data_30198 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position and 9th position ; _BMRB_accession_number 30198 _BMRB_flat_file_name bmr30198.str _Entry_type original _Submission_date 2016-10-26 _Accession_date 2016-10-26 _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 Hoppins J. J. . 2 Gruber D. R. . 3 Miears H. L. . 4 Kasymov R. D. . 5 Zharkov D. O. . 6 Smirnov S. L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 170 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-23 original BMRB . stop_ _Original_release_date 2016-11-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th position and 8-oxoguanine at the 4th position ; _Citation_status 'in preparation' _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 Hoppins J. J. . 2 Gruber D. R. . 3 Miears H. L. . 4 Kasymov R. D. . 5 Zharkov D. O. . 6 Smirnov S. L. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, chain 1' $entity_1 'entity_1, chain 2' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3')" _Molecular_mass 3693.419 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCXAATTXGCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DC 4 4 8OG 5 5 DA 6 6 DA 7 7 DT 8 8 DT 9 9 5CM 10 10 DG 11 11 DC 12 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_5CM _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE _BMRB_code 5CM _PDB_code 5CM _Standard_residue_derivative . _Molecular_mass 321.224 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C5A C5A C . 0 . ? C6 C6 C . 0 . ? O2 O2 O . 0 . ? N4 N4 N . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? O3' O3' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? H5A1 H5A1 H . 0 . ? H5A2 H5A2 H . 0 . ? H5A3 H5A3 H . 0 . ? H6 H6 H . 0 . ? HN41 HN41 H . 0 . ? HN42 HN42 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? HO3' HO3' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' 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 N1 C2 ? ? SING N1 C6 ? ? SING N1 C1' ? ? SING C2 N3 ? ? DOUB C2 O2 ? ? DOUB N3 C4 ? ? SING C4 C5 ? ? SING C4 N4 ? ? SING C5 C5A ? ? DOUB C5 C6 ? ? SING C5A H5A1 ? ? SING C5A H5A2 ? ? SING C5A H5A3 ? ? SING C6 H6 ? ? SING N4 HN41 ? ? SING N4 HN42 ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O3' HO3' ? ? SING C5' O5' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING O5' P ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING OP3 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 $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'), 100% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name AMBER _Version 12 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name NMRView _Version 9.0 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 500 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 500 _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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-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 'ionic strength' 120 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 120 . mM pH 6.8 . pH pressure 1 . atm temperature 274 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 4.768 internal direct . . . 