data_5385 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift assignments for the 8OG:G mismatched duplex ; _BMRB_accession_number 5385 _BMRB_flat_file_name bmr5385.str _Entry_type original _Submission_date 2002-06-05 _Accession_date 2002-06-05 _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 Thiviyanathan Varatharasa . . 2 Somasunderam Anoma D. . 3 Hazra Tapas . . 4 Mitra Sankar . . 5 Gorenstein David G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 116 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2003-02-20 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of a DNA Duplex containing 8-hydroxy-2'-deoxyguanosine Opposite Deoxyguanosine ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22387755 _PubMed_ID 12498794 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thiviyanathan Varatharasa . . 2 Somasunderam Anoma D. . 3 Hazra Tapas K. . 4 Mitra Sankar . . 5 Gorenstein David G. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 325 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 433 _Page_last 442 _Year 2003 _Details . loop_ _Keyword 8-oxoG 'DNA mismatch' MutY stop_ save_ ################################## # Molecular system description # ################################## save_system_8-OG _Saveframe_category molecular_system _Mol_system_name '8oxoG:G mismatch' _Abbreviation_common 8-OG _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '8-OG 1' $8-OG_duplex '8-OG 2' $8-OG_duplex stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 '8-OG 1' 2 '8-OG 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_8-OG_duplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA _Abbreviation_common DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCGAATTGGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DG 5 DA 6 DA 7 DT 8 DT 9 DG 10 DG 11 DC 12 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 $8-OG_duplex 'E. coli' 562 Eubacteria . Escherichia coli 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 $8-OG_duplex '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $8-OG_duplex . mM 1.8 2.2 . stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 6.0 loop_ _Task 'Molecular Dynamics' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity-Plus _Field_strength 750 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity-Plus _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D-TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 2D-TOCSY _Sample_label $sample_1 save_ save_31P-1H_HETCOR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '31P-1H HETCOR' _Sample_label $sample_1 save_ save_HEHAHA_5 _Saveframe_category NMR_applied_experiment _Experiment_name HEHAHA _Sample_label $sample_1 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 0.1 n/a temperature 298 1 K 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 HOD H 1 H ppm 4.76 internal direct spherical internal parallel_to_Bo 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_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 '8-OG 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 DC H41 H 8.13 0.1 2 2 . 1 DC H42 H 7.07 0.1 2 3 . 