data_50109 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Nonexchangeable proton shifts for d(GTATGGCCATAC)2 ; _BMRB_accession_number 50109 _BMRB_flat_file_name bmr50109.str _Entry_type original _Submission_date 2019-11-30 _Accession_date 2019-11-30 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Nonexchangeable proton shifts for d(GTATGGCCATAC)2' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lyon Rhiannon L. . 2 Southam Hannah M. . 3 Trevitt Clare R. . 4 Liao Chunyan . . 5 El-Khamisy Sherif . . 6 Poole Robert K. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 83 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-12-17 original BMRB . stop_ _Original_release_date 2019-12-02 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; CORM-3 induces DNA damage through Ru(II) binding to DNA ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lyon Rhiannon L. . 2 Southam Hannah M. . 3 Trevitt Clare R. . 4 Liao Chunyan . . 5 El-Khamisy Sherif . . 6 Poole Robert K. . 7 Williamson Mike P. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword 'ruthenium, CORM, DNA damage, NMR, cancer, cisplatin, antibacterial' stop_ save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 'd(GTATGGCCATAC)2 DNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA strand, 1' $entity_1 'DNA strand, 2' $entity_1 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 entity_1 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'synthetic oligonucleotide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; GTATGGCCATAC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DA 4 DT 5 DG 6 DG 7 DC 8 DC 9 DA 10 DT 11 DA 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $entity_1 'chemical synthesis' . . . . . 'Synthesised by Eurofins Genomics' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'potassium phosphate buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 5 mM 'natural abundance' 'potassium phosphate' 30 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TOPSPIN _Version 2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'NMR processing and display' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details 'Avance I' save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'standard conditions' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.8 0.1 pH pressure 1 . atm temperature 298 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details standard 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 'methyl protons' ppm 0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details 'nonexchangeable protons' loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'DNA strand, 1' _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 6.02 0.03 1 2 1 1 DG H2' H 2.80 0.03 2 3 1 1 DG H2'' H 2.69 0.03 2 4 1 1 DG H3' H 4.82 0.03 1 5 1 1 DG H4' H 3.80 0.03 1 6 1 1 DG H8 H 7.96 0.03 1 7 2 2 DT H1' H 5.88 0.03 1 8 2 2 DT H2' H 2.29 0.03 2 9 2 2 DT H2'' H 2.62 0.03 2 10 2 2 DT H3' H 4.94 0.03 1 11 2 2 DT H4' H 4.23 0.03 1 12 2 2 DT H6 H 7.47 0.03 1 13 2 2 DT H71 H 1.43 0.03 1 14 2 2 DT H72 H 1.43 0.03 1 15 2 2 DT H73 H 1.43 0.03 1 16 3 3 DA H1' H 6.31 0.03 1 17 3 3 DA H2 H 7.43 0.03 1 18 3 3 DA H2' H 2.71 0.03 2 19 3 3 DA H2'' H 2.97 0.03 2 20 3 3 DA H3' H 5.05 0.03 1 21 3 3 DA H4' H 4.45 0.03 1 22 3 3 DA H8 H 8.36 0.03 1 23 4 4 DT H1' H 5.70 0.03 1 24 4 4 DT H2' H 1.93 0.03 2 25 4 4 DT H2'' H 2.35 0.03 2 26 4 4 DT H3' H 4.86 0.03 1 27 4 4 DT H6 H 7.08 0.03 1 28 4 4 DT H71 H 1.40 0.03 1 29 4 4 DT H72 H 1.40 0.03 1 30 4 4 DT H73 H 1.40 0.03 1 31 5 5 DG H1' H 5.63 0.03 1 32 5 5 DG H2' H 2.63 0.03 2 33 5 5 DG H2'' H 2.71 0.03 2 34 5 5 DG H3' H 4.97 0.03 1 35 5 5 DG H4' H 4.05 0.03 1 36 5 5 DG H8 H 7.78 0.03 1 37 6 6 DG H1' H 5.86 0.03 1 38 6 6 DG H2' H 2.54 0.03 2 39 6 6 DG H2'' H 2.68 0.03 2 40 6 6 DG H3' H 4.94 0.03 1 41 6 6 DG H4' H 4.33 0.03 1 42 6 6 DG H8 H 7.68 0.03 1 43 7 7 DC H1' H 5.91 0.03 1 44 7 7 DC H2' H 2.06 0.03 2 45 7 7 DC H2'' H 2.46 0.03 2 46 7 7 DC H3' H 4.78 0.03 1 47 7 7 DC H5 H 5.22 0.03 1 48 7 7 DC H6 H 7.31 0.03 1 49 8 8 DC H1' H 5.48 0.03 1 50 8 8 DC H2' H 2.09 0.03 2 51 8 8 DC H2'' H 2.41 0.03 2 52 8 8 DC H3' H 4.82 0.03 1 53 8 8 DC H5 H 5.56 0.03 1 54 8 8 DC H6 H 7.46 0.03 1 55 9 9 DA H1' H 6.24 0.03 1 56 9 9 DA H2 H 7.60 0.03 1 57 9 9 DA H2' H 2.69 0.03 2 58 9 9 DA H2'' H 2.93 0.03 2 59 9 9 DA H3' H 5.00 0.03 1 60 9 9 DA H8 H 8.31 0.03 1 61 10 10 DT H1' H 5.64 0.03 1 62 10 10 DT H2' H 2.00 0.03 2 63 10 10 DT H2'' H 2.38 0.03 2 64 10 10 DT H3' H 4.86 0.03 1 65 10 10 DT H4' H 4.41 0.03 1 66 10 10 DT H6 H 7.18 0.03 1 67 10 10 DT H71 H 1.52 0.03 1 68 10 10 DT H72 H 1.52 0.03 1 69 10 10 DT H73 H 1.52 0.03 1 70 11 11 DA H1' H 6.25 0.03 1 71 11 11 DA H2 H 7.50 0.03 1 72 11 11 DA H2' H 2.66 0.03 2 73 11 11 DA H2'' H 2.86 0.03 2 74 11 11 DA H3' H 5.00 0.03 1 75 11 11 DA H4' H 4.26 0.03 1 76 11 11 DA H8 H 8.25 0.03 1 77 12 12 DC H1' H 6.07 0.03 1 78 12 12 DC H2' H 2.08 0.03 2 79 12 12 DC H2'' H 2.13 0.03 2 80 12 12 DC H3' H 4.47 0.03 1 81 12 12 DC H4' H 4.84 0.03 1 82 12 12 DC H5 H 5.40 0.03 1 83 12 12 DC H6 H 7.38 0.03 1 stop_ save_