data_5979 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A parallel stranded DNA duplex with an A-G mismatch base-pair ; _BMRB_accession_number 5979 _BMRB_flat_file_name bmr5979.str _Entry_type new _Submission_date 2003-10-21 _Accession_date 2003-10-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method 'theoretical calculation' _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Venkitakrishnan R. P. . 2 Bhaumik S. R. . 3 Chary K. V.R. . 4 Govil G. . . 5 Liu K. . . 6 Howard F. B. . 7 Miles T. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 229 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2003-01-20 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A Parallel Stranded DNA Duplex with an A-G Mismatch Base-Pair: (Ccataatttacc:Cctatgaaatcc) ; _Citation_status published _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 Venkitakrishnan R. P. . 2 Bhaumik S. R. . 3 Chary K. V.R. . 4 Govil G. . . 5 Liu K. . . 6 Howard F. B. . 7 Miles T. H. . stop_ _Journal_abbreviation 'Recent Trends in Biophys. Res.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1 _Page_last . _Year 2004 _Details . loop_ _Keyword ps-DNA 'A:G mismatch' 'parallel DNA duplex' stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA_duplex _Saveframe_category molecular_system _Mol_system_name DNA _Abbreviation_common 'A-G mismatch base-pair parallel DNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA strand A' $DNA_strand_A 'DNA 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 'A-G mismatch base-pair parallel DNA duplex, strand A' _Abbreviation_common 'DNA strand A' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CCATAATTTACC loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DT 5 DA 6 DA 7 DT 8 DT 9 DT 10 DA 11 DC 12 DC 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 'A-G mismatch base-pair parallel DNA duplex, strand B' _Abbreviation_common 'DNA strand B' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence CCTATGAAATCC loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DT 4 DA 5 DT 6 DG 7 DA 8 DA 9 DA 10 DT 11 DC 12 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 $DNA_strand_A . . . . . . $DNA_strand_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_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 5 mM . $DNA_strand_B 5 mM . 'sodium acetate buffer' 0.05 M [U-2H] NaCl 0.1 M . D2O 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_strand_A 5 mM . $DNA_strand_B 5 mM . 