data_18762 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing ; _BMRB_accession_number 18762 _BMRB_flat_file_name bmr18762.str _Entry_type original _Submission_date 2012-10-04 _Accession_date 2012-10-04 _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 Tang Yijin . . 2 Liu Zhi . . 3 Ding Shuang . . 4 Lin Chin H. . 5 Cai Yuqin . . 6 Rodriguez Fabian A. . 7 Sayer Jane M. . 8 Jerina Donald M. . 9 Amin Shantu . . 10 Broyde Suse . . 11 Geacintov Nicholas E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 154 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 update BMRB 'update entry citation' 2012-11-20 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Nuclear Magnetic Resonance Solution Structure of an N(2)-Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[a,l]pyrene: Intercalation from the Minor Groove with Ruptured Watson-Crick Base Pairing.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23121427 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tang Yijin . . 2 Liu Zhi . . 3 Ding Shuang . . 4 Lin Chin H. . 5 Cai Yuqin . . 6 Rodriguez Fabian A. . 7 Sayer Jane M. . 8 Jerina Donald M. . 9 Amin Shantu . . 10 Broyde Suse . . 11 Geacintov Nicholas E. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 51 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9751 _Page_last 9762 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')' $entity_1 'DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')' $entity_2 '1,3-DIAMINOBENZYL PHENYLALANINE' $entity_DBP stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')_ _Molecular_mass 3254.165 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence CCATCGCTACC loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DT 5 DC 6 DG 7 DC 8 DT 9 DA 10 DC 11 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')_ _Molecular_mass 3454.286 _Mol_thiol_state . _Details . _Residue_count 11 _Mol_residue_sequence GGTAGCGATGG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 12 DG 2 13 DG 3 14 DT 4 15 DA 5 16 DG 6 17 DC 7 18 DG 8 19 DA 9 20 DT 10 21 DG 11 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_DBP _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common '1,3-DIAMINOBENZYL PHENYLALANINE' _BMRB_code DBP _PDB_code DBP _Molecular_mass 122.168 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CB CB C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CG CG C . 0 . ? CZ CZ C . 0 . ? HB11 HB11 H . 0 . ? HB21 HB21 H . 0 . ? HC11 HC11 H . 0 . ? HC21 HC21 H . 0 . ? HCZ1 HCZ1 H . 0 . ? HD11 HD11 H . 0 . ? HE21 HE21 H . 0 . ? HE22 HE22 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? N N N . 0 . ? NE2 NE2 N . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CB ? ? SING N HN1 ? ? SING N HN21 ? ? SING CB CG ? ? SING CB HB11 ? ? SING CB HB21 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD11 ? ? DOUB CE1 CZ ? ? SING CE1 HC11 ? ? DOUB CD2 CE2 ? ? SING CD2 HC21 ? ? SING CE2 CZ ? ? SING CE2 NE2 ? ? SING CZ HCZ1 ? ? SING NE2 HE21 ? ? SING NE2 HE22 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . . . . . . $entity_2 . . . . . . 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 $entity_1 'chemical synthesis' . . . . . $entity_2 'chemical synthesis' . . . . . $entity_DBP '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 $assembly 1.5 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' DSS 25 nM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $assembly 1.5 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' DSS 25 nM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing collection stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_Chemical_shift_referencing _Saveframe_category chemical_shift_reference _Details . 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 _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $Chemical_shift_referencing _Mol_system_component_name 'DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')' _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 1 DC H1' H 5.932 . . 2 1 1 DC H2' H 2.072 . . 3 1 1 DC H2'' H 2.491 . . 4 1 1 DC H3' H 4.635 . . 5 1 1 DC H4' H 4.093 . . 6 1 1 DC H5 H 5.908 . . 7 1 1 DC H5' H 3.738 . . 8 1 1 DC H6 H 7.730 . . 9 2 2 DC H1' H 5.390 . . 10 2 2 DC H2' H 2.179 . . 11 2 2 DC H2'' H 2.420 . . 