data_5714 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H Chemical shift assignments of the major conformation of a 11-mer DNA duplex containing an AG Mismatch ; _BMRB_accession_number 5714 _BMRB_flat_file_name bmr5714.str _Entry_type new _Submission_date 2003-03-03 _Accession_date 2003-03-04 _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 Sanchez Ana M. . 2 Volk David E. . 3 Gorenstein David G. . 4 Lloyd R. Stephen . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 219 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2003-09-15 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Initiation of Repair of A/G Mismatches is Modulated by Sequence Context' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22775036 _PubMed_ID 12893083 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sanchez Ana M. . 2 Volk David E. . 3 Gorenstein David G. . 4 Lloyd R. Stephen . stop_ _Journal_abbreviation 'DNA Repair' _Journal_volume 2 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 863 _Page_last 878 _Year 2003 _Details . loop_ _Keyword 'AG Mismatch' 'DNA mismatch' 'DNA mispair' stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA_Duplex _Saveframe_category molecular_system _Mol_system_name 'Synthetic DNA duplex with an AG mismatch' _Abbreviation_common 'DNA Duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Strand A' $DNA_Strand_A 'Strand B' $DNA_Strand_B stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_Strand_A _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA Duplex' _Abbreviation_common 'DNA Duplex' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GCTTCAGTCGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DT 4 DT 5 DC 6 DA 7 DG 8 DT 9 DC 10 DG 11 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_Strand_B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA Duplex' _Abbreviation_common 'DNA Duplex' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 11 _Mol_residue_sequence ACGACGGAAGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 12 DA 2 13 DC 3 14 DG 4 15 DA 5 16 DC 6 17 DG 7 18 DG 8 19 DA 9 20 DA 10 21 DG 11 22 DC 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 _Details $DNA_Strand_A . . . . . . 'Synthetic DNA' $DNA_Strand_B . . . . . . 'Synthetic DNA' 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_Strand_A 'chemical synthesis' . . . . . $DNA_Strand_B '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_Strand_A 1.0 mM . $DNA_Strand_B 1.0 mM . 'Na Phosphate' 25.0 mM . NaCl 50.0 mM . EDTA 1.0 mM . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task processing 'volume determination' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITYplus _Field_strength 750 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITYplus _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOE_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOE' _Sample_label . save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOE' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_Condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 0.02 n/a temperature 298 1 K 'ionic strength' 0.11 0.02 mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $Sample_1 stop_ _Sample_conditions_label $Condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Strand A' _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 DG H8 H 7.84 0.01 1 2 . 