data_4409 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA DECAMER DUPLEX CONTAINING T-T DEWAR PHOTOPRODUCT ; _BMRB_accession_number 4409 _BMRB_flat_file_name bmr4409.str _Entry_type original _Submission_date 1999-09-16 _Accession_date 1999-09-16 _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 Lee J. -H. . 2 Bae S. -H. . 3 Choi B. -S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 163 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-09 update BMRB 'update non-standard residue based PDB entry 1QKG' 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-12-15 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The Dewar Photoproduct of the Thymidylyl(3' to 5')-thymidine (Dewar Product) Exhibits Mutagenic Behavior in Accordance with the "A rule" ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 10758155 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee J. H. . 2 Bae S. H. . 3 Choi B. S. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U. S. A.' _Journal_volume 97 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4591 _Page_last 4596 _Year 2000 _Details . loop_ _Keyword NMR 'DNA PHOTOPRODUCT' 'DEWAR PRODUCT(6-4) ADDUCT' MUTAGENESIS 'TRANSLESION REPLICATION' stop_ save_ ################################## # Molecular system description # ################################## save_system_DECAMER _Saveframe_category molecular_system _Mol_system_name 'DNA (5'-D(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)- 3')' _Abbreviation_common DECAMER _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA-DECAMER strand-1' $DECAMER-1 'DNA-DECAMER strand-2' $DECAMER-2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state heterodimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DECAMER-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)- 3')' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence CGCAXXACGC loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DA 5 64T 6 TA3 7 DA 8 DC 9 DG 10 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DECAMER-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*G11P*C12P*G13*T14P*G15P*A16P*T17P*G18P*C19P*G20)-3')' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence GCGTGATGCG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 DG 2 12 DC 3 13 DG 4 14 DT 5 15 DG 6 16 DA 7 17 DT 8 18 DG 9 19 DC 10 20 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_64T _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE _BMRB_code 64T _PDB_code 64T _Standard_residue_derivative . _Molecular_mass 340.224 _Mol_paramagnetic . _Details . 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 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3 H3 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 H . 0 . ? HO3' HO3' H . 0 . ? HO5 HO5 H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? O2 O2 O . 0 . ? O3' O3' O . 0 . ? O4 O4 O . 0 . ? O4' O4' O . 0 . ? O5 O5 O . 