data_15238 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Duplex DNA containing an abasic site with an opposite dC (alpha anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure) ; _BMRB_accession_number 15238 _BMRB_flat_file_name bmr15238.str _Entry_type original _Submission_date 2007-05-04 _Accession_date 2007-05-04 _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 Chen J. . . 2 Dupradeau F. Y. . 3 Case D. A. . 4 Turner C. J. . 5 Stubbe J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 205 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2008-02-20 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15239 AB_C_beta stop_ _Original_release_date 2007-05-07 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18025040 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chen J. . . 2 Dupradeau F. Y. . 3 Case D. A. . 4 Turner C. J. . 5 Stubbe J. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 36 _Journal_issue 1 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 253 _Page_last 262 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Ab_C_alpha _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 1st_strand $5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' 2nd_strand $5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'duplex DNA containing an abasic site with an opposite C (alpha anomer)' save_ ######################## # Monomeric polymers # ######################## save_5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence ; CCAAAGXACCGGG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DA 5 DA 6 DG 7 ORP 8 DA 9 DC 10 DC 11 DG 12 DG 13 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 13 _Mol_residue_sequence ; CCCGGTCCTTTGG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DC 4 DG 5 DG 6 DT 7 DC 8 DC 9 DT 10 DT 11 DT 12 DG 13 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ORP _Saveframe_category polymer_residue _Mol_type SACCHARIDE _Name_common 2-DEOXY-5-PHOSPHONO-RIBOSE _BMRB_code ORP _PDB_code ORP _Standard_residue_derivative . _Molecular_mass 214.110 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? O1 O1 O . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? O3 O3 O . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? O5 O5 O . 0 . ? P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? H1 H1 H . 0 . ? HO1 HO1 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3 H3 H . 0 . ? HO3 HO3 H . 0 . ? H4 H4 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING C1 O1 ? ? SING C1 C2 ? ? SING C1 O4 ? ? SING C1 H1 ? ? SING O1 HO1 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 O3 ? ? SING C3 C4 ? ? SING C3 H3 ? ? SING O3 HO3 ? ? SING C4 O4 ? ? SING C4 C5 ? ? SING C4 H4 ? ? SING C5 O5 ? ? SING C5 H51 ? ? SING C5 H52 ? ? SING O5 P ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O3P ? ? SING O2P HOP2 ? ? SING O3P HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' . . . . . . $5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-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 $5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' 'chemical synthesis' . . . . . $5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.5 mM duplex DNA' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' 2.5 mM 'natural abundance' $5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' 2.5 mM 'natural abundance' D2O 100 % '[U-100% 2H]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2.5 mM duplex DNA' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3' 2.5 mM 'natural abundance' $5'-D(*CP*CP*CP*GP*GP*TP*CP*CP*TP*TP*TP*GP*G)-3' 2.5 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 2001 loop_ _Vendor _Address _Electronic_address 'Accelrys Inc.