data_17562 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal ; _BMRB_accession_number 17562 _BMRB_flat_file_name bmr17562.str _Entry_type original _Submission_date 2011-03-31 _Accession_date 2011-03-31 _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 Huang Hai . . 2 Kozekov Ivan D. . 3 Wang Hao . . 4 Kozekova Albena . . 5 Rizzo Carmelo J. . 6 Stone Michael P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 150 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-04-02 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21916419 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang Hai . . 2 Wang Hao . . 3 Kozekova Albena . . 4 Rizzo Carmelo J. . 5 Stone Michael P. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 133 _Journal_issue 40 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 16101 _Page_last 16110 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')' $DNA_1 'DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')' $DNA_2 (2E,4R)-4-HYDROXYNON-2-ENAL $HNE 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 (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')' _Molecular_mass 3663.422 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GCTAGCGAGTCC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DT 4 DA 5 DG 6 DC 7 DG 8 DA 9 DG 10 DT 11 DC 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')' _Molecular_mass 3663.422 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GGACTCGCTAGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DG 2 14 DG 3 15 DA 4 16 DC 5 17 DT 6 18 DC 7 19 DG 8 20 DC 9 21 DT 10 22 DA 11 23 DG 12 24 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_HNE _Saveframe_category ligand _Mol_type non-polymer _Name_common "HNE ((2E,4R)-4-HYDROXYNON-2-ENAL)" _BMRB_code . _PDB_code HNE _Molecular_mass 156.224 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Apr 27 10:49:25 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? O10 O10 O . 0 . ? O11 O11 O . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5C1 H5C1 H . 0 . ? H5C2 H5C2 H . 0 . ? H10 H10 H . 0 . ? H6C1 H6C1 H . 0 . ? H6C2 H6C2 H . 0 . ? H7C1 H7C1 H . 0 . ? H7C2 H7C2 H . 0 . ? H8C1 H8C1 H . 0 . ? H8C2 H8C2 H . 0 . ? H9C1 H9C1 H . 0 . ? H9C2 H9C2 H . 0 . ? H9C3 H9C3 H . 0 . ? H1 H1 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 C1 C2 ? ? DOUB C1 O11 ? ? SING C1 H1 ? ? DOUB C2 C3 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O10 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 H5C1 ? ? SING C5 H5C2 ? ? SING C6 C7 ? ? SING C6 H6C1 ? ? SING C6 H6C2 ? ? SING C7 C8 ? ? SING C7 H7C1 ? ? SING C7 H7C2 ? ? SING C8 C9 ? ? SING C8 H8C1 ? ? SING C8 H8C2 ? ? SING C9 H9C1 ? ? SING C9 H9C2 ? ? SING C9 H9C3 ? ? SING O10 H10 ? ? 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 . . . . . . $DNA_2 . . . . . . 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' . . . . . $DNA_2 'chemical synthesis' . . . . . $HNE '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 1 mM 'natural abundance' $DNA_2 1 mM 'natural abundance' $HNE 1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.3 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 4.733 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_chem_shift_list_1_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(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-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 DG H1' H 5.912 . . 2 1 1 DG H2' H 2.560 . . 3 1 1 DG H2'' H 2.677 . 2 4 1 1 DG H3' H 4.736 . . 5 1 1 DG H5' H 3.628 . . 6 1 1 DG H8 H 7.885 . 1 7 2 2 DC H1' H 5.954 . . 8 2 2 DC H2' H 2.016 . . 9 2 2 DC H2'' H 2.409 . 2 10 2 2 DC H3' H 4.717 . . 11 2 2 DC H5 H 5.286 . 1 12 2 2 DC H6 H 7.433 . 1 13 3 3 DT H1' H 5.429 . . 14 3 3 DT H2' H 2.007 . . 15 3 3 DT H2'' H 2.282 . 2 16 3 3 DT H3' H 4.752 . . 17 3 3 DT H6 H 7.302 . 1 18 3 3 DT H71 H 1.566 . 1 19 3 3 DT H72 H 1.566 . 1 20 3 3 DT H73 H 1.566 . 