0 . ? O5' O5' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? SING C5 O5 ? ? SING C5 C6 ? ? SING C5M H71 ? ? SING C5M H72 ? ? SING C5M H73 ? ? SING O5 HO5 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING OP3 HOP3 ? ? stop_ save_ save_chem_comp_TA3 _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common (4S,5R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYL-1,3-DIAZABICYCLO[2.2.0]HEXAN-2-ONE _BMRB_code TA3 _PDB_code TA3 _Standard_residue_derivative . _Molecular_mass 308.225 _Mol_paramagnetic . _Details . 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 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H5 H5 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H6 H6 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 H . 0 . ? HO1P HO1P H . 0 . ? HO2P HO2P H . 0 . ? HO3' HO3' H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? O2 O2 O . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 OP3 P ? ? SING P OP2 ? ? SING P O5' ? ? SING P OP1 ? ? SING OP1 HO1P ? ? SING OP2 HO2P ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' C2' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 C6 ? ? SING C4 C5 ? ? SING C4 H41 ? ? SING C4 H42 ? ? SING C5 C5M ? ? SING C5 C6 ? ? SING C5 H5 ? ? SING C5M H71 ? ? SING C5M H72 ? ? SING C5M H73 ? ? SING C6 H6 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DECAMER-1 . . unclassified . . . 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 $DECAMER-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 $DECAMER-1 1.0 mM . $DECAMER-2 1.0 mM . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details NOESY save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.6 0.1 n/a temperature 274.0 1.0 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 TSP H 1 'methyl protons' ppm 0.00 internal direct cylindrical internal parallel_to_Bo 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_chem_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details 'chemical shift assignment for strand 1' loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA-DECAMER strand-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 DC H41 H 8.27 . . 2 . 1 DC H42 H 7.18 . . 3 . 1 DC H5 H 5.93 . . 4 . 1 DC H6 H 7.68 . . 5 . 1 DC H1' H 5.78 . . 6 . 1 DC H2' H 2.05 . . 7 . 1 DC H2'' H 2.46 . . 8 . 1 DC H3' H 4.76 . . 9 . 1 DC H4' H 4.12 . . 10 . 2 DG H1 H 13.16 . . 11 . 2 DG H8 H 8.01 . . 12 . 2 DG H1' H 5.93 . . 13 . 2 DG H2' H 2.76 . . 14 . 2 DG H2'' H 2.76 . . 15 . 2 DG H3' H 5.03 . . 16 . 2 DG H4' H 4.42 . . 17 . 3 DC H41 H 8.41 . . 18 . 3 DC H42 H 6.66 . . 19 . 3 DC H5 H 5.48 . . 20 . 3 DC H6 H 7.40 . . 21 . 3 DC H1' H 5.73 . . 22 . 3 DC H2' H 2.14 . . 23 . 3 DC H2'' H 2.45 . . 24 . 3 DC H3' H 4.89 . . 25 . 3 DC H4' H 4.28 . . 26 . 4 DA H2 H 7.83 . . 27 . 4 DA H8 H 8.36 . . 28 . 4 DA H1' H 6.35 . . 29 . 4 DA H2' H 2.78 . . 30 . 4 DA H2'' H 2.88 . . 31 . 4 DA H3' H 4.99 . . 32 . 4 DA H4' H 4.43 . . 33 . 5 64T H61 H 4.39 . . 34 . 5 64T H62 H 4.39 . . 35 . 5 64T H71 H 0.95 . . 36 . 5 64T H72 H 0.95 . . 37 . 5 64T H73 H 0.95 . . 38 . 5 64T H1' H 5.97 . . 39 . 5 64T H2' H 2.08 . . 40 . 5 64T H2'' H 2.45 . . 41 . 5 64T H3' H 4.43 . . 42 . 5 64T H4' H 4.00 . . 43 . 6 TA3 H6 H 4.75 . . 44 . 6 TA3 H71 H 1.78 . . 45 . 6 TA3 H72 H 1.78 . . 46 . 6 TA3 H73 H 1.78 . . 47 . 6 TA3 H1' H 5.31 . . 48 . 6 TA3 H2' H 2.08 . . 49 . 6 TA3 H2'' H 2.18 . . 