data_18199 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Structure of a Thymine bulge. ; _BMRB_accession_number 18199 _BMRB_flat_file_name bmr18199.str _Entry_type original _Submission_date 2012-01-23 _Accession_date 2012-01-23 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'NMR structure of a d(GGCCGCAGTGCC)sequence' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Morrow Janet R. . 2 Fountain Matthew A. . 3 'del Mundo' 'Imee Marie' A . 4 Siter Kevin E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-05-10 update BMRB 'update entry citation' 2012-05-08 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22507054 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'Del Mundo' 'Imee Marie A' . . 2 Siters Kevin E. . 3 Fountain Matthew A. . 4 Morrow Janet R. . stop_ _Journal_abbreviation 'Inorg. Chem.' _Journal_name_full 'Inorganic chemistry' _Journal_volume 51 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5444 _Page_last 5457 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DNA_1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_1 $DNA_1 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_1 _Molecular_mass 3664.409 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GGCCGCAGTGCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DC 4 4 DC 5 5 DG 6 6 DC 7 7 DA 8 8 DG 9 9 DT 10 10 DG 11 11 DC 12 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_1 . . . . . . 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.1M NaCl 0.02M HEPES Buffer pD(7.9)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_1 1.8 mM 'natural abundance' D2O 100 % 'natural abundance' NaCl 0.1 M 'natural abundance' HEPES 0.02 M 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.1M NaCl 0.02M HEPES Buffer pD(7.9)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_1 1.8 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' NaCl 0.1 M 'natural abundance' HEPES 0.02 M 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.14 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 273 . K pD 7.9 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 288 . K pD 7.9 . pH pressure 1 . atm 'ionic strength' 0.1 . M 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 4.80 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 DQF-COSY' '2D 1H-1H TOCSY' '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_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 6.135 . . 2 2 2 DG H2' H 2.749 . . 3 2 2 DG H2'' H 2.921 . . 4 2 2 DG H8 H 8.095 . . 5 3 3 DC H1' H 6.45 . . 6 3 3 DC H2' H 2.15 . . 7 3 3 DC H2'' H 2.394 . . 8 3 3 DC H5 H 5.693 . . 9 3 3 DC H6 H 7.753 . . 10 4 4 DC H1' H 6.287 . . 11 4 4 DC H2' H 1.84 . . 12 4 4 DC H2'' H 2.417 . . 13 4 4 DC H5 H 5.873 . . 14 4 4 DC H6 H 7.544 . . 15 5 5 DG H1' H 5.945 . . 16 5 5 DG H2' H 2.836 . . 17 5 5 DG H2'' H 2.647 . . 18 5 5 DG H3' H 5.024 . . 19 5 5 DG H8 H 8.29 . . 20 6 6 DC H1' H 5.875 . . 21 6 6 DC H2' H 1.657 . . 22 6 6 DC H2'' H 2.225 . . 23 6 6 DC H5 H 5.423 . . 24 6 6 DC H6 H 7.405 . . 25 7 7 DA H8 H 7.915 . . 26 8 8 DG H1' H 5.39 . . 27 8 8 DG H2' H 2.21 . . 28 8 8 DG H2'' H 2.723 . . 29 8 8 DG H3' H 5.099 . . 30 8 8 DG H8 H 8.079 . . 31 9 9 DT H1' H 6.724 . . 32 9 9 DT H2' H 2.563 . . 33 9 9 DT H2'' H 2.482 . . 34 9 9 DT H3' H 5.222 . . 35 9 9 DT H6 H 8.018 . . 36 9 9 DT H71 H 2.232 . . 37 9 9 DT H72 H 2.232 . . 38 9 9 DT H73 H 2.232 . . 39 10 10 DG H1' H 6.273 . . 40 10 10 DG H2' H 2.236 . . 41 10 10 DG H2'' H 2.313 . . 42 10 10 DG H3' H 4.562 . . 43 10 10 DG H8 H 7.652 . . 44 11 11 DC H1' H 5.726 . . 45 11 11 DC H2' H 2.406 . . 46 11 11 DC H2'' H 2.594 . . 47 11 11 DC H5 H 5.328 . . 48 11 11 DC H6 H 7.656 . . stop_ save_