data_19917 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of DNA dodecamer containing the 5-hydroxycytosine ; _BMRB_accession_number 19917 _BMRB_flat_file_name bmr19917.str _Entry_type original _Submission_date 2014-04-17 _Accession_date 2014-04-17 _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 Donahue Patrick S. . 2 Szulik Marta W. . 3 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 70 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-08 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 19925 'DNA dodecamer with A:C mismatch' stop_ _Original_release_date 2014-05-23 save_ ############################# # Citation for this entry # ############################# save_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Characterization of 5-hydroxycytosine in DNA ; _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 Szulik Marta . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _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 dodecamer containing the 5-hydroxycytosine' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_1" $DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') "DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_2" $DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-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(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') _Molecular_mass 3355.223 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCGAATTXGCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DC 4 4 DG 5 5 DA 6 6 DA 7 7 DT 8 8 DT 9 9 5OC 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_5OC _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common "2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate)" _BMRB_code 5OC _PDB_code 5OC _Standard_residue_derivative . _Molecular_mass 323.197 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? O5 O5 O . 0 . ? C6 C6 C . 0 . ? C1' C1' C . 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 . ? OP1 OP1 O . 0 . ? OP3 OP3 O . 0 . ? HN4 HN4 H . 0 . ? HN4A HN4A H . 0 . ? H6 H6 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H2'A H2'A H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'A H5'A H . 0 . ? HOP1 HOP1 H . 0 . ? OP2 OP2 O . 0 . ? H13 H13 H . 0 . ? HOP2 HOP2 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 P O5' ? ? DOUB P OP3 ? ? SING N1 C6 ? ? SING N1 C2 ? ? SING C2 N3 ? ? DOUB O2 C2 ? ? DOUB N3 C4 ? ? SING C4 N4 ? ? SING N4 HN4 ? ? SING N4 HN4A ? ? SING C5 C4 ? ? SING C5 O5 ? ? DOUB C6 C5 ? ? SING C6 H6 ? ? SING C1' N1 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING C2' H2' ? ? SING C2' H2'A ? ? SING C3' C2' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING O4' C4' ? ? SING C5' C4' ? ? SING C5' O5' ? ? SING C5' H5' ? ? SING C5' H5'A ? ? SING OP1 P ? ? SING OP1 HOP1 ? ? SING P OP2 ? ? SING O5 H13 ? ? SING OP2 HOP2 ? ? stop_ 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(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') Human 9606 Eukaryota Metazoa Homo sapiens 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(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-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(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3') 100 mM 'natural abundance' D2O 10 % 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium azide' 11 mM 'natural abundance' EDTA 0.05 mM 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details 0.1 save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model INOVA _Field_strength 900 _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 pH 7 . pH pressure 1 . atm temperature 288 . 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 water H 1 protons ppm 4.7 na direct . . . 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' 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(*CP*GP*CP*GP*AP*AP*TP*TP*(OHC)P*GP*CP*G)-3')_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 5.810 . 1 2 1 1 DC H2' H 2.024 . 1 3 1 1 DC H2'' H 2.462 . 1 4 1 1 DC H3' H 4.756 . 1 5 1 1 DC H5 H 5.964 . 1 6 1 1 DC H6 H 7.678 . 1 7 2 2 DG H1' H 5.916 . 1 8 2 2 DG H2' H 2.712 . 1 9 2 2 DG H2'' H 2.763 . 1 10 2 2 DG H3' H 5.021 . 1 11 2 2 DG H8 H 8.004 . 1 12 3 3 DC H1' H 5.719 . 1 13 3 3 DC H2' H 1.880 . 1 14 3 3 DC H2'' H 2.335 . 1 15 3 3 DC H5 H 5.434 . 1 16 3 3 DC H6 H 7.302 . 1 17 4 4 DG H1' H 5.278 . 1 18 4 4 DG H2' H 2.695 . 1 19 4 4 DG H2'' H 2.736 . 1 20 4 4 DG H3' H 5.023 . 1 21 4 4 DG H8 H 7.896 . 1 22 5 5 DA H1' H 6.054 . 1 23 5 5 DA H2 H 7.440 . 1 24 5 5 DA H2' H 2.806 . 1 25 5 5 DA H2'' H 3.001 . 1 26 5 5 DA H3' H 5.131 . 1 27 5 5 DA H8 H 8.211 . 1 28 6 6 DA H1' H 6.208 . 1 29 6 6 DA H2 H 7.616 . 1 30 6 6 DA H2' H 2.970 . 1 31 6 6 DA H2'' H 2.632 . 1 32 6 6 DA H3' H 5.064 . 1 33 6 6 DA H8 H 8.187 . 1 34 7 7 DT H1' H 5.938 . 1 35 7 7 DT H2' H 2.590 . 1 36 7 7 DT H2'' H 1.991 . 1 37 7 7 DT H6 H 7.161 . 1 38 7 7 DT H71 H 1.337 . 1 39 7 7 DT H72 H 1.337 . 1 40 7 7 DT H73 H 1.337 . 1 41 8 8 DT H1' H 6.111 . 1 42 8 8 DT H2' H 2.168 . 1 43 8 8 DT H2'' H 2.631 . 1 44 8 8 DT H3' H 4.949 . 1 45 8 8 DT H6 H 7.322 . 1 46 8 8 DT H71 H 1.582 . 1 47 8 8 DT H72 H 1.582 . 1 48 8 8 DT H73 H 1.582 . 1 49 9 9 5OC H1' H 5.572 . 1 50 9 9 5OC H2' H 2.163 . 1 51 9 9 5OC H2'' H 2.385 . 1 52 9 9 5OC H6 H 6.656 . 1 53 10 10 DG H1' H 5.933 . 1 54 10 10 DG H2' H 2.704 . 1 55 10 10 DG H2'' H 2.768 . 1 56 10 10 DG H3' H 5.046 . 1 57 10 10 DG H4' H 4.438 . 1 58 10 10 DG H5' H 4.172 . 1 59 10 10 DG H5'' H 4.094 . 1 60 10 10 DG H8 H 7.954 . 1 61 11 11 DC H1' H 5.797 . 1 62 11 11 DC H2' H 1.960 . 1 63 11 11 DC H2'' H 2.385 . 1 64 11 11 DC H5 H 5.503 . 1 65 11 11 DC H6 H 7.376 . 1 66 12 12 DG H1' H 6.207 . 1 67 12 12 DG H2' H 2.680 . 1 68 12 12 DG H2'' H 2.424 . 1 69 12 12 DG H3' H 4.731 . 1 70 12 12 DG H8 H 7.996 . 1 stop_ save_