data_5993 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H shifts for the DNA duplex containing 5-hydroxy Uracil lesion ; _BMRB_accession_number 5993 _BMRB_flat_file_name bmr5993.str _Entry_type original _Submission_date 2003-11-03 _Accession_date 2003-11-04 _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 Thiviyanathan Varatharasa . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 118 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2005-03-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title '5-hydroxyuracil can form stable base pairs with all four bases in a DNA duplex' _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 Thiviyanathan Varatharasa . . 2 Somasunderam Anoma D. . 3 Volk David E. . 4 Gorenstein David G. . stop_ _Journal_abbreviation 'Chem. Commun.' _Journal_volume . _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 400 _Page_last 402 _Year 2005 _Details . loop_ _Keyword 'oxidized cytosines' 'DNA damage' 'hydroxy uracil' NEIL stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA _Saveframe_category molecular_system _Mol_system_name 'DNA duplex' _Abbreviation_common DNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA chain A' $DNA 'DNA chain B' $DNA 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 'DNA chain A' 1 'DNA chain B' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA _Abbreviation_common DNA _Molecular_mass 3647 _Mol_thiol_state 'not present' _Details '5OHU is the 5 hydroxy-2'deoxy Uracil' ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCAAATTXGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DA 5 DA 6 DA 7 DT 8 DT 9 chem_comp_1 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 $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 '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 $DNA 0.6 mM 0.6 0.8 . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Task 'NMR data processing' 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_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_31P_HETCOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '31P HETCOR' _Sample_label $sample_1 save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 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 '31P HETCOR' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_cond_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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $entry_citation $entry_citation 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_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA chain 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 5.86 0.01 1 2 . 1 DC H6 H 7.60 0.01 1 3 . 1 DC H1' H 5.69 0.01 1 4 . 1 DC H2' H 1.92 0.01 1 5 . 1 DC H2'' H 2.35 0.01 1 6 . 1 DC H3' H 4.64 0.01 1 7 . 1 DC H4' H 4.01 0.01 1 8 . 1 DC H5' H 3.66 0.01 2 9 . 1 DC H5'' H 3.68 0.01 2 10 . 2 DG H1 H 13.01 0.01 1 11 . 2 DG H8 H 7.90 0.01 1 12 . 2 DG H1' H 5.78 0.01 1 13 . 2 DG H2' H 2.56 0.01 1 14 . 2 DG H2'' H 2.61 0.01 1 15 . 2 DG H3' H 4.90 0.01 1 16 . 