data_4416 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution-State Structure of a DNA Dodecamer Duplex Containing a Cis-Syn Thymine Cyclobutane Dimer. ; _BMRB_accession_number 4416 _BMRB_flat_file_name bmr4416.str _Entry_type original _Submission_date 1999-09-20 _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 McAteer K. . . 2 Jing Y. . . 3 Kao J. . . 4 Taylor J.-S. . . 5 Kennedy M. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 193 "31P chemical shifts" 22 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-06-17 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution-state Structure of a DNA Dodecamer Duplex Containing a Cis-Syn Thymine Cyclobutane Dimer, the Major UV photoproduct of DNA. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98428625 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 McAteer K. . . 2 Jing Y. . . 3 Kao J. . . 4 Taylor J.-S. . . 5 Kennedy M. A. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 282 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1013 _Page_last 1032 _Year 1998 _Details . loop_ _Keyword 'DNA structure' NMR UV-photoproducts 'BII backbone' stop_ save_ ################################## # Molecular system description # ################################## save_Cis-syn_thymine_cyclobutane_dimer _Saveframe_category molecular_system _Mol_system_name 'Cis-syn thymine cyclobutane dimer' _Abbreviation_common 'Cis-syn thymine cyclobutane dimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'strand 1' $Cis-syn_thymine_cyclobutane_dimer_strand_1 'strand 2' $Cis-syn_thymine_cyclobutane_dimer_strand_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details ; strand one, residues 1-12 strand two, residues 13-24 ; save_ ######################## # Monomeric polymers # ######################## save_Cis-syn_thymine_cyclobutane_dimer_strand_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'Cis-syn thymine cyclobutane dimer strand 1' _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GCACGAATTAAG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DA 4 DC 5 DG 6 DA 7 DA 8 DT 9 DT 10 DA 11 DA 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_Cis-syn_thymine_cyclobutane_dimer_strand_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'Cis-syn thymine cyclobutane dimer strand 2' _Molecular_mass . _Mol_thiol_state . _Details . _Residue_count 12 _Mol_residue_sequence CTTAATTCGTGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DC 2 14 DT 3 15 DT 4 16 DA 5 17 DA 6 18 DT 7 19 DT 8 20 DC 9 21 DG 10 22 DT 11 23 DG 12 24 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Cis-syn_thymine_cyclobutane_dimer_strand_1 . . . . . . $Cis-syn_thymine_cyclobutane_dimer_strand_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 $Cis-syn_thymine_cyclobutane_dimer_strand_1 'chemical synthesis' . . . . . $Cis-syn_thymine_cyclobutane_dimer_strand_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 $Cis-syn_thymine_cyclobutane_dimer 1.2 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Plus' _Field_strength 750 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Plus' _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_HELCO_3 _Saveframe_category NMR_applied_experiment _Experiment_name HELCO _Sample_label $sample_1 save_ save_hetero-TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name hetero-TOCSY _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name HELCO _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name hetero-TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_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 278 1 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 _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 DSS P 31 'methyl protons' ppm 0.0 . indirect . . . 0.404808636 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '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 DG H8 H 7.92 . 1 2 . 1 DG H1' H 5.95 . 1 3 . 1 DG H2' H 2.74 . 5 4 . 1 DG H2'' H 2.62 . 5 5 . 1 DG H3' H 5.06 . 1 6 . 1 DG H4' H 4.13 . 5 7 . 1 DG P P -4.17 . 1 8 . 2 DC H41 H 6.55 . 1 9 . 2 DC H42 H 8.44 . 1 10 . 2 DC H5 H 5.45 . 5 11 . 2 DC H6 H 7.52 . 1 12 . 2 DC H1' H 5.66 . 1 13 . 2 DC H2' H 2.62 . 5 14 . 2 DC H2'' H 2.82 . 5 15 . 2 DC H3' H 4.91 . 1 16 . 2 DC H4' H 4.22 . 5 17 . 2 DC P P -3.88 . 1 18 . 3 DA H2 H 7.79 . 1 19 . 3 DA H8 H 8.32 . 1 20 . 3 DA H1' H 6.24 . 1 21 . 3 DA H2' H 2.73 . 1 22 . 3 DA H2'' H 2.89 . 1 23 . 3 DA H3' H 4.82 . 5 24 . 3 DA H4' H 4.12 . 5 25 . 3 DA P P -4.20 . 1 26 . 4 DC H41 H 6.57 . 1 27 . 4 DC H42 H 8.21 . 1 28 . 4 DC H5 H 5.28 . 1 29 . 4 DC H6 H 7.22 . 5 30 . 4 DC H1' H 5.39 . 1 31 . 4 DC H2' H 1.83 . 1 32 . 4 DC H2'' H 2.21 . 1 33 . 4 DC H3' H 4.82 . 5 34 . 4 DC H4' H 4.11 . 1 35 . 4 DC P P -3.89 . 1 36 . 5 DG H1 H 12.55 . 1 37 . 5 DG H8 H 7.85 . 1 38 . 5 DG H1' H 5.45 . 1 39 . 5 DG H2' H 2.67 . 1 40 . 5 DG H2'' H 2.79 . 1 41 . 5 DG H3' H 4.88 . 5 42 . 5 DG H4' H 4.34 . 1 43 . 5 DG P P -4.12 . 1 44 . 6 DA H2 H 7.16 . 1 45 . 6 DA H8 H 8.14 . 1 46 . 6 DA H1' H 6.03 . 1 47 . 6 DA H2' H 2.72 . 1 48 . 6 DA H2'' H 2.98 . 5 49 . 6 DA H3' H 4.49 . 1 50 . 6 DA H4' H 4.26 . 1 51 . 6 DA P P -4.23 . 1 52 . 7 DA H2 H 7.60 . 5 53 . 7 DA H8 H 8.16 . 1 54 . 7 DA H1' H 6.19 . 1 55 . 7 DA H2' H 2.68 . 1 56 . 7 DA H2'' H 2.97 . 5 57 . 7 DA H3' H 4.53 . 5 58 . 7 DA H4' H 4.08 . 5 59 . 7 DA P P -4.29 . 5 60 . 8 DT H3 H 13.65 . 1 61 . 8 DT H6 H 7.19 . 1 62 . 8 DT H71 H 1.27 . 5 63 . 8 DT H72 H 1.27 . 5 64 . 8 DT H73 H 1.27 . 5 65 . 8 DT H1' H 5.95 . 1 66 . 8 DT H2' H 2.12 . 1 67 . 8 DT H2'' H 2.50 . 1 68 . 8 DT H3' H 4.87 . 1 69 . 8 DT H4' H 4.22 . 5 70 . 8 DT P P -4.36 . 5 71 . 9 DT H3 H 13.52 . 1 72 . 9 DT H6 H 7.38 . 1 73 . 9 DT H71 H 1.61 . 1 74 . 9 DT H72 H 1.61 . 1 75 . 9 DT H73 H 1.61 . 1 76 . 9 DT H1' H 5.79 . 5 77 . 9 DT H2' H 2.12 . 1 78 . 9 DT H2'' H 2.50 . 1 79 . 9 DT H3' H 4.88 . 5 80 . 9 DT H4' H 4.22 . 5 81 . 9 DT P P -4.20 . 1 82 . 10 DA H2 H 6.78 . 1 83 . 10 DA H8 H 8.30 . 1 84 . 10 DA H1' H 5.92 . 1 85 . 10 DA H2' H 2.78 . 1 86 . 10 DA H2'' H 2.94 . 1 87 . 10 DA H3' H 4.66 . 1 88 . 10 DA H4' H 4.45 . 1 89 . 10 DA P P -4.06 . 5 90 . 11 DA H2 H 7.59 . 1 91 . 11 DA H8 H 8.08 . 1 92 . 11 DA H1' H 6.04 . 1 93 . 11 DA H2' H 2.59 . 5 94 . 11 DA H2'' H 2.88 . 1 95 . 11 DA H3' H 4.64 . 5 96 . 11 DA H4' H 4.30 . 