data_4488 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA decamer duplex containing T-T (6-4) photoadduct ; _BMRB_accession_number 4488 _BMRB_flat_file_name bmr4488.str _Entry_type original _Submission_date 1999-03-20 _Accession_date 1999-12-06 _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 Hwang G. -S. . 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" 165 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-16 update BMRB 'update non-standard residue, and sequence 6 to DT in chain 1' 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-08-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of a DNA decamer duplex containing the stable 3' T.G base pair of the pyrimidine(6-4)pyrimidone photoproduct [(6-4) adduct]: implications for the highly specific 3' T --> C transition of the (6-4) adduct ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99289522 _PubMed_ID 10359763 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee J. H. . 2 Hwang G. -S. . 3 Choi B. -S. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. USA' _Journal_name_full 'Proceedings of the National Academy of Science, USA' _Journal_volume 96 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6632 _Page_last 6636 _Year 1999 _Details . loop_ _Keyword 'NMR, DNA photoproduct' '(6-4) adduct, mutagenesis' stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA_decamer _Saveframe_category molecular_system _Mol_system_name 'DNA decamer' _Abbreviation_common 'DNA decamer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA decamer strand 1' $DNA_decamer_1 'DNA decamer strand 2' $DNA_decamer_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'double strand' _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_decamer_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA decamer strand 1' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence CGCAXTACGC loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DA 5 64T 6 DT 7 DA 8 DC 9 DG 10 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_decamer_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA decamer strand 2' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence GCGTGATGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DT 5 DG 6 DA 7 DT 8 DG 9 DC 10 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_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_decamer_1 . . . . . . $DNA_decamer_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_decamer_1 'chemical synthesis' . . . . . $DNA_decamer_2 '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_decamer_1 . mM . $DNA_decamer_2 . mM . stop_ 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 . 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 . n/a temperature 274 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 . H 1 . ppm . . . . . . 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 . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference_one _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 0.01 1 2 . 1 DC H42 H 7.14 0.01 1 3 . 1 DC H5 H 5.89 0.005 1 4 . 1 DC H6 H 7.67 0.005 1 5 . 1 DC H1' H 5.79 0.005 1 6 . 1 DC H2' H 2.03 0.005 1 7 . 1 DC H2'' H 2.46 0.005 1 8 . 1 DC H3' H 4.75 0.005 1 9 . 1 DC H4' H 4.11 0.005 1 10 . 2 DG H1 H 13.14 0.01 1 11 . 2 DG H8 H 8.01 0.005 1 12 . 2 DG H1' H 5.92 0.005 1 13 . 2 DG H2' H 2.70 0.005 1 14 . 2 DG H2'' H 2.76 0.005 1 15 . 2 DG H3' H 5.02 0.005 1 16 . 2 DG H4' H 4.41 0.005 1 17 . 3 DC H41 H 8.42 0.01 1 18 . 3 DC H42 H 6.68 0.01 1 19 . 3 DC H5 H 5.44 0.005 1 20 . 3 DC H6 H 7.35 0.005 1 21 . 3 DC H1' H 5.77 0.005 1 22 . 3 DC H2' H 2.14 0.005 1 23 . 3 DC H2'' H 2.47 0.005 1 24 . 3 DC H3' H 4.85 0.005 1 25 . 3 DC H4' H 4.27 0.005 1 26 . 4 DA H2 H 7.77 0.005 1 27 . 4 DA H8 H 8.29 0.005 1 28 . 4 DA H1' H 6.40 0.005 1 29 . 4 DA H2' H 2.83 0.005 1 30 . 4 DA H2'' H 2.83 0.005 1 31 . 4 DA H3' H 4.97 0.005 1 32 . 4 DA H4' H 4.43 0.005 1 33 . 5 64T H3 H 13.14 0.01 1 34 . 5 64T H61 H 4.75 0.005 1 35 . 