2 DG H4' H 4.27 0.01 1 17 . 2 DG H5' H 4.00 0.01 2 18 . 2 DG H5'' H 3.91 0.01 2 19 . 3 DC H41 H 8.30 0.01 2 20 . 3 DC H42 H 6.53 0.01 2 21 . 3 DC H5 H 5.37 0.01 1 22 . 3 DC H6 H 7.30 0.01 1 23 . 3 DC H1' H 5.27 0.01 1 24 . 3 DC H2' H 1.81 0.01 1 25 . 3 DC H2'' H 2.14 0.01 1 26 . 3 DC H3' H 4.72 0.01 1 27 . 3 DC H4' H 4.04 0.01 1 28 . 3 DC H5' H 4.02 0.01 2 29 . 4 DA H2 H 7.06 0.01 1 30 . 4 DA H61 H 7.58 0.01 2 31 . 4 DA H62 H 5.97 0.01 2 32 . 4 DA H2' H 2.70 0.01 1 33 . 4 DA H2'' H 2.85 0.01 1 34 . 4 DA H3' H 4.98 0.01 1 35 . 4 DA H4' H 4.34 0.01 1 36 . 4 DA H5' H 4.05 0.01 2 37 . 4 DA H5'' H 3.94 0.01 2 38 . 5 DA H2 H 6.87 0.01 1 39 . 5 DA H61 H 7.21 0.01 2 40 . 5 DA H62 H 5.96 0.01 2 41 . 5 DA H8 H 8.06 0.01 1 42 . 5 DA H1' H 5.86 0.01 1 43 . 5 DA H2' H 2.60 0.01 1 44 . 5 DA H2'' H 2.89 0.01 1 45 . 5 DA H3' H 5.00 0.01 1 46 . 5 DA H4' H 4.42 0.01 1 47 . 5 DA H5' H 4.17 0.01 2 48 . 5 DA H5'' H 4.08 0.01 2 49 . 6 DA H2 H 7.50 0.01 1 50 . 6 DA H61 H 6.92 0.01 2 51 . 6 DA H62 H 6.04 0.01 2 52 . 6 DA H8 H 8.05 0.01 1 53 . 6 DA H1' H 6.08 0.01 1 54 . 6 DA H2' H 2.48 0.01 1 55 . 6 DA H2'' H 2.91 0.01 1 56 . 6 DA H3' H 4.95 0.01 1 57 . 6 DA H4' H 4.40 0.01 1 58 . 6 DA H5' H 4.25 0.01 2 59 . 6 DA H5'' H 4.19 0.01 2 60 . 7 DT H3 H 13.71 0.01 1 61 . 7 DT H6 H 7.10 0.01 1 62 . 7 DT H71 H 1.19 0.01 1 63 . 7 DT H72 H 1.19 0.01 1 64 . 7 DT H73 H 1.19 0.01 1 65 . 7 DT H1' H 5.88 0.01 1 66 . 7 DT H2' H 1.97 0.01 2 67 . 7 DT H2'' H 2.54 0.01 2 68 . 7 DT H3' H 4.80 0.01 1 69 . 7 DT H4' H 4.32 0.01 1 70 . 7 DT H5' H 4.17 0.01 2 71 . 7 DT H5'' H 4.09 0.01 2 72 . 8 DT H3 H 13.86 0.01 1 73 . 8 DT H6 H 7.31 0.01 1 74 . 8 DT H71 H 1.46 0.01 1 75 . 8 DT H72 H 1.46 0.01 1 76 . 8 DT H73 H 1.46 0.01 1 77 . 8 DT H1' H 6.09 0.01 1 78 . 8 DT H2' H 2.22 0.01 1 79 . 8 DT H2'' H 2.60 0.01 1 80 . 8 DT H3' H 4.89 0.01 1 81 . 8 DT H4' H 4.22 0.01 1 82 . 8 DT H5' H 4.09 0.01 2 83 . 8 DT H5'' H 3.97 0.01 2 84 . 9 chem_comp_1 H3 H 13.90 0.01 1 85 . 9 chem_comp_1 H6 H 6.88 0.01 1 86 . 9 chem_comp_1 H1' H 5.90 0.01 1 87 . 9 chem_comp_1 H2' H 1.99 0.01 1 88 . 9 chem_comp_1 H2'' H 2.45 0.01 1 89 . 9 chem_comp_1 H3' H 4.87 0.01 1 90 . 9 chem_comp_1 H4' H 4.16 0.01 1 91 . 9 chem_comp_1 H5' H 4.06 0.01 2 92 . 10 DG H1 H 12.67 0.01 1 93 . 10 DG H8 H 7.92 0.01 1 94 . 10 DG H1' H 5.76 0.01 1 95 . 10 DG H2' H 2.60 0.01 1 96 . 10 DG H2'' H 2.60 0.01 1 97 . 10 DG H3' H 4.95 0.01 1 98 . 10 DG H4' H 4.34 0.01 1 99 . 10 DG H5' H 4.10 0.01 2 100 . 10 DG H5'' H 4.01 0.01 2 101 . 11 DC H41 H 8.42 0.01 2 102 . 11 DC H42 H 6.63 0.01 2 103 . 11 DC H5 H 5.37 0.01 1 104 . 11 DC H6 H 7.31 0.01 1 105 . 11 DC H1' H 5.67 0.01 1 106 . 11 DC H2' H 1.85 0.01 1 107 . 11 DC H2'' H 2.28 0.01 1 108 . 11 DC H3' H 4.75 0.01 1 109 . 11 DC H4' H 4.16 0.01 1 110 . 11 DC H5' H 4.11 0.01 2 111 . 11 DC H5'' H 4.04 0.01 2 112 . 12 DG H8 H 7.92 0.01 1 113 . 12 DG H1' H 6.12 0.01 1 114 . 12 DG H2' H 2.30 0.01 1 115 . 12 DG H2'' H 2.58 0.01 1 116 . 12 DG H3' H 4.62 0.01 1 117 . 12 DG H4' H 4.12 0.01 1 118 . 12 DG H5' H 4.02 0.01 1 stop_ save_