code $strand_A 5 stop_ _Molecular_mass . _Mol_paramagnetic no _Details ; ABP is the modified nucleotide adduct derived from the trans addition of the exocyclic N6-amino group of deoxyadenosine to (+)-(7R,8S,9S,!0R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. ; save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $strand_A . . . . . . 'Model System' $strand_B . . . . . . 'Model System' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $strand_A 'chemical synthesis' . . . . . $strand_B 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 180 'A260 units' . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 5.1 loop_ _Task 'Data processing' 'peak picking' 'peak integration' stop_ _Details . save_ save_MORASS _Saveframe_category software _Name MORASS _Version 2.2 loop_ _Task ; Group developed software used to generate accurate distance restraints from NOE intensities utilizing full relaxation matrix theory. ; stop_ _Details . _Citation_label $ref_3 save_ save_AMBER _Saveframe_category software _Name AMBER _Version 4.1 loop_ _Task 'Structure calculation using noe restrained molecular dynamics and energy minimization.' stop_ _Details . _Citation_label $ref_4 save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 750 _Details . save_ save_NMR_spectrometer2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _Sample_label . save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_2D_exchange-only_spectra_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D exchange-only spectra' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D exchange-only spectra' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 0.1 n/a temperature 288 1 K 'ionic strength' 76 . mM pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_ref _Saveframe_category chemical_shift_reference _Details ; The chemical shifts reported for this entry are referenced to the chemical shift of the dC17 H5-H6 NOE cross peak from the major conformer of this molecule (reported as 5.18 and 7.18 ppm, respectively). The reference is Yeh, H. J. C. et al. (1995) Biochemistry 34, 1364-1375. ; loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis DNA H 1 'deoxycytidine H5' ppm 5.18 internal direct cylindrical internal parallel_to_Bo stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chem_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chem_shift_ref _Mol_system_component_name 'DNA Strand A' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 2 DG H8 H 7.80 . 1 2 . 2 DG H1' H 5.99 . 1 3 . 2 DG H2' H 2.60 . 2 4 . 2 DG H2'' H 2.75 . 2 5 . 2 DG H3' H 4.94 . 1 6 . 3 DT H3 H 13.50 . 1 7 . 3 DT H6 H 7.26 . 1 8 . 3 DT H71 H 1.33 . 1 9 . 3 DT H72 H 1.33 . 1 10 . 