12 2 2 DC H4' H 4.113 . . 13 2 2 DC H5 H 5.673 . . 14 2 2 DC H6 H 7.594 . . 15 3 3 DA H1' H 6.292 . . 16 3 3 DA H2 H 7.736 . . 17 3 3 DA H2' H 2.734 . . 18 3 3 DA H2'' H 2.940 . . 19 3 3 DA H3' H 5.026 . . 20 3 3 DA H4' H 4.443 . . 21 3 3 DA H5' H 4.147 . . 22 3 3 DA H5'' H 4.077 . . 23 3 3 DA H8 H 8.354 . . 24 4 4 DT H1' H 5.843 . . 25 4 4 DT H2' H 1.962 . . 26 4 4 DT H2'' H 2.404 . . 27 4 4 DT H6 H 7.102 . . 28 4 4 DT H71 H 1.302 . . 29 4 4 DT H72 H 1.302 . . 30 4 4 DT H73 H 1.302 . . 31 5 5 DC H1' H 5.630 . . 32 5 5 DC H2' H 1.567 . . 33 5 5 DC H2'' H 2.205 . . 34 5 5 DC H5 H 5.425 . . 35 5 5 DC H6 H 7.213 . . 36 6 6 DG H1' H 6.095 . . 37 6 6 DG H2'' H 2.825 . . 38 6 6 DG H8 H 8.038 . . 39 7 7 DC H1' H 5.723 . . 40 7 7 DC H2' H 2.112 . . 41 7 7 DC H2'' H 2.352 . . 42 7 7 DC H3' H 4.694 . . 43 7 7 DC H4' H 4.292 . . 44 7 7 DC H6 H 7.553 . . 45 8 8 DT H1' H 5.482 . . 46 8 8 DT H2' H 2.065 . . 47 8 8 DT H2'' H 2.399 . . 48 8 8 DT H6 H 7.297 . . 49 8 8 DT H71 H 1.492 . . 50 8 8 DT H72 H 1.492 . . 51 8 8 DT H73 H 1.492 . . 52 9 9 DA H1' H 6.181 . . 53 9 9 DA H2 H 7.423 . . 54 9 9 DA H2' H 2.699 . . 55 9 9 DA H2'' H 2.847 . . 56 9 9 DA H3' H 5.025 . . 57 9 9 DA H4' H 4.409 . . 58 9 9 DA H5' H 4.142 . . 59 9 9 DA H5'' H 4.057 . . 60 9 9 DA H8 H 8.259 . . 61 10 10 DC H1' H 5.881 . . 62 10 10 DC H2' H 2.023 . . 63 10 10 DC H2'' H 2.376 . . 64 10 10 DC H3' H 4.739 . . 65 10 10 DC H4' H 4.137 . . 66 10 10 DC H5 H 5.330 . . 67 10 10 DC H6 H 7.314 . . 68 11 11 DC H1' H 6.160 . . 69 11 11 DC H2'' H 2.215 . . 70 11 11 DC H3' H 4.510 . . 71 11 11 DC H4' H 3.988 . . 72 11 11 DC H5 H 5.636 . . 73 11 11 DC H6 H 7.565 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $Chemical_shift_referencing _Mol_system_component_name 'DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')' _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 12 1 DG H1' H 5.666 . . 2 12 1 DG H2' H 2.568 . . 3 12 1 DG H2'' H 2.679 . . 4 12 1 DG H3' H 4.788 . . 5 12 1 DG H4' H 4.159 . . 6 12 1 DG H5' H 3.664 . . 7 12 1 DG H8 H 7.858 . . 8 13 2 DG H1' H 5.971 . . 9 13 2 DG H2' H 2.601 . . 10 13 2 DG H2'' H 2.749 . . 11 13 2 DG H3' H 4.949 . . 12 13 2 DG H4' H 4.368 . . 13 13 2 DG H8 H 7.798 . . 14 14 3 DT H1' H 5.543 . . 15 14 3 DT H2' H 2.019 . . 16 14 3 DT H2'' H 2.303 . . 17 14 3 DT H6 H 7.205 . . 18 14 3 DT H71 H 1.358 . . 19 14 3 DT H72 H 1.358 . . 20 14 3 DT H73 H 1.358 . . 21 15 4 DA H1' H 5.991 . . 22 15 4 DA H2' H 2.569 . . 23 15 4 DA H2'' H 2.842 . . 24 15 4 DA H3' H 5.045 . . 25 15 4 DA H4' H 4.359 . . 26 15 4 DA H8 H 7.977 . . 27 16 5 DG H1' H 5.768 . . 28 16 5 DG H2' H 2.705 . . 29 16 5 DG H2'' H 2.865 . . 30 16 5 DG H3' H 5.118 . . 31 16 5 DG H4' H 4.377 . . 32 16 5 DG H8 H 7.658 . . 33 17 6 DC H2' H 1.456 . . 34 17 6 DC H2'' H 1.846 . . 35 17 6 DC H5 H 5.139 . . 36 17 6 DC H6 H 6.860 . . 37 18 7 DG H1' H 5.549 . . 38 18 7 DG H2' H 2.666 . . 39 18 7 DG H2'' H 2.757 . . 40 18 7 DG H8 H 7.709 . . 41 19 8 DA H1' H 6.191 . . 42 19 8 DA H2 H 7.700 . . 43 19 8 DA H2' H 2.575 . . 44 19 8 DA H2'' H 2.884 . . 45 19 8 DA H3' H 5.025 . . 46 19 8 DA H4' H 4.456 . . 47 19 8 DA H8 H 8.184 . . 48 20 9 DT H1' H 5.616 . . 49 20 9 DT H2' H 1.780 . . 50 20 9 DT H2'' H 2.164 . . 51 20 9 DT H3' H 4.803 . . 52 20 9 DT H4' H 4.083 . . 53 20 9 DT H6 H 7.044 . . 54 20 9 DT H71 H 1.377 . . 55 20 9 DT H72 H 1.377 . . 56 20 9 DT H73 H 1.377 . . 57 21 10 DG H1' H 5.600 . . 58 21 10 DG H2' H 2.615 . . 59 21 10 DG H2'' H 2.674 . . 60 21 10 DG H4' H 4.314 . . 61 21 10 DG H8 H 7.790 . . 62 22 11 DG H1' H 6.120 . . 63 22 11 DG H2' H 2.324 . . 64 22 11 DG H2'' H 2.490 . . 65 22 11 DG H3' H 4.626 . . 66 22 11 DG H4' H 4.194 . . 67 22 11 DG H8 H 7.773 . . stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $Chemical_shift_referencing _Mol_system_component_name '1,3-DIAMINOBENZYL PHENYLALANINE' _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 1 101 1 DBP H1 H 7.809 . . 2 101 1 DBP H10 H 7.940 . . 3 101 1 DBP H11 H 3.797 . . 4 101 1 DBP H12 H 5.101 . . 5 101 1 DBP H13 H 4.164 . . 6 101 1 DBP H14 H 6.483 . . 7 101 1 DBP H2 H 6.376 . . 8 101 1 DBP H3 H 6.767 . . 9 101 1 DBP H4 H 7.807 . . 10 101 1 DBP H5 H 8.042 . . 11 101 1 DBP H6 H 7.306 . . 12 101 1 DBP H7 H 7.345 . . 13 101 1 DBP H8 H 7.098 . . 14 101 1 DBP H9 H 7.256 . . stop_ save_