1 21 4 4 DA H1' H 5.874 . . 22 4 4 DA H2' H 2.631 . . 23 4 4 DA H2'' H 2.735 . 2 24 4 4 DA H3' H 4.915 . . 25 4 4 DA H8 H 8.111 . 1 26 5 5 DG H1' H 5.489 . . 27 5 5 DG H2' H 2.346 . . 28 5 5 DG H3' H 4.802 . . 29 5 5 DG H8 H 7.577 . 1 30 6 6 DC H1' H 5.203 . . 31 6 6 DC H2' H 1.426 . . 32 6 6 DC H2'' H 1.534 . 2 33 6 6 DC H3' H 4.530 . . 34 6 6 DC H5 H 5.150 . 1 35 6 6 DC H6 H 7.097 . 1 36 7 7 DG H1' H 5.104 . . 37 7 7 DG H2' H 2.623 . . 38 7 7 DG H2'' H 2.690 . 2 39 7 7 DG H3' H 4.828 . . 40 7 7 DG H4' H 4.129 . . 41 7 7 DG H8 H 7.690 . 1 42 8 8 DA H1' H 6.024 . . 43 8 8 DA H2 H 7.513 . 1 44 8 8 DA H2' H 2.671 . . 45 8 8 DA H2'' H 2.838 . 2 46 8 8 DA H3' H 4.926 . . 47 8 8 DA H4' H 4.269 . . 48 8 8 DA H8 H 8.054 . 1 49 9 9 DG H1' H 5.636 . . 50 9 9 DG H2' H 2.342 . . 51 9 9 DG H2'' H 2.557 . 2 52 9 9 DG H3' H 4.757 . . 53 9 9 DG H4' H 4.211 . . 54 9 9 DG H8 H 7.421 . 1 55 10 10 DT H1' H 5.875 . . 56 10 10 DT H2' H 1.991 . . 57 10 10 DT H2'' H 2.377 . 2 58 10 10 DT H3' H 4.698 . . 59 10 10 DT H6 H 7.062 . 1 60 10 10 DT H71 H 1.135 . 1 61 10 10 DT H72 H 1.135 . 1 62 10 10 DT H73 H 1.135 . 1 63 11 11 DC H1' H 5.963 . . 64 11 11 DC H2' H 2.099 . . 65 11 11 DC H2'' H 2.379 . 2 66 11 11 DC H3' H 4.708 . . 67 11 11 DC H5 H 5.582 . 1 68 11 11 DC H6 H 7.481 . 1 69 12 12 DC H1' H 6.144 . . 70 12 12 DC H2' H 2.152 . . 71 12 12 DC H3' H 4.446 . . 72 12 12 DC H5 H 5.715 . 1 73 12 12 DC H6 H 7.581 . 1 stop_ save_ save_assigned_chem_shift_list_1_2 _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(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-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 13 1 DG H1' H 5.527 . . 2 13 1 DG H2' H 2.353 . . 3 13 1 DG H2'' H 2.541 . 2 4 13 1 DG H3' H 4.698 . . 5 13 1 DG H5' H 3.534 . . 6 13 1 DG H8 H 7.726 . 1 7 14 2 DG H1' H 5.461 . . 8 14 2 DG H2' H 2.575 . . 9 14 2 DG H2'' H 2.664 . 2 10 14 2 DG H3' H 4.903 . . 11 14 2 DG H8 H 7.740 . 1 12 15 3 DA H1' H 6.147 . . 13 15 3 DA H2 H 7.800 . 1 14 15 3 DA H2' H 2.606 . . 15 15 3 DA H2'' H 2.792 . 2 16 15 3 DA H3' H 4.941 . . 17 15 3 DA H8 H 8.108 . 1 18 16 4 DC H1' H 5.705 . . 19 16 4 DC H2' H 1.809 . . 20 16 4 DC H2'' H 2.310 . 2 21 16 4 DC H3' H 4.566 . . 22 16 4 DC H5 H 5.130 . 1 23 16 4 DC H6 H 7.190 . 1 24 17 5 DT H1' H 5.866 . . 25 17 5 DT H2' H 1.926 . . 26 17 5 DT H2'' H 2.104 . 2 27 17 5 DT H3' H 4.693 . . 28 17 5 DT H6 H 7.210 . 1 29 17 5 DT H71 H 1.377 . 1 30 17 5 DT H72 H 1.377 . 1 31 17 5 DT H73 H 1.377 . 1 32 18 6 DC H1' H 4.850 . . 33 18 6 DC H2' H 1.968 . . 34 18 6 DC H2'' H 2.057 . 2 35 18 6 DC H5 H 5.422 . 1 36 18 6 DC H6 H 7.329 . 1 37 19 7 DG H1' H 6.011 . . 38 19 7 DG H2' H 2.703 . . 39 19 7 DG H2'' H 2.741 . 2 40 19 7 DG H3' H 4.905 . . 41 19 7 DG H4' H 4.227 . . 42 19 7 DG H8 H 7.864 . 1 43 20 8 DC H1' H 5.949 . . 44 20 8 DC H2' H 2.029 . . 45 20 8 DC H2'' H 2.359 . 2 46 20 8 DC H3' H 4.745 . . 47 20 8 DC H4' H 4.107 . . 48 20 8 DC H5 H 5.400 . 1 49 20 8 DC H5' H 4.016 . . 50 20 8 DC H6 H 7.452 . 1 51 21 9 DT H1' H 5.365 . . 52 21 9 DT H2' H 1.937 . . 53 21 9 DT H2'' H 2.222 . 2 54 21 9 DT H3' H 4.709 . . 55 21 9 DT H6 H 7.209 . 1 56 21 9 DT H71 H 1.566 . 1 57 21 9 DT H72 H 1.566 . 1 58 21 9 DT H73 H 1.566 . 1 59 22 10 DA H1' H 5.898 . . 60 22 10 DA H2' H 2.615 . . 61 22 10 DA H2'' H 2.737 . 2 62 22 10 DA H3' H 4.904 . . 63 22 10 DA H8 H 8.109 . 1 64 23 11 DG H1' H 5.696 . . 65 23 11 DG H2' H 2.348 . . 66 23 11 DG H2'' H 2.517 . 2 67 23 11 DG H3' H 4.811 . . 68 23 11 DG H8 H 7.564 . 1 69 24 12 DC H1' H 6.024 . . 70 24 12 DC H2' H 1.992 . . 71 24 12 DC H2'' H 2.064 . 2 72 24 12 DC H3' H 4.341 . . 73 24 12 DC H5 H 5.283 . 1 74 24 12 DC H6 H 7.307 . 1 stop_ save_ save_assigned_chem_shift_list_1_3 _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 (2E,4R)-4-HYDROXYNON-2-ENAL _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 25 1 HNE H1 H 5.739 . . 2 25 1 HNE H3 H 3.474 . . 3 25 1 HNE H4 H 3.613 . . stop_ save_