data_18780 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link ; _BMRB_accession_number 18780 _BMRB_flat_file_name bmr18780.str _Entry_type original _Submission_date 2012-10-11 _Accession_date 2012-10-11 _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 Denisov Alexey Y. . 2 McManus Francis P. . 3 Noronha Anne M. . 4 Wilds Christopher J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 89 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-10-14 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18781 'DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link' stop_ _Original_release_date 2013-10-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structures of DNA duplexes containing mispair-aligned O4U-heptylene-O4U and O6G-heptylene-O6G interstrand cross-links' _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 Denisov Alexey Y. . 2 McManus Francis P. . 3 O'Flaherty Derek K . 4 Noronha Anne M. . 5 Wilds Christopher J. . stop_ _Journal_abbreviation Biochemistry _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 duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_1 $DNA_1 DNA_2 $DNA_1 entity_HP6 $entity_HP6 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 3334.210 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence CGAAAUTTTCG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DA 4 4 DA 5 5 DA 6 6 DU 7 7 DT 8 8 DT 9 9 DT 10 10 DC 11 11 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_HP6 _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common HEPTANE _BMRB_code HP6 _PDB_code HP6 _Molecular_mass 100.202 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C20 C20 C . 0 . ? C21 C21 C . 0 . ? C22 C22 C . 0 . ? C23 C23 C . 0 . ? C24 C24 C . 0 . ? C25 C25 C . 0 . ? C26 C26 C . 0 . ? H201 H201 H . 0 . ? H202 H202 H . 0 . ? H203 H203 H . 0 . ? H211 H211 H . 0 . ? H212 H212 H . 0 . ? H221 H221 H . 0 . ? H222 H222 H . 0 . ? H231 H231 H . 0 . ? H232 H232 H . 0 . ? H241 H241 H . 0 . ? H242 H242 H . 0 . ? H251 H251 H . 0 . ? H252 H252 H . 0 . ? H261 H261 H . 0 . ? H262 H262 H . 0 . ? H263 H263 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 C20 C21 ? ? SING C20 H201 ? ? SING C20 H202 ? ? SING C20 H203 ? ? SING C21 C22 ? ? SING C21 H211 ? ? SING C21 H212 ? ? SING C22 C23 ? ? SING C22 H221 ? ? SING C22 H222 ? ? SING C23 C24 ? ? SING C23 H231 ? ? SING C23 H232 ? ? SING C24 C25 ? ? SING C24 H241 ? ? SING C24 H242 ? ? SING C25 C26 ? ? SING C25 H251 ? ? SING C25 H252 ? ? SING C26 H261 ? ? SING C26 H262 ? ? SING C26 H263 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_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 . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_1 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_1 0.5 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_NMRPipe _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_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Inova' _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Inova' _Field_strength 800 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 500 _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_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_1 save_ save_2D_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 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' 0.1 . M pH 7.5 . 