'sodium acetate buffer' 0.05 M [U-2H] NaCl 0.1 M . D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 3.1 loop_ _Task refinement stop_ _Details MSI save_ save_Insight _Saveframe_category software _Name Insight _Version II loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_jump_return_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'jump return NOESY' _Sample_label . save_ save_E-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'jump return NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . n/a temperature 298 . K 'ionic strength' 0.1 . M pressure 1 . atm stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.5 . n/a temperature 278 . K 'ionic strength' 0.1 . M pressure 1 . atm 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 . . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA 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 DC H5' H 3.60 0.2 1 2 . 1 DC H5'' H 3.75 0.2 1 3 . 1 DC H4' H 3.91 0.2 1 4 . 1 DC H1' H 5.77 0.2 1 5 . 1 DC H6 H 7.61 0.2 1 6 . 1 DC H5 H 5.96 0.2 1 7 . 1 DC H3' H 4.41 0.2 1 8 . 1 DC H2' H 2.24 0.2 1 9 . 1 DC H2'' H 2.04 0.2 1 10 . 2 DC H5' H 3.57 0.2 1 11 . 2 DC H5'' H 3.76 0.2 1 12 . 2 DC H4' H 3.98 0.2 1 13 . 2 DC H1' H 5.69 0.2 1 14 . 2 DC H6 H 7.62 0.2 1 15 . 2 DC H5 H 5.81 0.2 1 16 . 2 DC H3' H 4.40 0.2 1 17 . 2 DC H2' H 2.26 0.2 1 18 . 2 DC H2'' H 2.09 0.2 1 19 . 3 DA H5' H 3.47 0.2 1 20 . 3 DA H5'' H 3.74 0.2 1 21 . 3 DA H4' H 3.93 0.2 1 22 . 3 DA H1' H 5.83 0.2 1 23 . 3 DA H8 H 8.41 0.2 1 24 . 3 DA H2 H 8.10 0.2 1 25 . 3 DA H3' H 4.54 0.2 1 26 . 3 DA H2' H 2.53 0.2 1 27 . 3 DA H2'' H 2.56 0.2 1 28 . 4 DT H5' H 3.72 0.2 1 29 . 4 DT H5'' H 3.87 0.2 1 30 . 4 DT H4' H 4.02 0.2 1 31 . 4 DT H1' H 5.07 0.2 1 32 . 4 DT H6 H 7.16 0.2 1 33 . 4 DT H71 H 1.70 0.2 1 34 . 4 DT H72 H 1.70 0.2 1 35 . 4 DT H73 H 1.70 0.2 1 36 . 4 DT H3' H 4.42 0.2 1 37 . 4 DT H2' H 2.07 0.2 1 38 . 4 DT H2'' H 1.89 0.2 1 39 . 5 DA H5' H 3.61 0.2 1 40 . 5 DA H5'' H 3.80 0.2 1 41 . 5 DA H4' H 4.02 0.2 1 42 . 5 DA H1' H 5.47 0.2 1 43 . 5 DA H8 H 8.38 0.2 1 44 . 5 DA H2 H 8.13 0.2 1 45 . 5 DA H3' H 4.57 0.2 1 46 . 5 DA H2' H 2.37 0.2 1 47 . 5 DA H2'' H 2.46 0.2 1 48 . 6 DA H5' H 3.74 0.2 1 49 . 6 DA H5'' H 3.94 0.2 1 50 . 6 DA H4' H 4.19 0.2 1 51 . 6 DA H1' H 6.30 0.2 1 52 . 6 DA H8 H 8.54 0.2 1 53 . 6 DA H2 H 8.38 0.2 1 54 . 6 DA H3' H 4.67 0.2 1 55 . 6 DA H2' H 2.64 0.2 1 56 . 6 DA H2'' H 2.58 0.2 1 57 . 7 DT H5' H 3.96 0.2 1 58 . 