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address James . . stop_ loop_ _Task 'iterative matrix relaxation' stop_ _Details . save_ save_Amber _Saveframe_category software _Name AMBER _Version 8.0 loop_ _Vendor _Address _Electronic_address 'Case et al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Custom-built _Model Custom-built _Field_strength 591 _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_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label $sample_1 save_ save_H-P_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'H-P HSQC' _Sample_label $sample_1 save_ save_H3'-selective_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name "H3'-selective HSQC" _Sample_label $sample_1 save_ save_watergate-NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name watergate-NOESY _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 10 . mM pH 6.5 . pH pressure 1 . atm temperature 298 . K 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 DSS H 1 'methyl protons' ppm 0.00 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_ _Software_label $FELIX stop_ loop_ _Experiment_label '2D NOESY' '2D TOCSY' "H3'-selective HSQC" watergate-NOESY stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 1st_strand _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 DC H42 H 7.815 . . 2 1 1 DC H6 H 5.999 . . 3 1 1 DC H41 H 6.003 . . 4 1 1 DC H5 H 4.681 . . 5 1 1 DC H1' H 3.762 . . 6 1 1 DC H2' H 3.778 . . 7 1 1 DC H2'' H 7.099 . . 8 1 1 DC H3' H 7.983 . . 9 2 2 DC H42 H 7.556 . . 10 2 2 DC H6 H 5.756 . . 11 2 2 DC H41 H 5.371 . . 12 2 2 DC H5 H 2.041 . . 13 2 2 DC H1' H 2.316 . . 14 2 2 DC H2' H 4.832 . . 15 2 2 DC H2'' H 4.34 . . 16 2 2 DC H3' H 4.092 . . 17 2 2 DC H4' H 4.018 . . 18 2 2 DC H5' H 6.986 . . 19 2 2 DC H5'' H 8.732 . . 20 3 3 DA H62 H 8.248 . . 21 3 3 DA H61 H 5.808 . . 22 3 3 DA H8 H 2.757 . . 23 3 3 DA H2 H 2.837 . . 24 3 3 DA H1' H 5.045 . . 25 3 3 DA H2' H 4.368 . . 26 3 3 DA H2'' H 4.112 . . 27 3 3 DA H3' H 4.013 . . 28 4 4 DA H62 H 8.078 . . 29 4 4 DA H61 H 2.557 . . 30 4 4 DA H8 H 2.744 . . 31 4 4 DA H2 H 5.014 . . 32 4 4 DA H1' H 4.378 . . 33 4 4 DA H2' H 4.196 . . 34 5 5 DA H62 H 7.892 . . 35 5 5 DA H61 H 5.851 . . 36 5 5 DA H8 H 2.35 . . 37 5 5 DA H2 H 2.601 . . 38 5 5 DA H1' H 4.956 . . 39 5 5 DA H2' H 4.333 . . 40 5 5 DA H2'' H 4.204 . . 41 6 6 DG H8 H 7.504 . . 42 6 6 DG H22 H 5.689 . . 43 6 6 DG H21 H 4.979 . . 44 6 6 DG H1 H 4.502 . . 45 6 6 DG H1' H 4.129 . . 46 7 7 ORP H8 H 5.468 . . 47 7 7 ORP H6 H 2.221 . . 48 7 7 ORP H7 H 1.95 . . 49 7 7 ORP H5 H 4.515 . . 50 8 8 DA H62 H 8.146 . . 51 8 8 DA H61 H 6.219 . . 52 8 8 DA H8 H 2.792 . . 53 8 8 DA H2 H 2.887 . . 54 8 8 DA H1' H 4.929 . . 55 8 8 DA H2' H 4.494 . . 56 8 8 DA H2'' H 4.105 . . 57 8 8 DA H3' H 4.138 . . 58 9 9 DC H42 H 7.374 . . 59 9 9 DC H6 H 5.872 . . 60 9 9 DC H41 H 2.036 . . 61 9 9 DC H5 H 2.394 . . 62 9 9 DC H1' H 4.793 . . 63 9 9 DC H2' H 6.66 . . 64 9 9 DC H2'' H 8.114 . . 65 10 10 DC H42 H 7.412 . . 66 10 10 DC H6 H 5.553 . . 67 10 10 DC H41 H 5.51 . . 68 10 10 DC H5 H 1.931 . . 69 10 10 DC H1' H 2.276 . . 70 10 10 DC H2' H 4.805 . . 71 10 10 DC H2'' H 4.021 . . 72 10 10 DC H3' H 6.904 . . 73 10 10 DC H4' H 8.642 . . 74 11 11 DG H8 H 7.827 . . 75 11 11 DG H22 H 5.488 . . 76 11 11 DG H21 H 2.644 . . 77 11 11 DG H1 H 2.677 . . 78 11 11 DG H1' H 4.962 . . 79 11 11 DG H2' H 4.33 . . 80 11 11 DG H2'' H 4.041 . . 81 11 11 DG H3' H 3.929 . . 82 11 11 DG H4' H 13.263 . . 83 12 12 DG H8 H 7.738 . . 