data_18040 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA TT mismatch and 2,7-BisNP ; _BMRB_accession_number 18040 _BMRB_flat_file_name bmr18040.str _Entry_type original _Submission_date 2011-11-03 _Accession_date 2011-11-03 _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 JOURDAN Muriel . . 2 GRANZHAN Anton . . 3 GUILLOT Regis . . 4 DUMY Pascal . . 5 TEULADE-FICHOU Marie-Paule . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 202 "31P chemical shifts" 20 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-15 update BMRB 'update entry citation' 2012-03-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22362757 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jourdan Muriel . . 2 Granzhan Anton . . 3 Guillot Regis . . 4 Dumy Pascal . . 5 Teulade-Fichou Marie-Paule . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 40 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5115 _Page_last 5128 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DNA_1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_1 $DNA_1 DNA_2 $DNA_2 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3')_ _Molecular_mass 3365.224 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence CGTCGTAGTGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DT 4 4 DC 5 5 DG 6 6 DT 7 7 DA 8 8 DG 9 9 DT 10 10 DG 11 11 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3')_ _Molecular_mass 3334.213 _Mol_thiol_state 'not present' _Details . _Residue_count 11 _Mol_residue_sequence GCACTTCGACG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 12 DG 2 13 DC 3 14 DA 4 15 DC 5 16 DT 6 17 DT 7 18 DC 8 19 DG 9 20 DA 10 21 DC 11 22 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_1 . . . . . . 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_1 'chemical synthesis' . . . . . $DNA_2 '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_1 1.5 mM 'natural abundance' $DNA_2 1.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 10.1 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 283 . K pH 6 . pH pressure 1 . atm 'ionic strength' 0.06 . M 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 4.96 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D DQF-COSY' '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 DNA_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 DC H1' H 5.78 . 1 2 1 1 DC H2' H 2.50 . 2 3 1 1 DC H2'' H 2.12 . 2 4 1 1 DC H3' H 4.75 . 1 5 1 1 DC H4' H 4.09 . 1 6 1 1 DC H5 H 5.94 . 1 7 1 1 DC H5' H 3.76 . 2 8 1 1 DC H6 H 7.70 . 1 9 1 1 DC H41 H 7.13 . 2 10 1 1 DC H42 H 8.14 . 2 11 2 2 DG H1 H 12.94 . 1 12 2 2 DG H1' H 6.06 . 1 13 2 2 DG H2' H 2.86 . 2 14 2 2 DG H2'' H 2.75 . 2 15 2 2 DG H3' H 5.02 . 1 16 2 2 DG H4' H 4.42 . 1 17 2 2 DG H5' H 4.15 . 