data_4412 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT ; _BMRB_accession_number 4412 _BMRB_flat_file_name bmr4412.str _Entry_type original _Submission_date 1999-09-17 _Accession_date 1999-09-21 _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 Choi Y. -J. . 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" 169 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-09 update BMRB 'update non-standard residue based PDB entry 1QL5' 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-06-19 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Lee, J-H., Choi, Y-J., and Choi, B-S., "Solution Structure of the DNA Decamer Duplex Containing a 3'-T.T base pair of the cis-syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the cis-syn Dimer," Nuc. Acids Res. 28, 1794-1801 (2000). ; _Citation_title ; Solution Structure of the DNA Decamer Duplex Containing a 3'-T.T base pair of the cis-syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the cis-syn Dimer ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20200612 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee J. -H. . 2 Choi Y. -J. . 3 Choi B. -S. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic Acids Research' _Journal_volume 28 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1794 _Page_last 1801 _Year 2000 _Details . loop_ _Keyword NMR 'DNA PHOTOPRODUCT' 'cis-syn dimer' MUTAGENESIS 'DEOXYRIBONUCLEIC ACID' stop_ save_ ################################## # Molecular system description # ################################## save_cis-syn_dimer _Saveframe_category molecular_system _Mol_system_name 'DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3')' _Abbreviation_common 'cis-syn dimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label strand+ $strand+ strand- $strand- stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'heterodimer duplex' _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_strand+ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3')' _Name_variant none _Abbreviation_common 'cis-syn dimer' _Molecular_mass . _Mol_thiol_state 'not applicable' _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 PBT 6 PBT 7 DA 8 DC 9 DG 10 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_strand- _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common strand- _Abbreviation_common 'cis-syn dimer' _Molecular_mass . _Mol_thiol_state 'not applicable' _Details . _Residue_count 10 _Mol_residue_sequence GCGTTATGCG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 DG 2 12 DC 3 13 DG 4 14 DT 5 15 DT 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_PBT _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common '[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN PHOSPHATE' _BMRB_code PBT _PDB_code PBT _Standard_residue_derivative . _Molecular_mass 324.224 _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 . ? H1P H1P H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H2P H2P H . 