data_17787 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the duplex when (5'S)-8,5'-cyclo-2'-deoxyguanosine is placed opposite dA ; _BMRB_accession_number 17787 _BMRB_flat_file_name bmr17787.str _Entry_type original _Submission_date 2011-07-18 _Accession_date 2011-07-18 _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 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 164 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-25 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17786 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17788 'gamma-hydroxy-1,N2-propano-2'-deoxyguanosine adduct' 17789 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17790 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' 17791 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22309170 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Das Rajat S. . 3 Basu Ashis . . 4 Stone Michael P. . stop_ _Journal_abbreviation 'Chem. Res. Toxicol.' _Journal_volume 25 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 478 _Page_last 490 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name (5'S)-8,5'-cyclo-2'-deoxyguanosine _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')' $DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 'DNA (5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3')' $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') 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_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')_ _Molecular_mass 2752.830 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GTGCGTGTTTGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DG 4 DC 5 DG 6 DT 7 DG 8 DT 9 DT 10 DT 11 DG 12 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3')_ _Molecular_mass 3031.057 _Mol_thiol_state present _Details . _Residue_count 12 _Mol_residue_sequence ACAAACAAGCAC loop_ _Residue_seq_code _Residue_label 1 DA 2 DC 3 DA 4 DA 5 DA 6 DC 7 DA 8 DA 9 DG 10 DC 11 DA 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_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') . . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') . . . . . . 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_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') '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_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 1.0 mM 'natural abundance' $DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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 298 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 4.773 internal direct . . . 1.000000000 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 NOESY' '2D 1H-1H COSY' 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 (5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')' _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 DG H1' H 6.030 .003 . 2 1 1 DG H2' H 2.684 .003 . 3 1 1 DG H2'' H 2.829 .003 2 4 1 1 DG H3' H 4.838 .003 . 5 1 1 DG H4' H 4.254 .003 . 6 1 1 DG H8 H 7.983 .003 1 7 2 2 DT H1' H 5.981 .003 . 8 2 2 DT H2' H 2.202 .003 . 9 2 2 DT H2'' H 2.570 .003 2 10 2 2 DT H3' H 4.941 .003 . 11 2 2 DT H4' H 4.278 .003 . 12 2 2 DT H6 H 7.394 .003 1 13 2 2 DT H71 H 1.391 .003 1 14 2 2 DT H72 H 1.391 .003 1 15 2 2 DT H73 H 1.391 .003 1 16 3 3 DG H1' H 5.903 .003 . 17 3 3 DG H2' H 2.589 .003 . 18 3 3 DG H2'' H 2.750 .003 2 19 3 3 DG H3' H 5.002 .003 . 20 3 3 DG H4' H 4.378 .003 . 21 3 3 DG H8 H 7.875 .003 1 22 4 4 DC H1' H 5.930 .003 . 23 4 4 DC H2' H 2.218 .003 . 24 4 4 DC H2'' H 3.133 .003 2 25 4 4 DC H3' H 4.984 .003 . 26 4 4 DC H4' H 4.357 .003 . 27 4 4 DC H5 H 5.436 .003 1 28 4 4 DC H6 H 7.501 .003 1 29 5 5 DG H1' H 6.115 .003 . 30 5 5 DG H2' H 2.240 .003 . 31 5 5 DG H2'' H 2.306 .003 . 32 5 5 DG H3' H 5.019 .003 . 33 5 5 DG H4' H 5.136 .003 . 34 5 5 DG H5' H 5.503 .003 . 35 6 6 DT H1' H 5.881 .003 . 36 6 6 DT H2' H 2.254 .003 . 37 6 6 DT H2'' H 2.505 .003 2 38 6 6 DT H3' H 4.864 .003 . 39 6 6 DT H4' H 4.296 .003 . 