1 DC H5 H 5.89 0.1 1 4 . 1 DC H6 H 7.63 0.1 1 5 . 1 DC H1' H 5.77 0.1 1 6 . 1 DC H2' H 1.95 0.1 1 7 . 1 DC H2'' H 2.41 0.1 1 8 . 1 DC H3' H 4.71 0.1 1 9 . 1 DC H4' H 4.08 0.1 1 10 . 1 DC H5' H 3.74 0.1 1 11 . 1 DC H5'' H 3.72 0.1 1 12 . 2 DG H1 H 13.05 0.1 1 13 . 2 DG H8 H 7.97 0.1 1 14 . 2 DG H1' H 5.90 0.1 1 15 . 2 DG H2' H 2.70 0.1 1 16 . 2 DG H2'' H 2.77 0.1 1 17 . 2 DG H3' H 4.99 0.1 1 18 . 2 DG H4' H 4.37 0.1 1 19 . 3 DC H41 H 8.43 0.1 2 20 . 3 DC H42 H 6.36 0.1 2 21 . 3 DC H5 H 5.48 0.1 1 22 . 3 DC H6 H 7.38 0.1 1 23 . 3 DC H1' H 5.76 0.1 1 24 . 3 DC H2' H 2.05 0.1 1 25 . 3 DC H2'' H 2.42 0.1 1 26 . 3 DC H3' H 4.82 0.1 1 27 . 3 DC H4' H 4.25 0.1 1 28 . 3 DC H5' H 4.17 0.1 2 29 . 3 DC H5'' H 4.17 0.1 2 30 . 4 DG H1 H 10.70 0.1 1 31 . 4 DG H21 H 5.62 0.1 2 32 . 4 DG H8 H 7.76 0.1 1 33 . 4 DG H1' H 5.68 0.1 1 34 . 4 DG H2' H 2.66 0.1 1 35 . 4 DG H2'' H 2.78 0.1 1 36 . 4 DG H3' H 4.99 0.1 1 37 . 4 DG H4' H 4.11 0.1 1 38 . 4 DG H5' H 4.07 0.1 2 39 . 5 DA H2 H 7.35 0.1 1 40 . 5 DA H61 H 7.14 0.1 2 41 . 5 DA H62 H 6.15 0.1 2 42 . 5 DA H8 H 8.07 0.1 1 43 . 5 DA H1' H 5.95 0.1 1 44 . 5 DA H2' H 2.63 0.1 1 45 . 5 DA H2'' H 2.93 0.1 1 46 . 5 DA H3' H 5.06 0.1 1 47 . 5 DA H4' H 4.43 0.1 1 48 . 5 DA H5' H 4.23 0.1 2 49 . 5 DA H5'' H 4.20 0.1 2 50 . 6 DA H2 H 7.58 0.1 1 51 . 6 DA H61 H 7.15 0.1 1 52 . 6 DA H62 H 6.18 0.1 1 53 . 6 DA H8 H 8.16 0.1 1 54 . 6 DA H1' H 6.14 0.1 1 55 . 6 DA H2' H 2.60 0.1 1 56 . 6 DA H2'' H 2.91 0.1 1 57 . 6 DA H3' H 5.02 0.1 1 58 . 6 DA H4' H 4.47 0.1 1 59 . 6 DA H5' H 4.25 0.1 2 60 . 7 DT H3 H 13.59 0.1 1 61 . 7 DT H6 H 7.10 0.1 1 62 . 7 DT H71 H 1.31 0.1 1 63 . 7 DT H72 H 1.31 0.1 1 64 . 7 DT H73 H 1.31 0.1 1 65 . 7 DT H1' H 5.88 0.1 1 66 . 7 DT H2' H 1.98 0.1 1 67 . 7 DT H2'' H 2.51 0.1 1 68 . 7 DT H3' H 4.81 0.1 1 69 . 7 DT H4' H 4.20 0.1 1 70 . 7 DT H5' H 4.33 0.1 2 71 . 8 DT H3 H 13.65 0.1 1 72 . 8 DT H6 H 7.18 0.1 1 73 . 8 DT H71 H 1.54 0.1 1 74 . 8 DT H72 H 1.54 0.1 1 75 . 8 DT H73 H 1.54 0.1 1 76 . 8 DT H1' H 6.13 0.1 1 77 . 8 DT H2' H 1.91 0.1 1 78 . 8 DT H2'' H 2.81 0.1 1 79 . 8 DT H3' H 4.87 0.1 1 80 . 8 DT H4' H 4.24 0.1 1 81 . 8 DT H5' H 4.12 0.1 2 82 . 8 DT H5'' H 4.09 0.1 2 83 . 9 DG H1 H 11.38 0.1 1 84 . 9 DG H1' H 5.17 0.1 1 85 . 9 DG H2' H 3.27 0.1 1 86 . 9 DG H2'' H 2.34 0.1 1 87 . 9 DG H3' H 4.95 0.1 1 88 . 9 DG H4' H 4.11 0.1 1 89 . 9 DG H5' H 4.09 0.1 1 90 . 10 DG H1 H 13.01 0.1 1 91 . 10 DG H8 H 7.92 0.1 1 92 . 10 DG H1' H 5.93 0.1 1 93 . 10 DG H2' H 2.68 0.1 1 94 . 10 DG H2'' H 2.73 0.1 1 95 . 10 DG H3' H 5.03 0.1 1 96 . 10 DG H4' H 4.41 0.1 1 97 . 10 DG H5' H 4.14 0.1 2 98 . 10 DG H5'' H 4.05 0.1 2 99 . 11 DC H41 H 8.45 0.1 2 100 . 11 DC H42 H 6.63 0.1 2 101 . 11 DC H5 H 5.45 0.1 1 102 . 11 DC H6 H 7.33 0.1 1 103 . 11 DC H1' H 5.78 0.1 1 104 . 11 DC H2' H 1.92 0.1 1 105 . 11 DC H2'' H 2.34 0.1 1 106 . 11 DC H3' H 4.84 0.1 1 107 . 11 DC H4' H 4.15 0.1 1 108 . 11 DC H5' H 4.20 0.1 1 109 . 11 DC H5'' H 4.11 0.1 1 110 . 12 DG H8 H 7.94 0.1 1 111 . 12 DG H1' H 6.16 0.1 1 112 . 12 DG H2' H 2.39 0.1 1 113 . 12 DG H2'' H 2.64 0.1 1 114 . 12 DG H3' H 4.69 0.1 1 115 . 12 DG H4' H 4.18 0.1 1 116 . 12 DG H5' H 4.08 0.1 2 stop_ save_