3 DT H73 H 1.33 . 1 11 . 3 DT H1' H 6.05 . 1 12 . 3 DT H2' H 1.98 . 2 13 . 3 DT H2'' H 2.33 . 2 14 . 4 DC H41 H 8.15 . 2 15 . 4 DC H42 H 7.16 . 2 16 . 4 DC H5 H 5.82 . 1 17 . 4 DC H6 H 7.32 . 1 18 . 4 DC H1' H 5.45 . 1 19 . 4 DC H2' H 1.04 . 2 20 . 4 DC H2'' H 1.35 . 2 21 . 4 DC H3' H 4.69 . 1 22 . 5 ABP H2 H 7.93 . 1 23 . 5 ABP H61 H 7.36 . 1 24 . 5 ABP H8 H 8.73 . 1 25 . 5 ABP H1' H 6.44 . 1 26 . 5 ABP H2' H 3.23 . 2 27 . 5 ABP H2'' H 3.12 . 2 28 . 5 ABP H3' H 5.13 . 1 29 . 5 ABP H4' H 4.58 . 1 30 . 5 ABP HC21 H 6.14 . 1 31 . 5 ABP HC25 H 6.47 . 1 32 . 5 ABP HC27 H 6.91 . 1 33 . 5 ABP HC30 H 7.59 . 1 34 . 5 ABP HC32 H 7.66 . 1 35 . 5 ABP HC34 H 7.85 . 1 36 . 5 ABP HC40 H 6.95 . 1 37 . 5 ABP HC42 H 7.17 . 1 38 . 5 ABP HC44 H 7.83 . 1 39 . 5 ABP HC47 H 5.11 . 1 40 . 5 ABP HC51 H 3.85 . 1 41 . 5 ABP HC55 H 4.55 . 1 42 . 6 DC H41 H 8.17 . 2 43 . 6 DC H42 H 7.11 . 2 44 . 6 DC H5 H 6.06 . 1 45 . 6 DC H6 H 7.54 . 1 46 . 6 DC H1' H 5.68 . 1 47 . 6 DC H2' H 1.98 . 2 48 . 6 DC H2'' H 2.31 . 2 49 . 6 DC H3' H 4.92 . 1 50 . 7 DG H1 H 12.46 . 1 51 . 7 DG H8 H 7.90 . 1 52 . 7 DG H1' H 5.41 . 1 53 . 7 DG H2' H 2.68 . 2 54 . 7 DG H2'' H 2.71 . 2 55 . 8 DA H2 H 7.66 . 1 56 . 8 DA H8 H 8.05 . 1 57 . 8 DA H1' H 6.06 . 1 58 . 8 DA H2' H 2.61 . 2 59 . 8 DA H2'' H 2.87 . 2 60 . 9 DG H8 H 7.56 . 1 61 . 9 DG H1' H 5.90 . 1 62 . 9 DG H2' H 2.33 . 2 63 . 9 DG H2'' H 2.19 . 2 stop_ save_ save_chem_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chem_shift_ref _Mol_system_component_name 'DNA Strand B' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DC H5 H 5.86 . 1 2 . 1 DC H6 H 7.84 . 1 3 . 1 DC H1' H 5.75 . 1 4 . 1 DC H2' H 2.19 . 2 5 . 1 DC H2'' H 2.50 . 2 6 . 2 DT H3 H 13.84 . 1 7 . 2 DT H6 H 7.55 . 1 8 . 2 DT H71 H 1.58 . 1 9 . 2 DT H72 H 1.58 . 1 10 . 2 DT H73 H 1.58 . 1 11 . 2 DT H1' H 6.02 . 1 12 . 2 DT H2' H 2.07 . 2 13 . 2 DT H2'' H 2.40 . 2 14 . 3 DC H41 H 8.38 . 2 15 . 3 DC H42 H 6.82 . 2 16 . 3 DC H5 H 5.29 . 1 17 . 3 DC H6 H 7.05 . 1 18 . 3 DC H1' H 5.40 . 1 19 . 3 DC H2' H 1.62 . 2 20 . 3 DC H2'' H 1.98 . 2 21 . 3 DC H3' H 4.70 . 1 22 . 4 DG H1 H 11.28 . 1 23 . 4 DG H8 H 7.46 . 1 24 . 4 DG H1' H 5.14 . 1 25 . 4 DG H2' H 2.58 . 2 26 . 4 DG H2'' H 2.91 . 2 27 . 5 DG H1 H 9.88 . 1 28 . 5 DG H21 H 3.95 . 2 29 . 5 DG H22 H 3.95 . 2 30 . 5 DG H8 H 7.31 . 1 31 . 5 DG H1' H 5.02 . 1 32 . 6 DG H1 H 12.44 . 1 33 . 6 DG H8 H 7.57 . 1 34 . 6 DG H1' H 4.97 . 1 35 . 6 DG H2' H 2.42 . 2 36 . 6 DG H2'' H 2.45 . 2 37 . 7 DA H8 H 8.07 . 1 38 . 7 DA H1' H 6.19 . 1 39 . 7 DA H2' H 2.61 . 2 40 . 7 DA H2'' H 2.83 . 2 41 . 8 DC H5 H 5.19 . 1 42 . 8 DC H6 H 7.19 . 1 43 . 8 DC H1' H 5.85 . 1 44 . 9 DC H5 H 5.50 . 1 45 . 9 DC H6 H 7.48 . 1 46 . 9 DC H1' H 6.12 . 1 stop_ save_