data_17791 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT ; _BMRB_accession_number 17791 _BMRB_flat_file_name bmr17791.str _Entry_type original _Submission_date 2011-07-19 _Accession_date 2011-07-19 _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 Wang Hao . . 3 Kozekova Albena . . 4 LLoyd R. S. . 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" 141 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-08-30 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 17786 (5'S)-8,5'-cyclo-2'-deoxyguanosine 17787 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17788 'gamma-hydroxy-1,N2-propano-2'-deoxyguanosine adduct' 17789 (5'S)-8,5'-cyclo-2'-deoxyadenosine 17790 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' stop_ _Original_release_date 2012-08-30 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex' _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 Huang Hai . . 2 Wang Hao . . 3 Kozekova Albena . . 4 LLoyd R. S. . 5 Rizzo Carmelo J. . 6 Stone Michael P. . 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 '(6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct' _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_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') $DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') HNE $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_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') _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_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') _Molecular_mass 3678.433 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GGACTTGCTAGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DA 4 DC 5 DT 6 DT 7 DG 8 DC 9 DT 10 DA 11 DG 12 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 156.222 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Aug 4 15:36:21 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 . _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_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') . . . . . . $DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-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(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 'chemical synthesis' . . . . . $DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') '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_(5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 1 mM 'natural abundance' $DNA_(5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') 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 . 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 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 'ionic strength' 100 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . 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 4.773 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 6.052 . . 2 1 1 DG H2' H 2.711 . . 3 1 1 DG H2'' H 2.830 . 2 4 1 1 DG H3' H 4.886 . . 5 1 1 DG H8 H 8.020 . 1 6 2 2 DC H1' H 6.102 . . 7 2 2 DC H2' H 2.165 . . 8 2 2 DC H2'' H 2.554 . 2 9 2 2 DC H3' H 4.867 . . 10 2 2 DC H5 H 5.433 . 1 11 2 2 DC H6 H 7.574 . 1 12 3 3 DT H1' H 5.593 . . 13 3 3 DT H2' H 2.158 . . 14 3 3 DT H2'' H 2.435 . 2 15 3 3 DT H3' H 4.897 . . 16 3 3 DT H6 H 7.441 . 1 17 3 3 DT H71 H 1.713 . 1 18 3 3 DT H72 H 1.713 . 1 19 3 3 DT H73 H 1.713 . 1 20 4 4 DA H1' H 6.083 . . 21 4 4 DA H3' H 5.091 . . 22 4 4 DA H8 H 8.256 . 1 23 5 5 DG H1' H 5.676 . . 