7 DT H5'' H 3.99 0.2 1 59 . 7 DT H4' H 4.33 0.2 1 60 . 7 DT H1' H 5.94 0.2 1 61 . 7 DT H6 H 7.09 0.2 1 62 . 7 DT H71 H 1.56 0.2 1 63 . 7 DT H72 H 1.56 0.2 1 64 . 7 DT H73 H 1.56 0.2 1 65 . 7 DT H3' H 4.54 0.2 1 66 . 7 DT H2' H 2.35 0.2 1 67 . 7 DT H2'' H 2.03 0.2 1 68 . 8 DT H5' H 3.74 0.2 1 69 . 8 DT H5'' H 3.86 0.2 1 70 . 8 DT H4' H 4.11 0.2 1 71 . 8 DT H1' H 5.76 0.2 1 72 . 8 DT H6 H 7.23 0.2 1 73 . 8 DT H71 H 1.80 0.2 1 74 . 8 DT H72 H 1.80 0.2 1 75 . 8 DT H73 H 1.80 0.2 1 76 . 8 DT H3' H 4.41 0.2 1 77 . 8 DT H2' H 2.02 0.2 1 78 . 8 DT H2'' H 1.98 0.2 1 79 . 9 DT H5' H 3.51 0.2 1 80 . 9 DT H5'' H 3.66 0.2 1 81 . 9 DT H4' H 3.73 0.2 1 82 . 9 DT H1' H 4.73 0.2 1 83 . 9 DT H6 H 6.99 0.2 1 84 . 9 DT H71 H 1.74 0.2 1 85 . 9 DT H72 H 1.74 0.2 1 86 . 9 DT H73 H 1.74 0.2 1 87 . 9 DT H3' H 4.06 0.2 1 88 . 9 DT H2' H 1.23 0.2 1 89 . 9 DT H2'' H 0.78 0.2 1 90 . 10 DA H5' H 3.47 0.2 1 91 . 10 DA H5'' H 3.77 0.2 1 92 . 10 DA H4' H 4.06 0.2 1 93 . 10 DA H1' H 5.66 0.2 1 94 . 10 DA H8 H 8.31 0.2 1 95 . 10 DA H2 H 8.29 0.2 1 96 . 10 DA H3' H 4.47 0.2 1 97 . 10 DA H2' H 2.08 0.2 1 98 . 10 DA H2'' H 2.34 0.2 1 99 . 11 DC H5' H 3.66 0.2 1 100 . 11 DC H5'' H 3.80 0.2 1 101 . 11 DC H4' H 4.03 0.2 1 102 . 11 DC H1' H 5.80 0.2 1 103 . 11 DC H6 H 7.25 0.2 1 104 . 11 DC H5 H 5.44 0.2 1 105 . 11 DC H3' H 4.31 0.2 1 106 . 11 DC H2' H 1.99 0.2 1 107 . 11 DC H2'' H 1.51 0.2 1 108 . 12 DC H5' H 3.71 0.2 1 109 . 12 DC H5'' H 3.82 0.2 1 110 . 12 DC H4' H 4.05 0.2 1 111 . 12 DC H1' H 5.88 0.2 1 112 . 12 DC H6 H 7.73 0.2 1 113 . 12 DC H5 H 6.15 0.2 1 114 . 12 DC H3' H 4.62 0.2 1 115 . 12 DC H2' H 2.24 0.2 1 116 . 12 DC H2'' H 2.36 0.2 1 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA 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 DC H5' H 3.60 0.2 1 2 . 1 DC H5'' H 3.75 0.2 1 3 . 1 DC H4' H 3.91 0.2 1 4 . 1 DC H1' H 5.77 0.2 1 5 . 1 DC H6 H 7.61 0.2 1 6 . 1 DC H5 H 5.96 0.2 1 7 . 1 DC H3' H 4.41 0.2 1 8 . 1 DC H2' H 2.24 0.2 1 9 . 1 DC H2'' H 2.04 0.2 1 10 . 2 DC H5' H 3.57 0.2 1 11 . 2 DC H5'' H 3.76 0.2 1 12 . 2 DC H4' H 3.98 0.2 1 13 . 2 DC H1' H 5.69 0.2 1 14 . 2 DC H6 H 7.62 0.2 1 15 . 2 DC H5 H 5.81 0.2 1 16 . 2 DC H3' H 4.40 0.2 1 17 . 2 DC H2' H 2.26 0.2 1 18 . 2 DC H2'' H 2.09 0.2 1 19 . 3 DT H5' H 3.60 0.2 1 20 . 3 DT H5'' H 3.76 0.2 1 21 . 3 DT H4' H 3.96 0.2 1 22 . 3 DT H1' H 5.56 0.2 1 23 . 3 DT H6 H 7.33 0.2 1 24 . 3 DT H71 H 1.82 0.2 1 25 . 3 DT H72 H 1.82 0.2 1 26 . 