0 . ? H3 H3 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5 H5 H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H5M1 H5M1 H . 0 . ? H5M2 H5M2 H . 0 . ? H5M3 H5M3 H . 0 . ? H6C1 H6C1 H . 0 . ? H6C2 H6C2 H . 0 . ? HA HA H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? O1P O1P O . 0 . ? O2 O2 O . 0 . ? O2P O2P O . 0 . ? O3' O3' O . 0 . ? O3P O3P O . 0 . ? O4 O4 O . 0 . ? O4' O4' O . 0 . ? O5' O5' 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 SING P O1P ? ? SING P O2P ? ? DOUB P O3P ? ? SING P O5' ? ? SING O1P H1P ? ? SING O2P H2P ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HA ? ? SING C2' C1' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? 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 C6 ? ? SING C5 H5 ? ? SING C5M H5M1 ? ? SING C5M H5M2 ? ? SING C5M H5M3 ? ? SING C6 H6C1 ? ? SING C6 H6C2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $strand+ . . . . . . unclassified $strand- . . . . . . 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 $strand+ 'chemical synthesis' . . . . . $strand- '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 $strand+ 1.0 mM . $strand- 1.0 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 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 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_ref _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 TSP H 1 'methyl proton' ppm 0.00 internal direct cylindrical internal parallel_to_Bo . DSS H 1 'methyl protons' ppm 0.0 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_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 $chem_shift_ref _Mol_system_component_name strand+ _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 8.23 . . 2 . 1 DC H42 H 7.15 . . 3 . 1 DC H5 H 5.87 . . 4 . 1 DC H6 H 7.66 . . 5 . 1 DC H1' H 5.73 . . 6 . 1 DC H2' H 2.03 . . 7 . 1 DC H2'' H 2.45 . . 8 . 1 DC H3' H 4.74 . . 9 . 1 DC H4' H 4.11 . . 10 . 2 DG H1 H 13.14 . . 11 . 2 DG H8 H 8.01 . . 12 . 2 DG H1' H 5.95 . . 13 . 2 DG H2' H 2.70 . . 14 . 2 DG H2'' H 2.80 . . 15 . 2 DG H3' H 5.01 . . 16 . 2 DG H4' H 4.39 . . 17 . 3 DC H41 H 8.42 . . 18 . 3 DC H42 H 6.66 . . 19 . 3 DC H5 H 5.49 . . 20 . 3 DC H6 H 7.44 . . 21 . 3 DC H1' H 5.63 . . 22 . 3 DC H2' H 2.14 . . 23 . 3 DC H2'' H 2.46 . . 24 . 3 DC H3' H 4.89 . . 25 . 3 DC H4' H 4.24 . . 26 . 4 DA H2 H 7.87 . . 27 . 4 DA H8 H 8.38 . . 28 . 4 DA H1' H 6.41 . . 29 . 4 DA H2' H 2.73 . . 30 . 4 DA H2'' H 2.87 . . 31 . 4 DA H3' H 5.04 . . 32 . 4 DA H4' H 4.48 . . 33 . 5 PBT H3 H 11.94 . . 34 . 5 PBT H6C1 H 4.40 . . 35 . 5 PBT H6C2 H 4.40 . . 36 . 5 PBT H5M1 H 0.75 . . 37 . 5 PBT H5M2 H 0.75 . . 38 . 5 PBT H5M3 H 0.75 . . 39 . 5 PBT H1' H 5.45 . . 40 . 5 PBT H2'1 H 1.97 . . 41 . 5 PBT H2'2 H 2.37 . . 42 . 5 PBT H3' H 4.77 . . 43 . 5 PBT H4' H 4.23 . . 44 . 6 PBT H3 H 9.97 . . 45 . 6 PBT H6C1 H 4.05 . . 46 . 6 PBT H6C2 H 4.05 . . 47 . 6 PBT H5M1 H 1.45 . . 48 . 6 PBT H5M2 H 1.45 . . 49 . 6 PBT H5M3 H 1.45 . . 50 . 6 PBT H1' H 5.22 . . 51 . 6 PBT H2'1 H 1.72 . . 52 . 6 PBT H2'2 H 1.84 . . 53 . 6 PBT H3' H 4.72 . . 54 . 6 PBT H4' H 3.84 . . 55 . 7 DA H2 H 7.87 . . 