24 5 5 DG H2' H 2.525 . . 25 5 5 DG H2'' H 2.588 . 2 26 5 5 DG H3' H 4.990 . . 27 5 5 DG H8 H 7.727 . 1 28 6 6 DC H1' H 5.892 . . 29 6 6 DC H2' H 1.840 . . 30 6 6 DC H2'' H 2.206 . 2 31 6 6 DC H5 H 5.345 . 1 32 6 6 DC H6 H 7.269 . 1 33 7 7 DG H1' H 5.478 . . 34 7 7 DG H2' H 2.430 . . 35 7 7 DG H2'' H 2.569 . 2 36 7 7 DG H3' H 4.940 . . 37 7 7 DG H8 H 7.797 . 1 38 8 8 DA H1' H 5.999 . . 39 8 8 DA H2 H 7.611 . 1 40 8 8 DA H2' H 2.747 . . 41 8 8 DA H2'' H 2.828 . 2 42 8 8 DA H3' H 5.044 . . 43 8 8 DA H8 H 8.178 . 1 44 9 9 DG H1' H 5.966 . . 45 9 9 DG H2' H 2.553 . . 46 9 9 DG H2'' H 2.749 . 2 47 9 9 DG H3' H 4.899 . . 48 9 9 DG H8 H 7.633 . 1 49 10 10 DT H1' H 6.149 . . 50 10 10 DT H2' H 2.224 . . 51 10 10 DT H2'' H 2.588 . 2 52 10 10 DT H6 H 7.344 . 1 53 10 10 DT H71 H 1.287 . 1 54 10 10 DT H72 H 1.287 . 1 55 10 10 DT H73 H 1.287 . 1 56 11 11 DC H1' H 6.132 . . 57 11 11 DC H2' H 2.272 . . 58 11 11 DC H2'' H 2.538 . 2 59 11 11 DC H3' H 4.881 . . 60 11 11 DC H5 H 5.764 . 1 61 12 12 DC H1' H 6.298 . . 62 12 12 DC H2' H 2.318 . . 63 12 12 DC H3' H 4.605 . . 64 12 12 DC H5 H 5.868 . 1 65 12 12 DC H6 H 7.730 . 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*TP*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 5.678 . . 2 13 1 DG H2' H 2.506 . . 3 13 1 DG H2'' H 2.690 . 2 4 13 1 DG H3' H 4.845 . . 5 13 1 DG H8 H 7.864 . 1 6 14 2 DG H1' H 5.573 . . 7 14 2 DG H2' H 2.718 . . 8 14 2 DG H2'' H 2.809 . 2 9 14 2 DG H3' H 5.051 . . 10 14 2 DG H8 H 7.879 . 1 11 15 3 DA H1' H 6.325 . . 12 15 3 DA H2 H 7.992 . 1 13 15 3 DA H2' H 2.758 . . 14 15 3 DA H2'' H 2.958 . 2 15 15 3 DA H3' H 5.100 . . 16 15 3 DA H8 H 8.239 . 1 17 16 4 DC H1' H 5.892 . . 18 16 4 DC H2' H 1.953 . . 19 16 4 DC H5 H 5.262 . 1 20 16 4 DC H6 H 7.296 . 1 21 17 5 DT H1' H 6.169 . . 22 17 5 DT H2' H 2.072 . . 23 17 5 DT H2'' H 2.317 . 2 24 17 5 DT H3' H 4.910 . . 25 17 5 DT H6 H 7.330 . 1 26 17 5 DT H71 H 1.642 . 1 27 17 5 DT H72 H 1.642 . 1 28 17 5 DT H73 H 1.642 . 1 29 18 6 DT H1' H 6.032 . . 30 18 6 DT H2' H 2.125 . . 31 18 6 DT H2'' H 2.364 . 2 32 18 6 DT H3' H 4.837 . . 33 18 6 DT H6 H 7.551 . 1 34 18 6 DT H71 H 1.843 . 1 35 18 6 DT H72 H 1.843 . 1 36 18 6 DT H73 H 1.843 . 1 37 19 7 DG H1' H 5.980 . . 38 19 7 DG H2'' H 2.814 . 2 39 19 7 DG H3' H 4.993 . . 40 19 7 DG H8 H 8.002 . 1 41 20 8 DC H1' H 5.940 . . 42 20 8 DC H2' H 2.063 . . 43 20 8 DC H2'' H 2.489 . 2 44 20 8 DC H5 H 5.393 . 1 45 20 8 DC H6 H 7.449 . 1 46 21 9 DT H1' H 5.570 . . 47 21 9 DT H2' H 2.159 . . 48 21 9 DT H2'' H 2.446 . 2 49 21 9 DT H3' H 4.904 . . 50 21 9 DT H6 H 7.457 . 1 51 21 9 DT H71 H 1.692 . 1 52 21 9 DT H72 H 1.692 . 1 53 21 9 DT H73 H 1.692 . 1 54 22 10 DA H2 H 7.513 . 1 55 22 10 DA H8 H 8.249 . 1 56 23 11 DG H1' H 5.849 . . 57 23 11 DG H2' H 2.525 . . 58 23 11 DG H2'' H 2.684 . 2 59 23 11 DG H3' H 4.984 . . 60 23 11 DG H8 H 7.724 . 1 61 24 12 DC H1' H 6.173 . . 62 24 12 DC H2' H 2.151 . . 63 24 12 DC H2'' H 2.229 . 2 64 24 12 DC H3' H 4.496 . . 65 24 12 DC H5 H 5.438 . 1 66 24 12 DC H6 H 7.452 . 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 HNE _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 5.540 . . 2 25 1 HNE H2 H 1.416 . . 3 25 1 HNE H3 H 2.583 . . 4 25 1 HNE H4 H 2.888 . . 5 25 1 HNE H5C1 H 0.947 . . 6 25 1 HNE H5C2 H 1.164 . . 7 25 1 HNE H6C1 H 1.212 . . 8 25 1 HNE H6C2 H 1.212 . . 9 25 1 HNE H7C1 H 1.046 . . 10 25 1 HNE H7C2 H 1.046 . . stop_ save_