40 6 6 DT H6 H 7.559 .003 1 41 6 6 DT H71 H 1.659 .003 1 42 6 6 DT H72 H 1.659 .003 1 43 6 6 DT H73 H 1.659 .003 1 44 7 7 DG H1' H 6.057 .003 . 45 7 7 DG H2' H 2.675 .003 . 46 7 7 DG H2'' H 2.863 .003 2 47 7 7 DG H3' H 4.975 .003 . 48 7 7 DG H4' H 4.423 .003 . 49 7 7 DG H8 H 7.947 .003 1 50 8 8 DT H1' H 6.083 .003 . 51 8 8 DT H2' H 2.195 .003 . 52 8 8 DT H2'' H 2.616 .003 2 53 8 8 DT H3' H 4.900 .003 . 54 8 8 DT H4' H 4.284 .003 . 55 8 8 DT H6 H 7.324 .003 1 56 8 8 DT H71 H 1.361 .003 1 57 8 8 DT H72 H 1.361 .003 1 58 8 8 DT H73 H 1.361 .003 1 59 9 9 DT H1' H 6.134 .003 . 60 9 9 DT H2' H 2.181 .003 . 61 9 9 DT H2'' H 2.617 .003 2 62 9 9 DT H3' H 4.903 .003 . 63 9 9 DT H4' H 4.188 .003 . 64 9 9 DT H6 H 7.494 .003 1 65 9 9 DT H71 H 1.635 .003 1 66 9 9 DT H72 H 1.635 .003 1 67 9 9 DT H73 H 1.635 .003 1 68 10 10 DT H1' H 5.842 .003 . 69 10 10 DT H2' H 2.020 .003 . 70 10 10 DT H2'' H 2.403 .003 2 71 10 10 DT H3' H 4.910 .003 . 72 10 10 DT H4' H 4.138 .003 . 73 10 10 DT H6 H 7.339 .003 1 74 10 10 DT H71 H 1.733 .003 1 75 10 10 DT H72 H 1.733 .003 1 76 10 10 DT H73 H 1.733 .003 1 77 11 11 DG H1' H 6.075 .003 . 78 11 11 DG H2' H 2.733 .003 . 79 11 11 DG H3' H 5.016 .003 . 80 11 11 DG H4' H 4.425 .003 . 81 11 11 DG H8 H 8.001 .003 1 82 12 12 DT H1' H 6.264 .003 . 83 12 12 DT H2' H 2.264 .003 . 84 12 12 DT H3' H 4.564 .003 . 85 12 12 DT H4' H 4.104 .003 . 86 12 12 DT H6 H 7.431 .003 1 87 12 12 DT H71 H 1.625 .003 1 88 12 12 DT H72 H 1.625 .003 1 89 12 12 DT H73 H 1.625 .003 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' 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 (5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3')' _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 13 1 DA H1' H 6.199 .003 . 2 13 1 DA H2' H 2.625 .003 . 3 13 1 DA H2'' H 2.787 .003 2 4 13 1 DA H3' H 4.851 .003 . 5 13 1 DA H4' H 4.255 .003 . 6 13 1 DA H8 H 8.218 .003 1 7 14 2 DC H1' H 5.146 .003 . 8 14 2 DC H2' H 2.036 .003 . 9 14 2 DC H2'' H 2.255 .003 2 10 14 2 DC H3' H 4.806 .003 . 11 14 2 DC H4' H 4.104 .003 . 12 14 2 DC H5 H 5.477 .003 1 13 14 2 DC H6 H 7.423 .003 1 14 15 3 DA H1' H 5.789 .003 . 15 15 3 DA H2' H 2.767 .003 . 16 15 3 DA H2'' H 2.870 .003 2 17 15 3 DA H3' H 5.065 .003 . 18 15 3 DA H4' H 4.388 .003 . 19 15 3 DA H8 H 8.237 .003 1 20 16 4 DA H1' H 5.891 .003 . 21 16 4 DA H2' H 2.669 .003 . 22 16 4 DA H2'' H 2.864 .003 2 23 16 4 DA H3' H 5.071 .003 . 24 16 4 DA H4' H 4.460 .003 . 25 16 4 DA H8 H 8.146 .003 1 26 17 5 DA H1' H 6.025 .003 . 27 17 5 DA H2' H 2.507 .003 . 28 17 5 DA H2'' H 2.788 .003 2 29 17 5 DA H3' H 4.982 .003 . 30 17 5 DA H4' H 4.428 .003 . 31 17 5 DA H8 H 8.041 .003 1 32 18 6 DC H1' H 5.470 .003 . 33 18 6 DC H2' H 1.644 .003 . 34 18 6 DC H2'' H 2.172 .003 2 35 18 6 DC H3' H 4.711 .003 . 36 18 6 DC H4' H 4.072 .003 . 37 18 6 DC H5 H 5.136 .003 1 38 18 6 DC H6 H 7.060 .003 1 39 19 7 DA H1' H 5.905 .003 . 40 19 7 DA H2' H 2.364 .003 . 41 19 7 DA H2'' H 2.604 .003 2 42 19 7 DA H3' H 4.916 .003 . 43 19 7 DA H4' H 4.268 .003 . 44 19 7 DA H8 H 7.814 .003 1 45 20 8 DA H1' H 5.826 .003 . 46 20 8 DA H2' H 2.312 .003 . 47 20 8 DA H2'' H 2.417 .003 2 48 20 8 DA H3' H 4.919 .003 . 49 20 8 DA H4' H 4.236 .003 . 50 20 8 DA H8 H 7.751 .003 1 51 21 9 DG H1' H 5.831 .003 . 52 21 9 DG H2' H 2.606 .003 . 53 21 9 DG H2'' H 2.721 .003 2 54 21 9 DG H3' H 4.921 .003 . 55 21 9 DG H4' H 4.373 .003 . 56 21 9 DG H8 H 7.825 .003 1 57 22 10 DC H1' H 5.623 .003 . 58 22 10 DC H2' H 2.083 .003 . 59 22 10 DC H2'' H 2.406 .003 2 60 22 10 DC H3' H 4.814 .003 . 61 22 10 DC H4' H 4.196 .003 . 62 22 10 DC H5 H 5.333 .003 1 63 22 10 DC H6 H 7.360 .003 1 64 23 11 DA H1' H 6.282 .003 . 65 23 11 DA H2' H 2.690 .003 . 66 23 11 DA H2'' H 2.905 .003 2 67 23 11 DA H3' H 5.023 .003 . 68 23 11 DA H4' H 4.406 .003 . 69 23 11 DA H8 H 8.275 .003 1 70 24 12 DC H1' H 6.105 .003 . 71 24 12 DC H2' H 2.133 .003 . 72 24 12 DC H3' H 4.500 .003 . 73 24 12 DC H4' H 4.037 .003 . 74 24 12 DC H5 H 5.387 .003 1 75 24 12 DC H6 H 7.386 .003 1 stop_ save_