1 97 . 11 DA P P -4.02 . 1 98 . 12 DG H8 H 7.60 . 1 99 . 12 DG H1' H 6.00 . 1 100 . 12 DG H2' H 2.39 . 1 101 . 12 DG H2'' H 2.26 . 1 102 . 12 DG H3' H 4.64 . 5 103 . 12 DG H4' H 4.22 . 5 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '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 DC H5 H 5.94 . 1 2 . 1 DC H6 H 7.90 . 1 3 . 1 DC H1' H 5.87 . 1 4 . 1 DC H2' H 2.62 . 5 5 . 1 DC H2'' H 2.32 . 1 6 . 1 DC H3' H 4.67 . 5 7 . 1 DC H4' H 4.12 . 5 8 . 1 DC P P -4.14 . 1 9 . 2 DT H3 H 14.24 . 1 10 . 2 DT H6 H 7.68 . 1 11 . 2 DT H71 H 1.69 . 1 12 . 2 DT H72 H 1.69 . 1 13 . 2 DT H73 H 1.69 . 1 14 . 2 DT H1' H 6.18 . 5 15 . 2 DT H2' H 2.23 . 1 16 . 2 DT H2'' H 2.62 . 5 17 . 2 DT H3' H 4.92 . 5 18 . 2 DT H4' H 4.28 . 1 19 . 2 DT P P -4.32 . 5 20 . 3 DT H3 H 13.69 . 5 21 . 3 DT H6 H 7.50 . 5 22 . 3 DT H71 H 1.71 . 1 23 . 3 DT H72 H 1.71 . 1 24 . 3 DT H73 H 1.71 . 1 25 . 3 DT H1' H 5.72 . 1 26 . 3 DT H2' H 2.19 . 1 27 . 3 DT H2'' H 2.53 . 1 28 . 3 DT H3' H 4.92 . 5 29 . 3 DT H4' H 4.21 . 5 30 . 3 DT P P -4.06 . 5 31 . 4 DA H2 H 6.63 . 1 32 . 4 DA H8 H 8.33 . 1 33 . 4 DA H1' H 6.02 . 1 34 . 4 DA H2' H 2.74 . 5 35 . 4 DA H2'' H 2.98 . 5 36 . 4 DA H3' H 4.88 . 5 37 . 4 DA H4' H 4.21 . 5 38 . 4 DA P P -4.21 . 1 39 . 5 DA H2 H 7.53 . 1 40 . 5 DA H8 H 8.21 . 1 41 . 5 DA H1' H 6.21 . 1 42 . 5 DA H2' H 2.61 . 1 43 . 5 DA H2'' H 2.97 . 5 44 . 5 DA H3' H 4.53 . 5 45 . 5 DA H4' H 4.28 . 1 46 . 5 DA P P -4.29 . 5 47 . 6 DT H3 H 13.69 . 5 48 . 6 DT H6 H 7.21 . 1 49 . 6 DT H71 H 1.27 . 5 50 . 6 DT H72 H 1.27 . 5 51 . 6 DT H73 H 1.27 . 5 52 . 6 DT H1' H 5.96 . 5 53 . 6 DT H2' H 2.00 . 1 54 . 6 DT H2'' H 2.60 . 1 55 . 6 DT H3' H 4.88 . 5 56 . 6 DT H4' H 4.24 . 1 57 . 6 DT P P -4.36 . 1 58 . 7 DT H3 H 13.84 . 1 59 . 7 DT H6 H 7.43 . 1 60 . 7 DT H71 H 1.54 . 1 61 . 7 DT H72 H 1.54 . 1 62 . 7 DT H73 H 1.54 . 1 63 . 7 DT H1' H 6.18 . 5 64 . 7 DT H2' H 2.22 . 1 65 . 7 DT H2'' H 2.53 . 5 66 . 7 DT H3' H 4.53 . 5 67 . 7 DT H4' H 4.08 . 1 68 . 7 DT P P -4.32 . 5 69 . 8 DC H41 H 6.84 . 1 70 . 8 DC H42 H 8.33 . 1 71 . 8 DC H5 H 5.62 . 1 72 . 8 DC H6 H 7.50 . 5 73 . 8 DC H1' H 5.71 . 1 74 . 8 DC H2' H 2.14 . 1 75 . 8 DC H2'' H 2.69 . 1 76 . 8 DC H3' H 4.92 . 5 77 . 8 DC H4' H 4.22 . 5 78 . 8 DC P P -4.07 . 1 79 . 9 DG H1 H 12.64 . 1 80 . 9 DG H8 H 7.98 . 1 81 . 9 DG H1' H 5.96 . 1 82 . 9 DG H2' H 2.48 . 1 83 . 9 DG H2'' H 2.80 . 1 84 . 9 DG H3' H 4.40 . 1 85 . 9 DG H4' H 4.09 . 1 86 . 9 DG P P -4.33 . 1 87 . 10 DT H3 H 13.80 . 1 88 . 10 DT H6 H 7.22 . 1 89 . 10 DT H71 H 1.49 . 1 90 . 10 DT H72 H 1.49 . 1 91 . 10 DT H73 H 1.49 . 1 92 . 10 DT H1' H 5.79 . 1 93 . 10 DT H2' H 2.07 . 1 94 . 10 DT H2'' H 2.43 . 1 95 . 10 DT H3' H 4.89 . 1 96 . 10 DT H4' H 4.22 . 5 97 . 10 DT P P -3.80 . 1 98 . 11 DG H1 H 12.91 . 1 99 . 11 DG H8 H 7.95 . 1 100 . 11 DG H1' H 5.97 . 1 101 . 11 DG H2' H 2.63 . 1 102 . 11 DG H2'' H 2.74 . 5 103 . 11 DG H3' H 4.67 . 5 104 . 11 DG H4' H 4.13 . 5 105 . 11 DG P P -3.86 . 1 106 . 12 DC H5 H 5.45 . 5 107 . 12 DC H6 H 7.50 . 5 108 . 12 DC H1' H 6.17 . 1 109 . 12 DC H2' H 2.82 . 5 110 . 12 DC H2'' H 2.47 . 1 111 . 12 DC H3' H 4.92 . 5 112 . 12 DC H4' H 4.22 . 5 stop_ save_