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' 0.1 . M pH 7.5 . pH pressure 1 . atm temperature 273 . 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_ _Experiment_label '2D NOESY' '2D TOCSY' '2D DQF-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_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 5.60 0.01 1 2 1 1 DC H2' H 1.68 0.01 1 3 1 1 DC H2'' H 2.20 0.01 1 4 1 1 DC H3' H 4.55 0.01 1 5 1 1 DC H4' H 3.93 0.01 1 6 1 1 DC H5 H 5.80 0.01 1 7 1 1 DC H6 H 7.48 0.01 1 8 2 2 DG H1' H 5.17 0.01 1 9 2 2 DG H2' H 2.53 0.01 1 10 2 2 DG H2'' H 2.57 0.01 1 11 2 2 DG H3' H 4.85 0.01 1 12 2 2 DG H4' H 4.14 0.01 1 13 2 2 DG H8 H 7.81 0.01 1 14 3 3 DA H1' H 5.77 0.01 1 15 3 3 DA H2 H 7.29 0.01 1 16 3 3 DA H2' H 2.57 0.01 1 17 3 3 DA H2'' H 2.73 0.01 1 18 3 3 DA H3' H 4.95 0.01 1 19 3 3 DA H4' H 4.30 0.01 1 20 3 3 DA H8 H 8.04 0.01 1 21 4 4 DA H1' H 5.80 0.01 1 22 4 4 DA H2 H 7.25 0.01 1 23 4 4 DA H2' H 2.40 0.01 1 24 4 4 DA H2'' H 2.64 0.01 1 25 4 4 DA H3' H 4.91 0.01 1 26 4 4 DA H4' H 4.28 0.01 1 27 4 4 DA H8 H 7.90 0.01 1 28 5 5 DA H1' H 5.85 0.01 1 29 5 5 DA H2 H 7.55 0.01 1 30 5 5 DA H2' H 2.37 0.01 1 31 5 5 DA H2'' H 2.48 0.01 1 32 5 5 DA H3' H 4.83 0.01 1 33 5 5 DA H4' H 4.26 0.01 1 34 5 5 DA H8 H 7.82 0.01 1 35 6 6 DU H1' H 5.64 0.01 1 36 6 6 DU H2' H 2.06 0.01 1 37 6 6 DU H2'' H 2.40 0.01 1 38 6 6 DU H3' H 4.68 0.01 1 39 6 6 DU H4' H 4.13 0.01 1 40 6 6 DU H5 H 5.24 0.01 1 41 6 6 DU H6 H 7.36 0.01 1 42 7 7 DT H1' H 5.99 0.01 1 43 7 7 DT H2' H 2.11 0.01 1 44 7 7 DT H2'' H 2.46 0.01 1 45 7 7 DT H3' H 4.74 0.01 1 46 7 7 DT H4' H 4.16 0.01 1 47 7 7 DT H6 H 7.33 0.01 1 48 7 7 DT H71 H 1.40 0.01 1 49 7 7 DT H72 H 1.40 0.01 1 50 7 7 DT H73 H 1.40 0.01 1 51 8 8 DT H1' H 6.08 0.01 1 52 8 8 DT H2' H 2.15 0.01 1 53 8 8 DT H2'' H 2.54 0.01 1 54 8 8 DT H3' H 4.80 0.01 1 55 8 8 DT H4' H 4.15 0.01 1 56 8 8 DT H6 H 7.46 0.01 1 57 8 8 DT H71 H 1.56 0.01 1 58 8 8 DT H72 H 1.56 0.01 1 59 8 8 DT H73 H 1.56 0.01 1 60 9 9 DT H1' H 6.01 0.01 1 61 9 9 DT H2' H 2.06 0.01 1 62 9 9 DT H2'' H 2.43 0.01 1 63 9 9 DT H3' H 4.80 0.01 1 64 9 9 DT H4' H 4.10 0.01 1 65 9 9 DT H6 H 7.38 0.01 1 66 9 9 DT H71 H 1.60 0.01 1 67 9 9 DT H72 H 1.60 0.01 1 68 9 9 DT H73 H 1.60 0.01 1 69 10 10 DC H1' H 5.58 0.01 1 70 10 10 DC H2' H 1.92 0.01 1 71 10 10 DC H2'' H 2.24 0.01 1 72 10 10 DC H3' H 4.74 0.01 1 73 10 10 DC H4' H 4.04 0.01 1 74 10 10 DC H5 H 5.65 0.01 1 75 10 10 DC H6 H 7.43 0.01 1 76 11 11 DG H1' H 6.06 0.01 1 77 11 11 DG H2' H 2.51 0.01 1 78 11 11 DG H2'' H 2.27 0.01 1 79 11 11 DG H3' H 4.58 0.01 1 80 11 11 DG H4' H 4.07 0.01 1 81 11 11 DG H8 H 7.86 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' '2D DQF-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 entity_HP6 _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 1 101 1 HP6 H201 H 3.47 0.01 1 2 101 1 HP6 H202 H 3.62 0.01 1 3 101 1 HP6 H211 H 1.18 0.01 1 4 101 1 HP6 H212 H 1.18 0.01 1 5 101 1 HP6 H221 H 0.86 0.01 1 6 101 1 HP6 H222 H 0.86 0.01 1 7 101 1 HP6 H231 H 0.95 0.01 1 8 101 1 HP6 H232 H 0.95 0.01 1 stop_ save_