1 DG H1' H 5.84 0.01 1 3 . 1 DG H2' H 2.54 0.01 1 4 . 1 DG H2'' H 2.64 0.01 1 5 . 1 DG H3' H 4.71 0.01 1 6 . 1 DG H4' H 4.12 0.01 1 7 . 1 DG H5' H 3.59 0.01 2 8 . 1 DG H5'' H 3.59 0.01 2 9 . 2 DC H41 H 8.13 0.01 2 10 . 2 DC H42 H 6.56 0.01 2 11 . 2 DC H5 H 5.23 0.01 1 12 . 2 DC H6 H 7.43 0.01 1 13 . 2 DC H1' H 5.99 0.01 1 14 . 2 DC H2' H 2.09 0.01 1 15 . 2 DC H2'' H 2.44 0.01 1 16 . 2 DC H3' H 4.71 0.01 1 17 . 2 DC H4' H 4.15 0.01 1 18 . 2 DC H5' H 4.05 0.01 2 19 . 2 DC H5'' H 4.05 0.01 2 20 . 3 DT H3 H 14.00 0.01 1 21 . 3 DT H6 H 7.36 0.01 1 22 . 3 DT H71 H 1.48 0.01 1 23 . 3 DT H72 H 1.48 0.01 1 24 . 3 DT H73 H 1.48 0.01 1 25 . 3 DT H1' H 5.96 0.01 1 26 . 3 DT H2' H 2.07 0.01 1 27 . 3 DT H2'' H 2.48 0.01 1 28 . 3 DT H3' H 4.75 0.01 1 29 . 3 DT H4' H 4.08 0.01 1 30 . 3 DT H5' H 3.99 0.01 2 31 . 3 DT H5'' H 4.04 0.01 2 32 . 4 DT H3 H 13.75 0.01 1 33 . 4 DT H6 H 7.28 0.01 1 34 . 4 DT H71 H 1.52 0.01 1 35 . 4 DT H72 H 1.52 0.01 1 36 . 4 DT H73 H 1.52 0.01 1 37 . 4 DT H1' H 5.89 0.01 1 38 . 4 DT H2' H 1.99 0.01 1 39 . 4 DT H2'' H 2.36 0.01 1 40 . 4 DT H3' H 4.74 0.01 1 41 . 4 DT H4' H 4.02 0.01 1 42 . 5 DC H41 H 8.22 0.01 2 43 . 5 DC H42 H 6.69 0.01 2 44 . 5 DC H5 H 5.51 0.01 1 45 . 5 DC H6 H 7.19 0.01 1 46 . 5 DC H1' H 5.49 0.01 1 47 . 5 DC H2' H 1.46 0.01 1 48 . 5 DC H2'' H 1.97 0.01 1 49 . 5 DC H3' H 4.66 0.01 1 50 . 5 DC H4' H 3.89 0.01 1 51 . 5 DC H5' H 4.02 0.01 2 52 . 5 DC H5'' H 3.89 0.01 2 53 . 6 DA H2 H 7.64 0.01 1 54 . 6 DA H8 H 8.01 0.01 1 55 . 6 DA H1' H 5.66 0.01 1 56 . 6 DA H2' H 2.65 0.01 1 57 . 6 DA H2'' H 2.74 0.01 1 58 . 6 DA H3' H 4.85 0.01 1 59 . 6 DA H4' H 4.22 0.01 1 60 . 6 DA H5' H 3.89 0.01 2 61 . 6 DA H5'' H 4.03 0.01 2 62 . 7 DG H1 H 12.57 0.01 1 63 . 7 DG H8 H 7.59 0.01 1 64 . 7 DG H1' H 5.72 0.01 1 65 . 7 DG H2' H 2.43 0.01 1 66 . 7 DG H2'' H 2.59 0.01 1 67 . 7 DG H3' H 4.78 0.01 1 68 . 7 DG H4' H 4.25 0.01 1 69 . 7 DG H5' H 4.03 0.01 2 70 . 7 DG H5'' H 4.03 0.01 2 71 . 8 DT H3 H 13.55 0.01 1 72 . 8 DT H6 H 7.09 0.01 1 73 . 8 DT H71 H 1.18 0.01 1 74 . 8 DT H72 H 1.18 0.01 1 75 . 8 DT H73 H 1.18 0.01 1 76 . 8 DT H1' H 5.86 0.01 1 77 . 8 DT H2' H 1.96 0.01 1 78 . 8 DT H2'' H 2.32 0.01 1 79 . 8 DT H3' H 4.71 0.01 1 80 . 8 DT H4' H 4.05 0.01 1 81 . 8 DT H5' H 4.06 0.01 2 82 . 8 DT H5'' H 4.06 0.01 2 83 . 9 DC H41 H 8.35 0.01 2 84 . 9 DC H42 H 6.78 0.01 2 85 . 9 DC H5 H 5.47 0.01 1 86 . 9 DC H6 H 7.28 0.01 1 87 . 9 DC H1' H 5.48 0.01 1 88 . 9 DC H2' H 1.82 0.01 1 89 . 9 DC H2'' H 2.20 0.01 1 90 . 9 DC H3' H 4.68 0.01 1 91 . 9 DC H4' H 3.94 0.01 1 92 . 9 DC H5' H 3.97 0.01 2 93 . 9 DC H5'' H 3.94 0.01 2 94 . 10 DG H1 H 12.74 0.01 1 95 . 10 DG H8 H 7.83 0.01 1 96 . 10 DG H1' H 5.91 0.01 1 97 . 10 DG H2' H 2.54 0.01 1 98 . 10 DG H2'' H 2.58 0.01 1 99 . 10 DG H3' H 4.84 0.01 1 100 . 10 DG H4' H 4.23 0.01 1 101 . 10 DG H5' H 3.93 0.01 2 102 . 10 DG H5'' H 3.95 0.01 2 103 . 11 DT H6 H 7.23 0.01 1 104 . 11 DT H71 H 1.44 0.01 1 105 . 11 DT H72 H 1.44 0.01 1 106 . 11 DT H73 H 1.44 0.01 1 107 . 11 DT H1' H 6.08 0.01 1 108 . 11 DT H2' H 2.10 0.01 1 109 . 11 DT H2'' H 2.10 0.01 1 110 . 11 DT H3' H 4.40 0.01 1 111 . 11 DT H4' H 4.11 0.01 1 112 . 11 DT H5' H 3.92 0.01 2 113 . 