data_17814 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA Containing an Aristolactam II-dA Lesion. ; _BMRB_accession_number 17814 _BMRB_flat_file_name bmr17814.str _Entry_type original _Submission_date 2011-07-28 _Accession_date 2011-07-28 _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 Lukin Mark . . 2 Zaliznyak Tanya . . 3 Johnson Francis . . 4 'de los Santos' Carlos . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-04-06 update BMRB 'update entry citation' 2011-12-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22121223 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lukin Mark . . 2 Zaliznyak Tanya . . 3 Johnson Francis . . 4 'de Los Santos' Carlos . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 40 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2759 _Page_last 2770 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA Containing an Aristolactam II-dA Lesion' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_11m_dupl_ALII $DNA_11m_dupl_ALII 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_DNA_11m_dupl_ALII _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_11m_dupl_ALII _Molecular_mass 111.103 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GCATGTGTACG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DA 4 DT 5 DG 6 DT 7 DG 8 DT 9 DA 10 DC 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 $DNA_11m_dupl_ALII . . . . . . 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 $DNA_11m_dupl_ALII 'chemical synthesis' . . . . no 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_11m_dupl_ALII 0.25 mM 'natural abundance' 'sodium phosphate' 25 mM 'natural abundance' 'sodium chloride' 50 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 $DNA_11m_dupl_ALII 0.25 mM 'natural abundance' 'sodium phosphate' 25 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 'structure solution' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_HYPER _Saveframe_category software _Name HYPER _Version . loop_ _Vendor _Address _Electronic_address 'Tejero, Monleon, Celda, Powers and Montelione' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_1_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.5 . pH pressure 1 . atm stop_ save_ save_sample_2_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.5 . pH pressure 1 . atm 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 water H 1 protons ppm 4.707 internal direct . . . 1 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_1_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name DNA_11m_dupl_ALII _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 5.929 0.004 . 2 1 1 DG H2' H 2.735 0.004 . 3 1 1 DG H2'' H 2.562 0.004 . 4 1 1 DG H3' H 4.797 0.005 . 5 1 1 DG H4' H 4.184 0.005 . 6 1 1 DG H8 H 7.903 0.003 . 7 2 2 DC H1' H 5.609 0.004 . 8 2 2 DC H2' H 2.409 0.004 . 9 2 2 DC H2'' H 2.099 0.004 . 10 2 2 DC H3' H 4.823 0.003 . 11 2 2 DC H4' H 4.158 0 . 12 2 2 DC H5 H 5.386 0.003 . 13 2 2 DC H6 H 7.416 0.004 . 14 3 3 DA H1' H 6.146 0.003 . 15 3 3 DA H2 H 7.541 0.088 . 16 3 3 DA H2' H 2.793 0.004 . 17 3 3 DA H2'' H 2.575 0.004 . 18 3 3 DA H3' H 4.931 0.004 . 19 3 3 DA H4' H 4.341 0.004 . 20 3 3 DA H8 H 8.225 0.003 . 21 4 4 DT H1' H 5.488 0.004 . 22 4 4 DT H2' H 1.948 0.004 . 23 4 4 DT H2'' H 1.558 0.005 . 24 4 4 DT H3' H 4.658 0.004 . 25 4 4 DT H5' H 4.144 0 . 26 4 4 DT H6 H 6.774 0.004 . 27 4 4 DT H71 H 1.142 0.006 . 28 4 4 DT H72 H 1.142 0.006 . 29 4 4 DT H73 H 1.142 0.006 . 30 5 5 DG H5'' H 3.889 0 . 31 5 5 DG H1' H 5.622 0.007 . 32 5 5 DG H2' H 2.218 0.006 . 33 5 5 DG H2'' H 2.284 0.006 . 34 5 5 DG H3' H 4.997 0.005 . 35 5 5 DG H4' H 4.237 0.004 . 36 5 5 DG H8 H 7.18 0.004 . 37 6 6 DT H1' H 6.579 0.004 . 38 6 6 DT H2' H 2.587 0.005 . 39 6 6 DT H2'' H 2.459 0.004 . 40 6 6 DT H3' H 5.064 0.003 . 41 6 6 DT H4' H 4.708 0.004 . 42 6 6 DT H5' H 4.357 0.004 . 43 6 6 DT H5'' H 4.23 0.004 . 44 6 6 DT H6 H 7.934 0.003 . 45 6 6 DT H71 H 2.023 0.004 . 46 6 6 DT H72 H 2.023 0.004 . 47 6 6 DT H73 H 2.023 0.004 . 48 7 7 DG H1' H 5.894 0.005 . 49 7 7 DG H2' H 2.625 0.004 . 50 7 7 DG H2'' H 2.389 0.005 . 51 7 7 DG H3' H 4.602 0.004 . 52 7 7 DG H4' H 4.339 0.004 . 53 7 7 DG H8 H 7.688 0.003 . 54 8 8 DT H1' H 5.76 0.004 . 55 8 8 DT H2' H 2.509 0.001 . 56 8 8 DT H2'' H 2.133 0.006 . 57 8 8 DT H3' H 4.852 0.004 . 58 8 8 DT H4' H 4.262 0.004 . 59 8 8 DT H5' H 4.095 0.005 . 60 8 8 DT H6 H 7.409 0.004 . 61 8 8 DT H71 H 1.168 0.005 . 62 8 8 DT H72 H 1.168 0.005 . 63 8 8 DT H73 H 1.168 0.005 . 64 9 9 DA H2 H 7.263 0.004 . 65 9 9 DA H2' H 2.736 0.005 . 66 9 9 DA H2'' H 2.529 0.006 . 67 9 9 DA H3' H 4.933 0.004 . 68 9 9 DA H4' H 4.288 0.004 . 69 9 9 DA H8 H 8.136 0.003 . 70 10 10 DC H1' H 5.585 0.005 . 71 10 10 DC H2' H 2.216 0.004 . 72 10 10 DC H2'' H 1.807 0.005 . 73 10 10 DC H3' H 4.72 0.004 . 74 10 10 DC H4' H 4.063 0.001 . 75 10 10 DC H5 H 5.236 0.005 . 76 10 10 DC H6 H 7.201 0.004 . 77 11 11 DG H1' H 6.076 0.003 . 78 11 11 DG H2' H 2.298 0.004 . 79 11 11 DG H2'' H 2.515 0.003 . 80 11 11 DG H3' H 4.589 0.004 . 81 11 11 DG H4' H 4.099 0 . 82 11 11 DG H8 H 7.823 0.003 . stop_ save_