data_19620 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of DNA duplex containing N3T-ethylene-N1I interstrand cross-link ; _BMRB_accession_number 19620 _BMRB_flat_file_name bmr19620.str _Entry_type original _Submission_date 2013-11-18 _Accession_date 2013-11-18 _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 O'Flaherty Derek K . 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" 116 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-12-01 update BMRB 'update sequence based on PDB 2MH6' 2014-09-30 update BMRB 'update entry citation' 2014-06-30 original author 'original release' stop_ _Original_release_date 2013-12-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR Structure of an Ethylene Interstrand Cross-Linked DNA which Mimics the Lesion Formed by 1,3-Bis(2-chloroethyl)-1-nitrosourea. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24931822 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 O'Flaherty Derek K. . 2 Denisov Alexey Y. . 3 Noronha Anne M. . 4 Wilds Christopher J. . stop_ _Journal_abbreviation ChemMedChem _Journal_name_full ChemMedChem _Journal_volume 9 _Journal_issue 9 _Journal_ISSN 1860-7187 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2099 _Page_last 2103 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA duplex containing N3T-ethylene-N1I' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3')" $DNA_(5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') "DNA (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3')" $DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*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*AP*GP*TP*TP*CP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') _Molecular_mass 2386.612 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; CAGTTCCA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DA 3 3 DG 4 4 DT 5 5 DT 6 6 DC 7 7 DC 8 8 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') _Molecular_mass 2467.646 _Mol_thiol_state 'not present' _Details . _Residue_count 8 _Mol_residue_sequence ; TGGAXCTG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DG 3 3 DG 4 4 DA 5 5 EDI 6 6 DC 7 7 DT 8 8 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_EDI _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 2'-deoxy-1-(2-iodoethyl)inosine _BMRB_code EDI _PDB_code EDI _Standard_residue_derivative . _Molecular_mass 486.156 _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 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C11 C11 C . 0 . ? C12 C12 C . 0 . ? OP3 OP3 O . 0 . ? H1 H1 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? H3 H3 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? H2 H2 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H15 H15 H . 0 . ? H14 H14 H . 0 . ? H5 H5 H . 0 . ? I1 I1 I . 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 DOUB OP1 P ? ? SING C5' C4' ? ? SING C5' O5' ? ? SING P O5' ? ? SING P OP2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING N3 C4 ? ? DOUB N3 C2 ? ? DOUB C4 C5 ? ? SING C2 N1 ? ? SING N7 C5 ? ? SING C5 C6 ? ? SING N1 C6 ? ? SING N1 C12 ? ? DOUB C6 O6 ? ? SING C12 C11 ? ? SING P OP3 ? ? SING OP2 H1 ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING O3' H3 ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' H1' ? ? SING C8 H8 ? ? SING C2 H2 ? ? SING C11 H11 ? ? SING C11 H12 ? ? SING C12 H15 ? ? SING C12 H14 ? ? SING OP3 H5 ? ? SING C11 I1 ? ? 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*AP*GP*TP*TP*CP*CP*A)-3') . . . . . . $DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*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 $DNA_(5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*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*AP*GP*TP*TP*CP*CP*A)-3') 0.5 mM 'natural abundance' $DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 0.5 mM 'natural abundance' NaCl 100 mM 'natural abundance' 'sodium phosphate' 15 mM 'natural abundance' D2O 100 % '[U-100% 2H]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3') 0.5 mM 'natural abundance' $DNA_(5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3') 0.5 mM 'natural abundance' NaCl 100 mM 'natural abundance' 'sodium phosphate' 15 mM 'natural