50 . 6 TA3 H3' H 4.75 . . 51 . 6 TA3 H4' H 3.99 . . 52 . 7 DA H2 H 7.96 . . 53 . 7 DA H8 H 8.54 . . 54 . 7 DA H1' H 6.30 . . 55 . 7 DA H2' H 2.84 . . 56 . 7 DA H2'' H 2.95 . . 57 . 7 DA H3' H 5.07 . . 58 . 7 DA H4' H 4.48 . . 59 . 8 DC H41 H 8.32 . . 60 . 8 DC H42 H 6.82 . . 61 . 8 DC H5 H 5.40 . . 62 . 8 DC H6 H 7.36 . . 63 . 8 DC H1' H 5.63 . . 64 . 8 DC H2' H 2.03 . . 65 . 8 DC H2'' H 2.37 . . 66 . 8 DC H3' H 4.87 . . 67 . 8 DC H4' H 4.19 . . 68 . 9 DG H1 H 13.14 . . 69 . 9 DG H8 H 7.92 . . 70 . 9 DG H1' H 6.00 . . 71 . 9 DG H2' H 2.63 . . 72 . 9 DG H2'' H 2.77 . . 73 . 9 DG H3' H 5.02 . . 74 . 9 DG H4' H 4.42 . . 75 . 10 DC H41 H 8.33 . . 76 . 10 DC H42 H 6.72 . . 77 . 10 DC H5 H 5.34 . . 78 . 10 DC H6 H 7.42 . . 79 . 10 DC H1' H 6.19 . . 80 . 10 DC H2' H 2.25 . . 81 . 10 DC H2'' H 2.66 . . 82 . 10 DC H3' H 4.56 . . 83 . 10 DC H4' H 4.06 . . stop_ save_ save_chem_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details 'chemical shift assignment for strand 2' loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA-DECAMER strand-2' _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 DG H1 H 13.10 . . 2 . 1 DG H8 H 8.03 . . 3 . 1 DG H1' H 6.03 . . 4 . 1 DG H2' H 2.71 . . 5 . 1 DG H2'' H 2.84 . . 6 . 1 DG H3' H 4.92 . . 7 . 1 DG H4' H 4.34 . . 8 . 2 DC H41 H 8.52 . . 9 . 2 DC H42 H 6.69 . . 10 . 2 DC H5 H 5.43 . . 11 . 2 DC H6 H 7.48 . . 12 . 2 DC H1' H 5.81 . . 13 . 2 DC H2' H 2.23 . . 14 . 2 DC H2'' H 2.52 . . 15 . 2 DC H3' H 4.96 . . 16 . 2 DC H4' H 4.26 . . 17 . 3 DG H1 H 12.97 . . 18 . 3 DG H8 H 8.02 . . 19 . 3 DG H1' H 6.02 . . 20 . 3 DG H2' H 2.69 . . 21 . 3 DG H2'' H 2.82 . . 22 . 3 DG H3' H 5.05 . . 23 . 3 DG H4' H 4.44 . . 24 . 4 DT H3 H 13.79 . . 25 . 4 DT H6 H 7.10 . . 26 . 4 DT H71 H 1.52 . . 27 . 4 DT H72 H 1.52 . . 28 . 4 DT H73 H 1.52 . . 29 . 4 DT H1' H 5.94 . . 30 . 4 DT H2' H 1.85 . . 31 . 4 DT H2'' H 2.37 . . 32 . 4 DT H3' H 4.87 . . 33 . 4 DT H4' H 4.26 . . 34 . 5 DG H1 H 10.24 . . 35 . 5 DG H8 H 7.92 . . 36 . 5 DG H1' H 5.44 . . 37 . 5 DG H2' H 2.31 . . 38 . 5 DG H2'' H 2.44 . . 39 . 5 DG H3' H 5.00 . . 40 . 5 DG H4' H 4.17 . . 41 . 6 DA H2 H 7.69 . . 42 . 6 DA H8 H 8.29 . . 43 . 6 DA H1' H 6.13 . . 44 . 6 DA H2' H 2.71 . . 45 . 6 DA H2'' H 2.77 . . 46 . 6 DA H3' H 5.01 . . 47 . 6 DA H4' H 4.38 . . 48 . 7 DT H3 H 13.44 . . 49 . 7 DT H6 H 7.21 . . 50 . 7 DT H71 H 1.35 . . 51 . 7 DT H72 H 1.35 . . 52 . 7 DT H73 H 1.35 . . 53 . 7 DT H1' H 5.74 . . 54 . 7 DT H2' H 2.19 . . 55 . 7 DT H2'' H 2.40 . . 56 . 7 DT H3' H 4.89 . . 57 . 7 DT H4' H 4.16 . . 58 . 8 DG H1 H 12.74 . . 59 . 8 DG H8 H 7.95 . . 60 . 8 DG H1' H 5.95 . . 61 . 8 DG H2' H 2.70 . . 62 . 8 DG H2'' H 2.73 . . 63 . 8 DG H3' H 5.03 . . 64 . 8 DG H4' H 4.43 . . 65 . 9 DC H41 H 8.52 . . 66 . 9 DC H42 H 6.74 . . 67 . 9 DC H5 H 5.48 . . 68 . 9 DC H6 H 7.43 . . 69 . 9 DC H1' H 5.85 . . 70 . 9 DC H2' H 2.01 . . 71 . 9 DC H2'' H 2.42 . . 72 . 9 DC H3' H 4.90 . . 73 . 9 DC H4' H 4.26 . . 74 . 10 DG H1 H 13.25 . . 75 . 10 DG H8 H 8.02 . . 76 . 10 DG H1' H 6.21 . . 77 . 10 DG H2' H 2.42 . . 78 . 10 DG H2'' H 2.70 . . 79 . 10 DG H3' H 4.75 . . 80 . 10 DG H4' H 4.25 . . stop_ save_