56 . 7 DA H8 H 8.35 . . 57 . 7 DA H1' H 6.19 . . 58 . 7 DA H2' H 2.74 . . 59 . 7 DA H2'' H 2.82 . . 60 . 7 DA H3' H 5.01 . . 61 . 7 DA H4' H 4.37 . . 62 . 8 DC H41 H 8.28 . . 63 . 8 DC H42 H 6.74 . . 64 . 8 DC H5 H 5.29 . . 65 . 8 DC H6 H 7.36 . . 66 . 8 DC H1' H 5.55 . . 67 . 8 DC H2' H 2.05 . . 68 . 8 DC H2'' H 2.35 . . 69 . 8 DC H3' H 4.85 . . 70 . 8 DC H4' H 4.16 . . 71 . 9 DG H1 H 13.12 . . 72 . 9 DG H8 H 7.88 . . 73 . 9 DG H1' H 6.00 . . 74 . 9 DG H2' H 2.61 . . 75 . 9 DG H2'' H 2.76 . . 76 . 9 DG H3' H 5.01 . . 77 . 9 DG H4' H 4.40 . . 78 . 10 DC H41 H 8.30 . . 79 . 10 DC H42 H 7.30 . . 80 . 10 DC H5 H 5.17 . . 81 . 10 DC H6 H 7.34 . . 82 . 10 DC H1' H 6.16 . . 83 . 10 DC H2' H 2.23 . . 84 . 10 DC H2'' H 2.23 . . 85 . 10 DC H3' H 4.54 . . 86 . 10 DC H4' H 4.04 . . 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 $chem_shift_ref _Mol_system_component_name strand- _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 13.11 . . 2 . 1 DG H8 H 8.00 . . 3 . 1 DG H1' H 5.99 . . 4 . 1 DG H2' H 2.66 . . 5 . 1 DG H2'' H 2.82 . . 6 . 1 DG H3' H 4.88 . . 7 . 1 DG H4' H 4.41 . . 8 . 2 DC H41 H 8.50 . . 9 . 2 DC H42 H 6.64 . . 10 . 2 DC H5 H 5.35 . . 11 . 2 DC H6 H 7.40 . . 12 . 2 DC H1' H 5.82 . . 13 . 2 DC H2' H 2.10 . . 14 . 2 DC H2'' H 2.48 . . 15 . 2 DC H3' H 4.92 . . 16 . 2 DC H4' H 4.31 . . 17 . 3 DG H1 H 13.00 . . 18 . 3 DG H8 H 8.01 . . 19 . 3 DG H1' H 6.06 . . 20 . 3 DG H2' H 2.71 . . 21 . 3 DG H2'' H 2.81 . . 22 . 3 DG H3' H 5.01 . . 23 . 3 DG H4' H 4.42 . . 24 . 4 DT H3 H 14.16 . . 25 . 4 DT H6 H 7.34 . . 26 . 4 DT H71 H 1.59 . . 27 . 4 DT H72 H 1.59 . . 28 . 4 DT H73 H 1.59 . . 29 . 4 DT H1' H 6.05 . . 30 . 4 DT H2' H 2.21 . . 31 . 4 DT H2'' H 2.53 . . 32 . 4 DT H3' H 4.85 . . 33 . 4 DT H4' H 4.31 . . 34 . 5 DT H3 H 9.77 . . 35 . 5 DT H6 H 1.61 . . 36 . 5 DT H71 H 7.20 . . 37 . 5 DT H72 H 7.20 . . 38 . 5 DT H73 H 7.20 . . 39 . 5 DT H1' H 5.72 . . 40 . 5 DT H2' H 1.80 . . 41 . 5 DT H2'' H 2.12 . . 42 . 5 DT H3' H 4.87 . . 43 . 5 DT H4' H 4.05 . . 44 . 6 DA H2 H 7.72 . . 45 . 6 DA H8 H 8.34 . . 46 . 6 DA H1' H 6.19 . . 47 . 6 DA H2' H 2.75 . . 48 . 6 DA H2'' H 2.86 . . 49 . 6 DA H3' H 5.00 . . 50 . 6 DA H4' H 4.37 . . 51 . 7 DT H3 H 13.69 . . 52 . 7 DT H6 H 7.23 . . 53 . 7 DT H71 H 1.50 . . 54 . 7 DT H72 H 1.50 . . 55 . 7 DT H73 H 1.50 . . 56 . 7 DT H1' H 5.65 . . 57 . 7 DT H2' H 2.10 . . 58 . 7 DT H2'' H 2.41 . . 59 . 7 DT H3' H 4.87 . . 60 . 7 DT H4' H 4.17 . . 61 . 8 DG H1 H 12.78 . . 62 . 8 DG H8 H 7.92 . . 63 . 8 DG H1' H 5.91 . . 64 . 8 DG H2' H 2.65 . . 65 . 8 DG H2'' H 2.71 . . 66 . 8 DG H3' H 5.00 . . 67 . 8 DG H4' H 4.41 . . 68 . 9 DC H41 H 8.50 . . 69 . 9 DC H42 H 6.73 . . 70 . 9 DC H5 H 5.45 . . 71 . 9 DC H6 H 7.40 . . 72 . 9 DC H1' H 5.78 . . 73 . 9 DC H2' H 1.96 . . 74 . 9 DC H2'' H 2.37 . . 75 . 9 DC H3' H 4.86 . . 76 . 9 DC H4' H 4.21 . . 77 . 10 DG H1 H 13.22 . . 78 . 10 DG H8 H 7.98 . . 79 . 10 DG H1' H 6.18 . . 80 . 10 DG H2' H 2.39 . . 81 . 10 DG H2'' H 2.39 . . 82 . 10 DG H3' H 4.72 . . 83 . 10 DG H4' H 4.21 . . stop_ save_