data_18453 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein ; _BMRB_accession_number 18453 _BMRB_flat_file_name bmr18453.str _Entry_type original _Submission_date 2012-05-09 _Accession_date 2012-05-09 _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 Zaliznyak Tanya . . 2 'de los Santos' Carlos . . 3 Lukin Mark . . 4 El-khateeb Mahmoud . . 5 Bonala Rahda . . 6 Johnson Francis . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 150 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-11 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18454 'duplex DNA containing the -OH-PdG dA base pair' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR structure of duplex DNA containing the -OH-PdG dA base pair: A mutagenic intermediate of acrolein' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20049919 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zaliznyak Tanya . . 2 'de los Santos' Carlos . . 3 Lukin Mark . . 4 El-khateeb Mahmoud . . 5 Bonala Rahda . . 6 Johnson Francis . . stop_ _Journal_abbreviation Biopolymers _Journal_volume 93 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 391 _Page_last 401 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 11_mer_oligonucleotide-B _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 11_mer_oligonucleotide-B $11_mer_oligonucleotide-B 11_mer_oligonucleotide-D $11_mer_oligonucleotide-D 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_11_mer_oligonucleotide-B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 11_mer_oligonucleotide-B _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence CGTACGCATGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DT 4 4 DA 5 5 DC 6 6 DG 7 7 DC 8 8 DA 9 9 DT 10 10 DG 11 11 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_11_mer_oligonucleotide-D _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 11_mer_oligonucleotide-D _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 11 _Mol_residue_sequence GCATGAGTACG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DC 3 3 DA 4 4 DT 5 5 DG 6 6 DA 7 7 DG 8 8 DT 9 9 DA 10 10 DC 11 11 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $11_mer_oligonucleotide-B . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $11_mer_oligonucleotide-B 'chemical synthesis' . . . . n/a n/a 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 $11_mer_oligonucleotide-B 0.5 mM '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 $11_mer_oligonucleotide-B 0.5 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY45_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY45' _Sample_label $sample_1 save_ save_2D_DQF-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _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 temperature 273 . K pH 6.6 . pH pressure 1 . atm stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.6 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 TSP H 1 'methylene protons' ppm 0 internal direct . . . 1.0 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_reference_1 _Mol_system_component_name 11_mer_oligonucleotide-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 1 DC H1' H 5.74 . . 2 1 1 DC H2' H 1.98 . . 3 1 1 DC H2'' H 2.39 . . 4 1 1 DC H3' H 4.67 . . 5 1 1 DC H4' H 4.03 . . 6 1 1 DC H5 H 5.86 . . 7 1 1 DC H6 H 7.60 . . 8 2 2 DG H1' H 5.93 . . 9 2 2 DG H2' H 2.64 . . 10 2 2 DG H2'' H 2.74 . . 11 2 2 DG H3' H 4.94 . . 12 2 2 DG H4' H 4.32 . . 13 2 2 DG H8 H 7.93 . . 14 3 3 DT H1' H 5.61 . . 15 3 3 DT H2' H 2.02 . . 16 3 3 DT H2'' H 2.37 . . 17 3 3 DT H3' H 4.84 . . 