84 12 12 DG H22 H 5.772 . . 85 12 12 DG H21 H 2.592 . . 86 12 12 DG H1 H 2.742 . . 87 12 12 DG H1' H 4.987 . . 88 12 12 DG H2' H 4.38 . . 89 12 12 DG H2'' H 4.13 . . 90 12 12 DG H3' H 4.198 . . 91 12 12 DG H4' H 13.233 . . 92 13 13 DG H8 H 7.771 . . 93 13 13 DG H22 H 6.139 . . 94 13 13 DG H21 H 2.506 . . 95 13 13 DG H1 H 2.361 . . 96 13 13 DG H1' H 4.648 . . 97 13 13 DG H2' H 4.38 . . 98 13 13 DG H2'' H 4.203 . . 99 13 13 DG H3' H 4.127 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $FELIX stop_ loop_ _Experiment_label '2D NOESY' '2D TOCSY' "H3'-selective HSQC" watergate-NOESY stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 2nd_strand _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 14 1 DC H42 H 7.813 . . 2 14 1 DC H6 H 6 . . 3 14 1 DC H41 H 6.01 . . 4 14 1 DC H5 H 4.688 . . 5 14 1 DC H1' H 4.213 . . 6 14 1 DC H2' H 3.773 . . 7 14 1 DC H2'' H 3.811 . . 8 14 1 DC H3' H 7.132 . . 9 14 1 DC H4' H 7.975 . . 10 15 2 DC H42 H 7.643 . . 11 15 2 DC H6 H 5.711 . . 12 15 2 DC H41 H 6.003 . . 13 15 2 DC H5 H 4.869 . . 14 15 2 DC H1' H 4.061 . . 15 15 2 DC H2' H 6.934 . . 16 15 2 DC H2'' H 8.481 . . 17 16 3 DC H42 H 7.43 . . 18 16 3 DC H6 H 5.666 . . 19 16 3 DC H41 H 5.611 . . 20 16 3 DC H5 H 2.033 . . 21 16 3 DC H1' H 2.384 . . 22 16 3 DC H2' H 4.85 . . 23 16 3 DC H2'' H 4.084 . . 24 16 3 DC H3' H 4.117 . . 25 16 3 DC H4' H 6.986 . . 26 16 3 DC H5' H 8.646 . . 27 17 4 DG H8 H 7.858 . . 28 17 4 DG H22 H 5.666 . . 29 17 4 DG H21 H 4.994 . . 30 17 4 DG H1 H 13.138 . . 31 18 5 DG H8 H 7.655 . . 32 18 5 DG H22 H 5.915 . . 33 18 5 DG H21 H 2.474 . . 34 18 5 DG H1 H 2.632 . . 35 18 5 DG H1' H 4.916 . . 36 18 5 DG H2' H 4.368 . . 37 18 5 DG H2'' H 4.198 . . 38 18 5 DG H3' H 4.136 . . 39 18 5 DG H4' H 12.85 . . 40 19 6 DT H6 H 7.223 . . 41 19 6 DT H3 H 5.963 . . 42 19 6 DT H71 H 2.319 . . 43 19 6 DT H72 H 2.319 . . 44 19 6 DT H73 H 2.319 . . 45 19 6 DT H1' H 4.892 . . 46 19 6 DT H2' H 4.37 . . 47 19 6 DT H2'' H 4.099 . . 48 19 6 DT H3' H 4.145 . . 49 20 7 DC H42 H 7.757 . . 50 20 7 DC H6 H 5.807 . . 51 20 7 DC H41 H 6.172 . . 52 20 7 DC H5 H 2.271 . . 53 20 7 DC H1' H 2.516 . . 54 21 8 DC H42 H 7.893 . . 55 21 8 DC H6 H 5.949 . . 56 21 8 DC H41 H 6.023 . . 57 21 8 DC H5 H 2.068 . . 58 21 8 DC H1' H 2.522 . . 59 21 8 DC H2' H 4.741 . . 60 22 9 DT H6 H 7.594 . . 61 22 9 DT H3 H 6.036 . . 62 22 9 DT H71 H 2.273 . . 63 22 9 DT H72 H 2.273 . . 64 22 9 DT H73 H 2.273 . . 65 22 9 DT H1' H 2.59 . . 66 22 9 DT H2' H 4.901 . . 67 22 9 DT H2'' H 4.254 . . 68 22 9 DT H3' H 4.178 . . 69 22 9 DT H4' H 4.145 . . 70 22 9 DT H5' H 14.093 . . 71 23 10 DT H6 H 7.521 . . 72 23 10 DT H3 H 6.078 . . 73 23 10 DT H71 H 2.138 . . 74 23 10 DT H72 H 2.138 . . 75 23 10 DT H73 H 2.138 . . 76 23 10 DT H1' H 2.56 . . 77 23 10 DT H2' H 4.895 . . 78 23 10 DT H2'' H 4.264 . . 79 23 10 DT H3' H 4.173 . . 80 23 10 DT H4' H 4.185 . . 81 23 10 DT H5' H 14.097 . . 82 24 11 DT H6 H 7.357 . . 83 24 11 DT H3 H 5.721 . . 84 24 11 DT H71 H 1.971 . . 85 24 11 DT H72 H 1.971 . . 86 24 11 DT H73 H 1.971 . . 87 24 11 DT H1' H 2.299 . . 88 24 11 DT H2' H 4.861 . . 89 24 11 DT H2'' H 4.184 . . 90 24 11 DT H3' H 14.11 . . 91 25 12 DG H8 H 7.863 . . 92 25 12 DG H22 H 5.679 . . 93 25 12 DG H21 H 2.682 . . 94 25 12 DG H1 H 2.734 . . 95 25 12 DG H1' H 4.977 . . 96 25 12 DG H2' H 4.355 . . 97 25 12 DG H2'' H 4.206 . . 98 25 12 DG H3' H 12.996 . . 99 26 13 DG H8 H 7.813 . . 100 26 13 DG H22 H 6.151 . . 101 26 13 DG H21 H 2.506 . . 102 26 13 DG H1 H 2.361 . . 103 26 13 DG H1' H 4.647 . . 104 26 13 DG H2' H 4.211 . . 105 26 13 DG H2'' H 4.141 . . 106 26 13 DG H3' H 4.049 . . stop_ save_