2 18 2 2 DG H5'' H 4.07 . 2 19 2 2 DG H8 H 8.05 . 1 20 2 2 DG P P -4.62 . 1 21 3 3 DT H1' H 6.10 . 1 22 3 3 DT H2' H 2.54 . 2 23 3 3 DT H2'' H 2.19 . 2 24 3 3 DT H3 H 13.86 . 1 25 3 3 DT H3' H 4.90 . 1 26 3 3 DT H4' H 4.28 . 1 27 3 3 DT H5' H 4.12 . 2 28 3 3 DT H5'' H 4.07 . 2 29 3 3 DT H6 H 7.34 . 1 30 3 3 DT H71 H 1.45 . 1 31 3 3 DT H72 H 1.45 . 1 32 3 3 DT H73 H 1.45 . 1 33 3 3 DT P P -4.84 . 1 34 4 4 DC H1' H 5.62 . 1 35 4 4 DC H2' H 2.43 . 2 36 4 4 DC H2'' H 2.04 . 2 37 4 4 DC H3' H 4.84 . 1 38 4 4 DC H4' H 4.13 . 1 39 4 4 DC H5 H 5.62 . 1 40 4 4 DC H6 H 7.46 . 1 41 4 4 DC H41 H 6.96 . 2 42 4 4 DC H42 H 8.52 . 2 43 4 4 DC P P -4.84 . 1 44 5 5 DG H1 H 13.00 . 1 45 5 5 DG H1' H 6.00 . 1 46 5 5 DG H2' H 2.73 . 2 47 5 5 DG H2'' H 2.60 . 2 48 5 5 DG H3' H 4.83 . 1 49 5 5 DG H4' H 4.28 . 1 50 5 5 DG H5' H 4.12 . 2 51 5 5 DG H5'' H 4.07 . 2 52 5 5 DG H8 H 7.92 . 1 53 5 5 DG P P -4.51 . 1 54 6 6 DT H1' H 5.52 . 1 55 6 6 DT H2' H 2.00 . 2 56 6 6 DT H2'' H 1.29 . 2 57 6 6 DT H3 H 10.56 . 1 58 6 6 DT H3' H 4.77 . 1 59 6 6 DT H4' H 4.30 . 1 60 6 6 DT H5' H 4.04 . 2 61 6 6 DT H5'' H 4.10 . 2 62 6 6 DT H6 H 6.95 . 1 63 6 6 DT H71 H 1.50 . 1 64 6 6 DT H72 H 1.50 . 1 65 6 6 DT H73 H 1.50 . 1 66 6 6 DT P P -5.03 . 1 67 7 7 DA H1' H 6.07 . 1 68 7 7 DA H2 H 7.79 . 1 69 7 7 DA H2' H 2.92 . 2 70 7 7 DA H2'' H 2.92 . 2 71 7 7 DA H3' H 5.04 . 1 72 7 7 DA H4' H 4.21 . 1 73 7 7 DA H8 H 8.29 . 1 74 7 7 DA P P -4.61 . 1 75 8 8 DG H1 H 12.82 . 1 76 8 8 DG H1' H 5.88 . 1 77 8 8 DG H2' H 2.73 . 2 78 8 8 DG H2'' H 2.51 . 2 79 8 8 DG H3' H 4.88 . 1 80 8 8 DG H4' H 4.40 . 1 81 8 8 DG H8 H 7.63 . 1 82 8 8 DG P P -4.51 . 1 83 9 9 DT H1' H 5.88 . 1 84 9 9 DT H2' H 2.46 . 2 85 9 9 DT H2'' H 2.04 . 2 86 9 9 DT H3 H 13.79 . 1 87 9 9 DT H3' H 4.89 . 1 88 9 9 DT H4' H 4.22 . 1 89 9 9 DT H6 H 7.17 . 1 90 9 9 DT H71 H 1.29 . 1 91 9 9 DT H72 H 1.29 . 1 92 9 9 DT H73 H 1.29 . 1 93 9 9 DT P P -4.84 . 1 94 10 10 DG H1 H 12.94 . 1 95 10 10 DG H1' H 5.96 . 1 96 10 10 DG H2' H 2.75 . 2 97 10 10 DG H2'' H 2.65 . 2 98 10 10 DG H3' H 5.01 . 1 99 10 10 DG H4' H 4.40 . 1 100 10 10 DG H8 H 7.92 . 1 101 10 10 DG P P -4.82 . 1 102 11 11 DC H1' H 6.21 . 1 103 11 11 DC H2' H 2.21 . 2 104 11 11 DC H2'' H 2.21 . 2 105 11 11 DC H3' H 4.52 . 1 106 11 11 DC H4' H 4.28 . 1 107 11 11 DC H5 H 5.45 . 1 108 11 11 DC H5' H 4.09 . 2 109 11 11 DC H5'' H 4.13 . 2 110 11 11 DC H6 H 7.48 . 1 111 11 11 DC H41 H 6.77 . 2 112 11 11 DC H42 H 8.27 . 2 113 11 11 DC P P -4.50 . 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D DQF-COSY' '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 DNA_2 _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 13.12 . 1 2 12 1 DG H1' H 5.99 . 1 3 12 1 DG H2' H 2.65 . 2 4 12 1 DG H2'' H 2.81 . 2 5 12 1 DG H3' H 4.87 . 