18 3 3 DT H6 H 7.20 . . 19 3 3 DT H71 H 1.46 . . 20 3 3 DT H72 H 1.46 . . 21 3 3 DT H73 H 1.46 . . 22 4 4 DA H1' H 6.08 . . 23 4 4 DA H2 H 7.38 . . 24 4 4 DA H2' H 2.67 . . 25 4 4 DA H2'' H 2.76 . . 26 4 4 DA H3' H 4.99 . . 27 4 4 DA H4' H 4.37 . . 28 4 4 DA H8 H 8.25 . . 29 5 5 DC H1' H 5.62 . . 30 5 5 DC H2' H 1.69 . . 31 5 5 DC H2'' H 2.41 . . 32 5 5 DC H3' H 4.66 . . 33 5 5 DC H4' H 4.11 . . 34 5 5 DC H5 H 5.19 . . 35 5 5 DC H6 H 7.07 . . 36 6 6 DG H1' H 5.81 . . 37 6 6 DG H2' H 2.48 . . 38 6 6 DG H3' H 4.84 . . 39 6 6 DG H4' H 4.24 . . 40 6 6 DG H8 H 7.71 . . 41 7 7 DC H1' H 5.41 . . 42 7 7 DC H2' H 2.14 . . 43 7 7 DC H2'' H 2.33 . . 44 7 7 DC H3' H 4.85 . . 45 7 7 DC H5 H 5.43 . . 46 7 7 DC H6 H 7.44 . . 47 8 8 DA H1' H 6.16 . . 48 8 8 DA H2 H 7.51 . . 49 8 8 DA H2' H 2.62 . . 50 8 8 DA H2'' H 2.88 . . 51 8 8 DA H3' H 4.98 . . 52 8 8 DA H4' H 4.37 . . 53 8 8 DA H8 H 8.22 . . 54 9 9 DT H1' H 5.67 . . 55 9 9 DT H2' H 1.91 . . 56 9 9 DT H2'' H 2.30 . . 57 9 9 DT H3' H 4.81 . . 58 9 9 DT H4' H 4.04 . . 59 9 9 DT H6 H 7.03 . . 60 9 9 DT H71 H 1.36 . . 61 9 9 DT H72 H 1.36 . . 62 9 9 DT H73 H 1.36 . . 63 10 10 DG H1' H 5.87 . . 64 10 10 DG H2' H 2.55 . . 65 10 10 DG H2'' H 2.65 . . 66 10 10 DG H3' H 4.92 . . 67 10 10 DG H4' H 4.31 . . 68 10 10 DG H8 H 7.8 . . 69 11 11 DC H1' H 6.14 . . 70 11 11 DC H2' H 2.13 . . 71 11 11 DC H2'' H 2.13 . . 72 11 11 DC H3' H 4.45 . . 73 11 11 DC H5 H 5.36 . . 74 11 11 DC H6 H 7.40 . . 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_reference_1 _Mol_system_component_name 11_mer_oligonucleotide-D _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 DG H1' H 5.94 . . 2 1 1 DG H2' H 2.58 . . 3 1 1 DG H2'' H 2.74 . . 4 1 1 DG H3' H 4.81 . . 5 1 1 DG H4' H 4.20 . . 6 1 1 DG H8 H 7.90 . . 7 2 2 DC H1' H 5.64 . . 8 2 2 DC H2' H 2.12 . . 9 2 2 DC H2'' H 2.44 . . 10 2 2 DC H3' H 4.86 . . 11 2 2 DC H4' H 4.18 . . 12 2 2 DC H5 H 5.39 . . 13 2 2 DC H6 H 7.43 . . 14 3 3 DA H1' H 6.24 . . 15 3 3 DA H2 H 7.65 . . 16 3 3 DA H2' H 2.68 . . 17 3 3 DA H2'' H 2.91 . . 18 3 3 DA H3' H 5.01 . . 19 3 3 DA H4' H 4.40 . . 20 3 3 DA H8 H 8.30 . . 21 4 4 DT H1' H 5.68 . . 22 4 4 DT H2' H 1.87 . . 23 4 4 DT H2'' H 2.31 . . 24 4 4 DT H3' H 4.82 . . 25 4 4 DT H4' H 4.11 . . 26 4 4 DT H6 H 7.03 . . 27 4 4 DT H71 H 1.42 . . 28 4 4 DT H72 H 1.42 . . 29 4 4 DT H73 H 1.42 . . 30 5 5 DG H1' H 5.42 . . 31 5 5 DG H2' H 2.60 . . 32 5 5 DG H2'' H 2.72 . . 33 5 5 DG H3' H 4.95 . . 34 5 5 DG H4' H 4.27 . . 35 5 5 DG H8 H 7.83 . . 36 6 6 DA H1' H 6.08 . . 37 6 6 DA H2 H 7.83 . . 38 6 6 DA H2' H 2.71 . . 39 6 6 DA H2'' H 2.92 . . 40 6 6 DA H3' H 5.03 . . 41 6 6 DA H4' H 4.43 . . 42 6 6 DA H8 H 8.26 . . 43 7 7 DG H1' H 5.83 . . 44 7 7 DG H2' H 2.51 . . 45 7 7 DG H2'' H 2.71 . . 46 7 7 DG H3' H 4.95 . . 47 7 7 DG H4' H 4.35 . . 48 7 7 DG H8 H 7.72 . . 49 8 8 DT H1' H 5.60 . . 50 8 8 DT H2' H 1.98 . . 51 8 8 DT H2'' H 2.34 . . 52 8 8 DT H3' H 4.83 . . 53 8 8 DT H6 H 7.09 . . 54 8 8 DT H71 H 1.35 . . 55 8 8 DT H72 H 1.35 . . 56 8 8 DT H73 H 1.35 . . 57 9 9 DA H1' H 6.16 . . 58 9 9 DA H2 H 7.55 . . 59 9 9 DA H2' H 2.66 . . 60 9 9 DA H2'' H 2.81 . . 61 9 9 DA H3' H 4.99 . . 62 9 9 DA H4' H 4.37 . . 63 9 9 DA H8 H 8.24 . . 64 10 10 DC H1' H 5.61 . . 65 10 10 DC H2' H 1.81 . . 66 10 10 DC H2'' H 2.24 . . 67 10 10 DC H3' H 4.74 . . 68 10 10 DC H4' H 4.10 . . 69 10 10 DC H5 H 5.32 . . 70 10 10 DC H6 H 7.22 . . 71 11 11 DG H1' H 6.09 . . 72 11 11 DG H2' H 2.54 . . 73 11 11 DG H2'' H 2.32 . . 74 11 11 DG H3' H 4.62 . . 75 11 11 DG H4' H 4.12 . . 76 11 11 DG H8 H 7.85 . . stop_ save_