3 DT H73 H 1.82 0.2 1 27 . 3 DT H3' H 4.42 0.2 1 28 . 3 DT H2' H 2.32 0.2 1 29 . 3 DT H2'' H 2.09 0.2 1 30 . 4 DA H5' H 3.62 0.2 1 31 . 4 DA H5'' H 3.85 0.2 1 32 . 4 DA H4' H 4.16 0.2 1 33 . 4 DA H1' H 6.19 0.2 1 34 . 4 DA H8 H 8.35 0.2 1 35 . 4 DA H2 H 8.32 0.2 1 36 . 4 DA H3' H 4.61 0.2 1 37 . 4 DA H2' H 2.66 0.2 1 38 . 4 DA H2'' H 2.57 0.2 1 39 . 5 DT H5' H 3.84 0.2 1 40 . 5 DT H5'' H 3.90 0.2 1 41 . 5 DT H4' H 4.12 0.2 1 42 . 5 DT H1' H 5.32 0.2 1 43 . 5 DT H6 H 6.86 0.2 1 44 . 5 DT H71 H 1.85 0.2 1 45 . 5 DT H72 H 1.85 0.2 1 46 . 5 DT H73 H 1.85 0.2 1 47 . 5 DT H3' H 4.42 0.2 1 48 . 5 DT H2' H 1.97 0.2 1 49 . 5 DT H2'' H 1.85 0.2 1 50 . 6 DG H5' H 3.54 0.2 1 51 . 6 DG H5'' H 3.85 0.2 1 52 . 6 DG H4' H 4.03 0.2 1 53 . 6 DG H1' H 5.50 0.2 1 54 . 6 DG H8 H 7.71 0.2 1 55 . 6 DG H3' H 4.56 0.2 1 56 . 6 DG H2' H 2.43 0.2 1 57 . 6 DG H2'' H 2.34 0.2 1 58 . 7 DA H5' H 3.68 0.2 1 59 . 7 DA H5'' H 3.87 0.2 1 60 . 7 DA H4' H 4.05 0.2 1 61 . 7 DA H1' H 5.59 0.2 1 62 . 7 DA H8 H 8.07 0.2 1 63 . 7 DA H2 H 7.36 0.2 1 64 . 7 DA H3' H 4.53 0.2 1 65 . 7 DA H2' H 2.23 0.2 1 66 . 7 DA H2'' H 2.25 0.2 1 67 . 8 DA H5' H 3.65 0.2 1 68 . 8 DA H5'' H 3.86 0.2 1 69 . 8 DA H4' H 4.08 0.2 1 70 . 8 DA H1' H 5.51 0.2 1 71 . 8 DA H8 H 8.53 0.2 1 72 . 8 DA H2 H 7.72 0.2 1 73 . 8 DA H3' H 4.60 0.2 1 74 . 8 DA H2' H 2.47 0.2 1 75 . 8 DA H2'' H 2.59 0.2 1 76 . 9 DA H5' H 3.75 0.2 1 77 . 9 DA H5'' H 3.90 0.2 1 78 . 9 DA H4' H 4.16 0.2 1 79 . 9 DA H1' H 6.10 0.2 1 80 . 9 DA H8 H 8.35 0.2 1 81 . 9 DA H2 H 8.26 0.2 1 82 . 9 DA H3' H 4.58 0.2 1 83 . 9 DA H2' H 2.41 0.2 1 84 . 9 DA H2'' H 2.49 0.2 1 85 . 10 DT H5' H 3.84 0.2 1 86 . 10 DT H5'' H 3.83 0.2 1 87 . 10 DT H4' H 4.07 0.2 1 88 . 10 DT H1' H 5.38 0.2 1 89 . 10 DT H6 H 6.84 0.2 1 90 . 10 DT H71 H 1.45 0.2 1 91 . 10 DT H72 H 1.45 0.2 1 92 . 10 DT H73 H 1.45 0.2 1 93 . 10 DT H3' H 4.36 0.2 1 94 . 10 DT H2' H 1.97 0.2 1 95 . 10 DT H2'' H 1.83 0.2 1 96 . 11 DC H5' H 3.66 0.2 1 97 . 11 DC H5'' H 3.80 0.2 1 98 . 11 DC H4' H 4.03 0.2 1 99 . 11 DC H1' H 5.80 0.2 1 100 . 11 DC H6 H 7.25 0.2 1 101 . 11 DC H5 H 5.44 0.2 1 102 . 11 DC H3' H 4.31 0.2 1 103 . 11 DC H2' H 1.99 0.2 1 104 . 11 DC H2'' H 1.51 0.2 1 105 . 12 DC H5' H 3.71 0.2 1 106 . 12 DC H5'' H 3.82 0.2 1 107 . 12 DC H4' H 4.05 0.2 1 108 . 12 DC H1' H 5.88 0.2 1 109 . 12 DC H6 H 7.73 0.2 1 110 . 12 DC H5 H 6.15 0.2 1 111 . 12 DC H3' H 4.62 0.2 1 112 . 12 DC H2' H 2.24 0.2 1 113 . 12 DC H2'' H 2.36 0.2 1 stop_ save_