1 6 12 1 DG H4' H 4.27 . 1 7 12 1 DG H5' H 3.73 . 2 8 12 1 DG H5'' H 3.73 . 2 9 12 1 DG H8 H 7.98 . 1 10 13 2 DC H1' H 5.66 . 1 11 13 2 DC H2' H 2.16 . 2 12 13 2 DC H2'' H 2.47 . 2 13 13 2 DC H3' H 4.90 . 1 14 13 2 DC H4' H 4.23 . 1 15 13 2 DC H5 H 5.45 . 1 16 13 2 DC H5' H 4.15 . 2 17 13 2 DC H6 H 7.48 . 1 18 13 2 DC H41 H 6.62 . 2 19 13 2 DC H42 H 8.53 . 2 20 13 2 DC P P -5.03 . 1 21 14 3 DA H1' H 6.29 . 1 22 14 3 DA H2 H 7.80 . 1 23 14 3 DA H2' H 2.81 . 2 24 14 3 DA H2'' H 2.95 . 2 25 14 3 DA H3' H 5.07 . 1 26 14 3 DA H4' H 4.49 . 1 27 14 3 DA H5' H 4.12 . 2 28 14 3 DA H8 H 8.34 . 1 29 14 3 DA P P -4.50 . 1 30 15 4 DC H1' H 5.85 . 1 31 15 4 DC H2' H 2.06 . 2 32 15 4 DC H2'' H 2.55 . 2 33 15 4 DC H3' H 4.70 . 1 34 15 4 DC H4' H 4.28 . 1 35 15 4 DC H5 H 5.26 . 1 36 15 4 DC H6 H 7.34 . 1 37 15 4 DC H41 H 6.80 . 2 38 15 4 DC H42 H 8.07 . 2 39 15 4 DC P P -4.82 . 1 40 16 5 DT H1' H 6.07 . 1 41 16 5 DT H2' H 2.19 . 2 42 16 5 DT H2'' H 2.57 . 2 43 16 5 DT H3 H 13.79 . 1 44 16 5 DT H3' H 4.86 . 1 45 16 5 DT H4' H 4.25 . 1 46 16 5 DT H6 H 7.42 . 1 47 16 5 DT H71 H 1.57 . 1 48 16 5 DT H72 H 1.57 . 1 49 16 5 DT H73 H 1.57 . 1 50 16 5 DT P P -4.96 . 1 51 17 6 DT H1' H 5.75 . 1 52 17 6 DT H2' H 1.89 . 2 53 17 6 DT H2'' H 2.33 . 2 54 17 6 DT H3 H 10.61 . 1 55 17 6 DT H3' H 4.87 . 1 56 17 6 DT H4' H 4.11 . 1 57 17 6 DT H6 H 7.31 . 1 58 17 6 DT H71 H 1.59 . 1 59 17 6 DT H72 H 1.59 . 1 60 17 6 DT H73 H 1.59 . 1 61 17 6 DT P P -5.14 . 1 62 18 7 DC H1' H 5.01 . 1 63 18 7 DC H2' H 2.42 . 2 64 18 7 DC H2'' H 2.42 . 2 65 18 7 DC H3' H 4.88 . 1 66 18 7 DC H4' H 4.21 . 1 67 18 7 DC H5 H 5.75 . 1 68 18 7 DC H6 H 7.68 . 1 69 18 7 DC H41 H 7.13 . 2 70 18 7 DC H42 H 8.47 . 2 71 18 7 DC P P -3.72 . 1 72 19 8 DG H1 H 12.82 . 1 73 19 8 DG H1' H 5.66 . 1 74 19 8 DG H2' H 2.72 . 2 75 19 8 DG H2'' H 2.83 . 2 76 19 8 DG H3' H 5.05 . 1 77 19 8 DG H4' H 4.35 . 1 78 19 8 DG H8 H 7.93 . 1 79 19 8 DG P P -3.72 . 1 80 20 9 DA H1' H 6.24 . 1 81 20 9 DA H2 H 7.92 . 1 82 20 9 DA H2' H 2.69 . 2 83 20 9 DA H2'' H 2.92 . 2 84 20 9 DA H3' H 5.06 . 1 85 20 9 DA H4' H 4.48 . 1 86 20 9 DA H5' H 4.24 . 2 87 20 9 DA H5'' H 4.18 . 2 88 20 9 DA H8 H 8.24 . 1 89 20 9 DA P P -4.87 . 1 90 21 10 DC H1' H 5.63 . 1 91 21 10 DC H2' H 1.87 . 2 92 21 10 DC H2'' H 2.30 . 2 93 21 10 DC H3' H 4.82 . 1 94 21 10 DC H4' H 4.26 . 1 95 21 10 DC H5 H 5.31 . 1 96 21 10 DC H5' H 4.13 . 2 97 21 10 DC H6 H 7.26 . 1 98 21 10 DC H41 H 6.77 . 2 99 21 10 DC H42 H 8.39 . 2 100 21 10 DC P P -4.84 . 1 101 22 11 DG H1 H 12.92 . 1 102 22 11 DG H1' H 6.17 . 1 103 22 11 DG H2' H 2.62 . 2 104 22 11 DG H2'' H 2.37 . 2 105 22 11 DG H3' H 4.69 . 1 106 22 11 DG H4' H 4.19 . 1 107 22 11 DG H5' H 4.11 . 2 108 22 11 DG H8 H 7.93 . 1 109 22 11 DG P P -4.51 . 1 stop_ save_