abundance' D2O 10 % '[U-100% 2H]' 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 VNMRS _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 ; The enthane group of EDI has the following assignment: EHN H1 H 1 3.36 0.01 2 EHN H2 H 1 3.72 0.01 2 EHN H4 H 1 2.85 0.01 2 EHN H5 H 1 3.72 0.01 2 ; loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H 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 (5'-D(*CP*AP*GP*TP*TP*CP*CP*A)-3')" _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 5.53 0.01 1 2 1 1 DC H2' H 1.70 0.01 1 3 1 1 DC H2'' H 2.22 0.01 1 4 1 1 DC H3' H 4.59 0.01 1 5 1 1 DC H4' H 3.95 0.01 1 6 1 1 DC H5 H 5.85 0.01 1 7 1 1 DC H6 H 7.56 0.01 1 8 2 2 DA H1' H 5.93 0.01 1 9 2 2 DA H2 H 7.70 0.01 1 10 2 2 DA H2' H 2.70 0.01 1 11 2 2 DA H2'' H 2.78 0.01 1 12 2 2 DA H3' H 4.94 0.01 1 13 2 2 DA H4' H 4.29 0.01 1 14 2 2 DA H8 H 8.18 0.01 1 15 3 3 DG H1' H 5.79 0.01 1 16 3 3 DG H2' H 2.34 0.01 1 17 3 3 DG H2'' H 2.58 0.01 1 18 3 3 DG H3' H 4.79 0.01 1 19 3 3 DG H4' H 4.28 0.01 1 20 3 3 DG H8 H 7.59 0.01 1 21 4 4 DT H1' H 5.97 0.01 1 22 4 4 DT H2' H 1.95 0.01 1 23 4 4 DT H2'' H 2.42 0.01 1 24 4 4 DT H3' H 4.69 0.01 1 25 4 4 DT H4' H 4.14 0.01 1 26 4 4 DT H6 H 7.22 0.01 1 27 4 4 DT H71 H 1.38 0.01 1 28 4 4 DT H72 H 1.38 0.01 1 29 4 4 DT H73 H 1.38 0.01 1 30 5 5 DT H1' H 6.02 0.01 1 31 5 5 DT H2' H 2.14 0.01 1 32 5 5 DT H2'' H 2.45 0.01 1 33 5 5 DT H3' H 4.81 0.01 1 34 5 5 DT H4' H 4.15 0.01 1 35 5 5 DT H6 H 7.45 0.01 1 36 5 5 DT H71 H 1.52 0.01 1 37 5 5 DT H72 H 1.52 0.01 1 38 5 5 DT H73 H 1.52 0.01 1 39 6 6 DC H1' H 5.84 0.01 1 40 6 6 DC H2' H 2.01 0.01 1 41 6 6 DC H2'' H 2.29 0.01 1 42 6 6 DC H3' H 4.72 0.01 1 43 6 6 DC H4' H 4.06 0.01 1 44 6 6 DC H5 H 5.63 0.01 1 45 6 6 DC H6 H 7.49 0.01 1 46 7 7 DC H1' H 5.71 0.01 1 47 7 7 DC H2' H 1.95 0.01 1 48 7 7 DC H2'' H 2.21 0.01 1 49 7 7 DC H3' H 4.71 0.01 1 50 7 7 DC H4' H 3.98 0.01 1 51 7 7 DC H5 H 5.66 0.01 1 52 7 7 DC H6 H 7.41 0.01 1 53 8 8 DA H1' H 6.25 0.01 1 54 8 8 DA H2 H 7.76 0.01 1 55 8 8 DA H2' H 2.61 0.01 1 56 8 8 DA H2'' H 2.39 0.01 1 57 8 8 DA H3' H 4.61 0.01 1 58 8 8 DA H4' H 4.10 0.01 1 59 8 8 DA H8 H 8.19 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details ; The enthane group of EDI has the following assignment: EHN H1 H 1 3.36 0.01 2 EHN H2 H 1 3.72 0.01 2 EHN H4 H 1 2.85 0.01 2 EHN H5 H 1 3.72 0.01 2 ; loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H 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 (5'-D(*TP*GP*GP*AP*IP*CP*TP*G)-3')" _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 9 1 DT H1' H 5.74 0.01 1 2 9 1 DT H2' H 1.61 0.01 1 3 9 1 DT H2'' H 2.07 0.01 1 4 9 1 DT H3' H 4.49 0.01 1 5 9 1 DT H4' H 3.90 0.01 1 6 9 1 DT H6 H 7.24 0.01 1 7 9 1 DT H71 H 1.50 0.01 1 8 9 1 DT H72 H 1.50 0.01 1 9 9 1 DT H73 H 1.50 0.01 1 10 10 2 DG H1' H 5.37 0.01 1 11 10 2 DG H2' H 2.62 0.01 1 12 10 2 DG H2'' H 2.64 0.01 1 13 10 2 DG H3' H 4.85 0.01 1 14 10 2 DG H4' H 4.20 0.01 1 15 10 2 DG H8 H 7.83 0.01 1 16 11 3 DG H1' H 5.39 0.01 1 17 11 3 DG H2' H 2.49 0.01 1 18 11 3 DG H2'' H 2.56 0.01 1 19 11 3 DG H3' H 4.90 0.01 1 20 11 3 DG H4' H 4.24 0.01 1 21 11 3 DG H8 H 7.70 0.01 1 22 12 4 DA H1' H 5.67 0.01 1 23 12 4 DA H2 H 7.58 0.01 1 24 12 4 DA H2' H 2.51 0.01 1 25 12 4 DA H2'' H 2.65 0.01 1 26 12 4 DA H3' H 4.96 0.01 1 27 12 4 DA H4' H 4.29 0.01 1 28 12 4 DA H8 H 8.08 0.01 1 29 13 5 EDI H1' H 6.12 0.01 1 30 13 5 EDI H2 H 7.74 0.01 1 31 13 5 EDI H2' H 2.68 0.01 1 32 13 5 EDI H2'' H 2.81 0.01 1 33 13 5 EDI H3' H 4.95 0.01 1 34 13 5 EDI H4' H 4.40 0.01 1 35 13 5 EDI H8 H 8.26 0.01 1 36 14 6 DC H1' H 5.68 0.01 1 37 14 6 DC H2' H 1.78 0.01 1 38 14 6 DC H2'' H 2.35 0.01 1 39 14 6 DC H3' H 4.59 0.01 1 40 14 6 DC H4' H 4.08 0.01 1 41 14 6 DC H5 H 5.02 0.01 1 42 14 6 DC H6 H 7.07 0.01 1 43 15 7 DT H1' H 5.78 0.01 1 44 15 7 DT H2' H 1.94 0.01 1 45 15 7 DT H2'' H 2.30 0.01 1 46 15 7 DT H3' H 4.78 0.01 1 47 15 7 DT H4' H 4.05 0.01 1 48 15 7 DT H6 H 7.28 0.01 1 49 15 7 DT H71 H 1.51 0.01 1 50 15 7 DT H72 H 1.51 0.01 1 51 15 7 DT H73 H 1.51 0.01 1 52 16 8 DG H1' H 6.08 0.01 1 53 16 8 DG H2' H 2.54 0.01 1 54 16 8 DG H2'' H 2.28 0.01 1 55 16 8 DG H3' H 4.60 0.01 1 56 16 8 DG H4' H 4.09 0.01 1 57 16 8 DG H8 H 7.84 0.01 1 stop_ save_