1.0 stop_ save_ save_chem_shift_reference_2 _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 5.040 internal direct . . . 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_assigned_chemical_shifts_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, chain 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 1 DC H1' H 5.76493 . . 2 1 1 DC H2' H 1.96953 . . 3 1 1 DC H2'' H 2.40736 . . 4 1 1 DC H3' H 4.70072 . . 5 1 1 DC H5 H 5.92119 . . 6 1 1 DC H6 H 7.63251 . . 7 2 2 DG H1' H 5.88909 . . 8 2 2 DG H2' H 2.65046 . . 9 2 2 DG H2'' H 2.72252 . . 10 2 2 DG H3' H 4.96684 . . 11 2 2 DG H8 H 7.96021 . . 12 3 3 DC H1' H 6.0166 . . 13 3 3 DC H2' H 1.84534 . . 14 3 3 DC H2'' H 2.595 . . 15 3 3 DC H3' H 4.85751 . . 16 3 3 DC H5 H 5.39741 . . 17 3 3 DC H6 H 7.38215 . . 18 4 4 8OG H1' H 5.14408 . . 19 4 4 8OG H2' H 3.34432 . . 20 4 4 8OG H2'' H 2.38815 . . 21 4 4 8OG H3' H 4.85392 . . 22 5 5 DA H1' H 5.99607 . . 23 5 5 DA H2 H 7.23198 . . 24 5 5 DA H2' H 2.7002 . . 25 5 5 DA H2'' H 2.92828 . . 26 5 5 DA H3' H 5.06151 . . 27 5 5 DA H8 H 8.19956 . . 28 6 6 DA H1' H 6.16747 . . 29 6 6 DA H2 H 7.61197 . . 30 6 6 DA H2' H 2.56536 . . 31 6 6 DA H2'' H 2.93081 . . 32 6 6 DA H3' H 5.00414 . . 33 6 6 DA H8 H 8.13321 . . 34 7 7 DT H1' H 5.92019 . . 35 7 7 DT H2' H 1.98018 . . 36 7 7 DT H2'' H 2.55576 . . 37 7 7 DT H3' H 4.8352 . . 38 7 7 DT H6 H 7.10671 . . 39 7 7 DT H71 H 1.26667 . . 40 7 7 DT H72 H 1.26667 . . 41 7 7 DT H73 H 1.26667 . . 42 8 8 DT H1' H 6.1025 . . 43 8 8 DT H2' H 2.10332 . . 44 8 8 DT H2'' H 2.59877 . . 45 8 8 DT H3' H 4.89334 . . 46 8 8 DT H6 H 7.39713 . . 47 8 8 DT H71 H 1.52375 . . 48 8 8 DT H72 H 1.52375 . . 49 8 8 DT H73 H 1.52375 . . 50 9 9 5CM H1' H 5.65334 . . 51 9 9 5CM H2' H 2.03405 . . 52 9 9 5CM H2'' H 2.34513 . . 53 9 9 5CM H3' H 4.85602 . . 54 9 9 5CM H5A1 H 1.72909 . . 55 9 9 5CM H5A2 H 1.72909 . . 56 9 9 5CM H5A3 H 1.72909 . . 57 9 9 5CM H6 H 7.25068 . . 58 10 10 DG H1' H 5.83349 . . 59 10 10 DG H2' H 2.65983 . . 60 10 10 DG H3' H 4.96905 . . 61 10 10 DG H8 H 7.85825 . . 62 11 11 DC H1' H 5.76798 . . 63 11 11 DC H2' H 1.88219 . . 64 11 11 DC H2'' H 2.33298 . . 65 11 11 DC H3' H 4.79676 . . 66 11 11 DC H5 H 5.42977 . . 67 11 11 DC H6 H 7.31823 . . 68 12 12 DG H1' H 6.15658 . . 69 12 12 DG H2' H 2.60225 . . 70 12 12 DG H2'' H 2.36107 . . 71 12 12 DG H3' H 4.66706 . . 72 12 12 DG H8 H 7.93653 . . stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, chain 2' _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 DC H1' H 5.76493 . . 2 13 1 DC H2' H 1.96953 . . 3 13 1 DC H2'' H 2.40736 . . 4 13 1 DC H3' H 4.70072 . . 5 13 1 DC H5 H 5.92119 . . 6 13 1 DC H6 H 7.63251 . . 7 14 2 DG H1' H 5.88909 . . 8 14 2 DG H2' H 2.65046 . . 9 14 2 DG H2'' H 2.72252 . . 10 14 2 DG H3' H 4.96684 . . 