11 DT H5'' H 3.92 0.01 2 stop_ save_ save_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $Sample_1 stop_ _Sample_conditions_label $Condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Strand 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 DA H2 H 7.86 0.01 1 2 . 1 DA H8 H 8.06 0.01 1 3 . 1 DA H1' H 6.07 0.01 1 4 . 1 DA H2' H 2.48 0.01 1 5 . 1 DA H2'' H 2.64 0.01 1 6 . 1 DA H3' H 4.71 0.01 1 7 . 1 DA H4' H 4.12 0.01 1 8 . 1 DA H5' H 3.58 0.01 2 9 . 1 DA H5'' H 3.58 0.01 2 10 . 2 DC H41 H 8.14 0.01 2 11 . 2 DC H42 H 6.56 0.01 2 12 . 2 DC H5 H 5.25 0.01 1 13 . 2 DC H6 H 7.25 0.01 1 14 . 2 DC H1' H 5.17 0.01 1 15 . 2 DC H2' H 1.95 0.01 1 16 . 2 DC H2'' H 2.18 0.01 1 17 . 2 DC H3' H 4.68 0.01 1 18 . 2 DC H4' H 3.98 0.01 1 19 . 2 DC H5' H 3.94 0.01 2 20 . 3 DG H1 H 12.68 0.01 1 21 . 3 DG H8 H 7.76 0.01 1 22 . 3 DG H1' H 5.40 0.01 1 23 . 3 DG H2' H 2.57 0.01 1 24 . 3 DG H2'' H 2.65 0.01 1 25 . 3 DG H3' H 4.88 0.01 1 26 . 3 DG H4' H 4.20 0.01 1 27 . 3 DG H5' H 3.97 0.01 2 28 . 3 DG H5'' H 3.87 0.01 2 29 . 4 DA H2 H 7.65 0.01 1 30 . 4 DA H61 H 5.85 0.01 2 31 . 4 DA H62 H 5.70 0.01 2 32 . 4 DA H8 H 8.06 0.01 1 33 . 4 DA H1' H 6.06 0.01 1 34 . 4 DA H2' H 2.53 0.01 1 35 . 4 DA H2'' H 2.73 0.01 1 36 . 4 DA H3' H 4.90 0.01 1 37 . 4 DA H4' H 4.32 0.01 1 38 . 4 DA H5' H 4.03 0.01 2 39 . 4 DA H5'' H 4.07 0.01 2 40 . 5 DC H41 H 7.91 0.01 2 41 . 5 DC H42 H 6.43 0.01 2 42 . 5 DC H5 H 5.13 0.01 1 43 . 5 DC H6 H 7.02 0.01 1 44 . 5 DC H1' H 5.41 0.01 1 45 . 5 DC H2' H 1.49 0.01 1 46 . 5 DC H2'' H 1.84 0.01 1 47 . 5 DC H3' H 4.60 0.01 1 48 . 5 DC H4' H 4.11 0.01 1 49 . 5 DC H5' H 3.94 0.01 2 50 . 5 DC H5'' H 3.85 0.01 2 51 . 6 DG H1 H 12.04 0.01 1 52 . 6 DG H8 H 7.70 0.01 1 53 . 6 DG H1' H 5.28 0.01 1 54 . 6 DG H2' H 2.52 0.01 1 55 . 6 DG H2'' H 2.52 0.01 1 56 . 6 DG H3' H 4.78 0.01 1 57 . 6 DG H4' H 4.14 0.01 1 58 . 6 DG H5' H 3.88 0.01 2 59 . 6 DG H5'' H 3.76 0.01 2 60 . 7 DG H1 H 12.42 0.01 1 61 . 7 DG H8 H 7.59 0.01 1 62 . 7 DG H1' H 5.36 0.01 1 63 . 7 DG H2' H 2.46 0.01 1 64 . 7 DG H2'' H 2.59 0.01 1 65 . 7 DG H3' H 4.85 0.01 1 66 . 7 DG H4' H 4.20 0.01 1 67 . 7 DG H5' H 3.92 0.01 2 68 . 7 DG H5'' H 3.99 0.01 2 69 . 8 DA H2 H 7.09 0.01 1 70 . 8 DA H61 H 5.88 0.01 2 71 . 8 DA H62 H 5.66 0.01 2 72 . 8 DA H8 H 7.98 0.01 1 73 . 8 DA H1' H 5.70 0.01 1 74 . 8 DA H2' H 2.54 0.01 1 75 . 8 DA H2'' H 2.73 0.01 1 76 . 8 DA H3' H 4.90 0.01 1 77 . 8 DA H4' H 4.26 0.01 1 78 . 8 DA H5' H 3.98 0.01 2 79 . 8 DA H5'' H 4.04 0.01 2 80 . 9 DA H2 H 7.37 0.01 1 81 . 9 DA H8 H 7.86 0.01 1 82 . 9 DA H1' H 5.78 0.01 1 83 . 9 DA H2' H 2.42 0.01 1 84 . 9 DA H2'' H 2.65 0.01 1 85 . 9 DA H3' H 4.86 0.01 1 86 . 9 DA H4' H 4.25 0.01 1 87 . 9 DA H5' H 4.05 0.01 2 88 . 9 DA H5'' H 4.05 0.01 2 89 . 10 DG H1 H 12.81 0.01 1 90 . 10 DG H8 H 7.41 0.01 1 91 . 10 DG H1' H 5.63 0.01 1 92 . 10 DG H2' H 2.24 0.01 1 93 . 10 DG H2'' H 2.47 0.01 1 94 . 10 DG H3' H 4.76 0.01 1 95 . 10 DG H4' H 4.17 0.01 1 96 . 10 DG H5' H 4.05 0.01 2 97 . 10 DG H5'' H 4.02 0.01 2 98 . 11 DC H41 H 8.01 0.01 2 99 . 11 DC H42 H 6.42 0.01 2 100 . 11 DC H5 H 5.07 0.01 1 101 . 11 DC H6 H 7.18 0.01 1 102 . 11 DC H1' H 5.95 0.01 1 103 . 11 DC H2' H 1.98 0.01 1 104 . 11 DC H2'' H 2.02 0.01 1 105 . 11 DC H3' H 4.32 0.01 1 106 . 11 DC H5' H 3.88 0.01 2 stop_ save_