5 64T H62 H 4.75 0.005 1 36 . 5 64T H71 H 1.26 0.005 2 37 . 5 64T H72 H 1.26 0.005 2 38 . 5 64T H73 H 1.26 0.005 2 39 . 5 64T H1' H 5.54 0.005 1 40 . 5 64T H2' H 0.94 0.005 1 41 . 5 64T H2'' H 1.86 0.005 1 42 . 5 64T H3' H 4.75 0.005 1 43 . 5 64T H4' H 3.90 0.005 1 44 . 6 DT H6 H 7.96 0.005 1 45 . 6 DT H71 H 2.28 0.005 2 46 . 6 DT H72 H 2.28 0.005 2 47 . 6 DT H73 H 2.28 0.005 2 48 . 6 DT H1' H 6.24 0.005 1 49 . 6 DT H2' H 2.64 0.005 1 50 . 6 DT H2'' H 3.03 0.005 1 51 . 6 DT H3' H 5.01 0.005 1 52 . 6 DT H4' H 3.89 0.005 1 53 . 7 DA H2 H 7.83 0.005 1 54 . 7 DA H8 H 8.45 0.005 1 55 . 7 DA H1' H 6.35 0.005 1 56 . 7 DA H2' H 2.82 0.005 1 57 . 7 DA H2'' H 3.00 0.005 1 58 . 7 DA H3' H 5.09 0.005 1 59 . 7 DA H4' H 4.48 0.005 1 60 . 8 DC H41 H 8.34 0.01 1 61 . 8 DC H42 H 6.78 0.01 1 62 . 8 DC H5 H 5.37 0.005 1 63 . 8 DC H6 H 7.33 0.005 1 64 . 8 DC H1' H 5.59 0.005 1 65 . 8 DC H2' H 2.02 0.005 1 66 . 8 DC H2'' H 2.35 0.005 1 67 . 8 DC H3' H 4.88 0.005 1 68 . 8 DC H4' H 4.16 0.005 1 69 . 9 DG H1 H 13.15 0.01 1 70 . 9 DG H8 H 7.89 0.005 1 71 . 9 DG H1' H 5.98 0.005 1 72 . 9 DG H2' H 2.61 0.005 1 73 . 9 DG H2'' H 2.75 0.005 1 74 . 9 DG H3' H 5.01 0.005 1 75 . 9 DG H4' H 4.40 0.005 1 76 . 10 DC H41 H 8.29 0.01 1 77 . 10 DC H42 H 6.65 0.01 1 78 . 10 DC H5 H 5.19 0.005 1 79 . 10 DC H6 H 7.36 0.005 1 80 . 10 DC H1' H 6.16 0.005 1 81 . 10 DC H2' H 2.26 0.005 1 82 . 10 DC H2'' H 2.30 0.005 1 83 . 10 DC H3' H 4.54 0.005 1 84 . 10 DC H4' H 4.04 0.005 1 stop_ save_ save_chem_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference_one _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 13.09 0.01 1 2 . 1 DG H8 H 8.00 0.005 1 3 . 1 DG H1' H 6.00 0.005 1 4 . 1 DG H2' H 2.67 0.005 1 5 . 1 DG H2'' H 2.83 0.005 1 6 . 1 DG H3' H 4.90 0.005 1 7 . 1 DG H4' H 4.33 0.005 1 8 . 2 DC H41 H 8.49 0.01 1 9 . 2 DC H42 H 6.67 0.01 1 10 . 2 DC H5 H 5.38 0.005 1 11 . 2 DC H6 H 7.44 0.005 1 12 . 2 DC H1' H 5.79 0.005 1 13 . 2 DC H2' H 2.18 0.005 1 14 . 2 DC H2'' H 2.50 0.005 1 15 . 2 DC H3' H 4.93 0.005 1 16 . 2 DC H4' H 4.24 0.005 1 17 . 3 DG H1 H 12.98 0.01 1 18 . 3 DG H8 H 8.01 0.005 1 19 . 3 DG H1' H 6.02 0.005 1 20 . 3 DG H2' H 2.70 0.005 1 21 . 3 DG H2'' H 2.83 0.005 1 22 . 3 DG H3' H 5.04 0.005 1 23 . 3 DG H4' H 4.43 0.005 1 24 . 4 DT H3 H 13.67 0.005 1 25 . 4 DT H6 H 7.15 0.005 1 26 . 4 DT H71 H 1.52 0.005 2 27 . 4 DT H72 H 1.52 0.005 2 28 . 4 DT H73 H 1.52 0.005 2 29 . 4 DT H1' H 5.95 0.005 1 30 . 4 DT H2' H 1.98 0.005 1 31 . 4 DT H2'' H 2.46 0.005 1 32 . 4 DT H3' H 4.89 0.005 1 33 . 4 DT H4' H 4.26 0.005 1 34 . 5 DG H1 H 10.30 0.01 1 35 . 5 DG H21 H 7.84 0.01 1 36 . 5 DG H8 H 7.76 0.005 1 37 . 5 DG H1' H 5.46 0.005 1 38 . 5 DG H2' H 2.22 0.005 1 39 . 5 DG H2'' H 2.35 0.005 1 40 . 5 DG H3' H 4.93 0.005 1 41 . 5 DG H4' H 4.18 0.005 1 42 . 6 DA H2 H 7.62 0.005 1 43 . 6 DA H8 H 8.28 0.005 1 44 . 6 DA H1' H 6.09 0.005 1 45 . 6 DA H2' H 2.70 0.005 1 46 . 6 DA H2'' H 2.79 0.005 1 47 . 6 DA H3' H 5.02 0.005 1 48 . 6 DA H4' H 4.37 0.005 1 49 . 7 DT H3 H 13.37 0.01 1 50 . 7 DT H6 H 7.23 0.005 1 51 . 7 DT H71 H 1.46 0.005 2 52 . 7 DT H72 H 1.46 0.005 2 53 . 7 DT H73 H 1.46 0.005 2 54 . 7 DT H1' H 5.69 0.005 1 55 . 7 DT H2' H 2.17 0.005 1 56 . 7 DT H2'' H 2.39 0.005 1 57 . 7 DT H3' H 4.83 0.005 1 58 . 7 DT H4' H 4.19 0.005 1 59 . 8 DG H1 H 12.72 0.01 1 60 . 8 DG H8 H 7.96 0.005 1 61 . 8 DG H1' H 5.96 0.005 1 62 . 8 DG H2' H 2.68 0.005 1 63 . 8 DG H2'' H 2.68 0.005 1 64 . 8 DG H3' H 5.03 0.005 1 65 . 8 DG H4' H 4.44 0.005 1 66 . 9 DC H41 H 8.53 0.01 1 67 . 9 DC H42 H 6.74 0.01 1 68 . 9 DC H5 H 5.45 0.005 1 69 . 9 DC H6 H 7.43 0.005 1 70 . 9 DC H1' H 5.81 0.005 1 71 . 9 DC H2' H 2.01 0.005 1 72 . 9 DC H2'' H 2.40 0.005 1 73 . 9 DC H3' H 4.90 0.005 1 74 . 9 DC H4' H 4.24 0.005 1 75 . 10 DG H1 H 13.23 0.01 1 76 . 10 DG H8 H 7.99 0.005 1 77 . 10 DG H1' H 6.20 0.005 1 78 . 10 DG H2' H 2.41 0.005 1 79 . 10 DG H2'' H 2.70 0.005 1 80 . 10 DG H3' H 4.74 0.005 1 81 . 10 DG H4' H 4.24 0.005 1 stop_ save_