11 14 2 DG H8 H 7.96021 . . 12 15 3 DC H1' H 6.0166 . . 13 15 3 DC H2' H 1.84534 . . 14 15 3 DC H2'' H 2.595 . . 15 15 3 DC H3' H 4.85751 . . 16 15 3 DC H5 H 5.39741 . . 17 15 3 DC H6 H 7.38215 . . 18 16 4 8OG H1' H 5.14408 . . 19 16 4 8OG H2' H 3.34432 . . 20 16 4 8OG H2'' H 2.38815 . . 21 16 4 8OG H3' H 4.85392 . . 22 17 5 DA H1' H 5.99607 . . 23 17 5 DA H2 H 7.23198 . . 24 17 5 DA H2' H 2.7002 . . 25 17 5 DA H2'' H 2.92828 . . 26 17 5 DA H3' H 5.06151 . . 27 17 5 DA H8 H 8.19956 . . 28 18 6 DA H1' H 6.16747 . . 29 18 6 DA H2 H 7.61197 . . 30 18 6 DA H2' H 2.56536 . . 31 18 6 DA H2'' H 2.93081 . . 32 18 6 DA H3' H 5.00414 . . 33 18 6 DA H8 H 8.13321 . . 34 19 7 DT H1' H 5.92019 . . 35 19 7 DT H2' H 1.98018 . . 36 19 7 DT H2'' H 2.55576 . . 37 19 7 DT H3' H 4.8352 . . 38 19 7 DT H6 H 7.10671 . . 39 19 7 DT H71 H 1.26667 . . 40 19 7 DT H72 H 1.26667 . . 41 19 7 DT H73 H 1.26667 . . 42 20 8 DT H1' H 6.1025 . . 43 20 8 DT H2' H 2.10332 . . 44 20 8 DT H2'' H 2.59877 . . 45 20 8 DT H3' H 4.89334 . . 46 20 8 DT H6 H 7.39713 . . 47 20 8 DT H71 H 1.52375 . . 48 20 8 DT H72 H 1.52375 . . 49 20 8 DT H73 H 1.52375 . . 50 21 9 5CM H1' H 5.65334 . . 51 21 9 5CM H2' H 2.03405 . . 52 21 9 5CM H2'' H 2.34513 . . 53 21 9 5CM H3' H 4.85602 . . 54 21 9 5CM H5A1 H 1.72909 . . 55 21 9 5CM H5A2 H 1.72909 . . 56 21 9 5CM H5A3 H 1.72909 . . 57 21 9 5CM H6 H 7.25068 . . 58 22 10 DG H1' H 5.83349 . . 59 22 10 DG H2' H 2.65983 . . 60 22 10 DG H3' H 4.96905 . . 61 22 10 DG H8 H 7.85825 . . 62 23 11 DC H1' H 5.76798 . . 63 23 11 DC H2' H 1.88219 . . 64 23 11 DC H2'' H 2.33298 . . 65 23 11 DC H3' H 4.79676 . . 66 23 11 DC H5 H 5.42977 . . 67 23 11 DC H6 H 7.31823 . . 68 24 12 DG H1' H 6.15658 . . 69 24 12 DG H2' H 2.60225 . . 70 24 12 DG H2'' H 2.36107 . . 71 24 12 DG H3' H 4.66706 . . 72 24 12 DG H8 H 7.93653 . . stop_ save_ save_assigned_chemical_shifts_2_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_2 _Mol_system_component_name 'entity_1, chain 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 2 2 DG H1 H 13.11577 0 . 2 3 3 DC H41 H 8.37884 0 . 3 3 3 DC H42 H 6.4348 0 . 4 4 4 8OG H1 H 12.96057 0 . 5 5 5 DA H2 H 7.14443 0 . 6 6 6 DA H2 H 7.58476 0 . 7 7 7 DT H3 H 13.83849 0 . 8 8 8 DT H3 H 13.7995 0 . 9 9 9 5CM HN41 H 8.60389 0 . 10 9 9 5CM HN42 H 6.56331 0 . 11 10 10 DG H1 H 12.815 0 . 12 11 11 DC H41 H 8.48851 0 . 13 11 11 DC H42 H 6.69043 0 . stop_ save_ save_assigned_chemical_shifts_2_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_2 _Mol_system_component_name 'entity_1, chain 2' _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 2 DG H1 H 13.11577 0 . 2 15 3 DC H41 H 8.37884 0 . 3 15 3 DC H42 H 6.4348 0 . 4 16 4 8OG H1 H 12.96057 0 . 5 17 5 DA H2 H 7.14443 0 . 6 18 6 DA H2 H 7.58476 0 . 7 19 7 DT H3 H 13.83849 0 . 8 20 8 DT H3 H 13.7995 0 . 9 21 9 5CM HN41 H 8.60389 0 . 10 21 9 5CM HN42 H 6.56331 0 . 11 22 10 DG H1 H 12.815 0 . 12 23 11 DC H41 H 8.48851 0 . 13 23 11 DC H42 H 6.69043 0 . stop_ save_