data_15027 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC ; _BMRB_accession_number 15027 _BMRB_flat_file_name bmr15027.str _Entry_type new _Submission_date 2006-11-13 _Accession_date 2006-11-13 _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 Wang F. . . 2 DeMuro N. E. . 3 Elmquist C. E. . 4 Stover J. S. . 5 Rizzo C. J. . 6 Stone M. P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 203 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2009-10-09 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15026 'IQ-modified Dodecame' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16881637 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang F. . . 2 DeMuro N. E. . 3 Elmquist C. E. . 4 Stover J. S. . 5 Rizzo C. J. . 6 Stone M. P. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 128 _Journal_issue . _Journal_ASTM JACSAT _Journal_ISSN 0002-7863 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10085 _Page_last 10095 _Year 2006 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Nar1 Duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 'subunit 2' $5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' _Molecular_mass . _Mol_thiol_state 'not available' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CTCGGCGCCATC loop_ _Residue_seq_code _Residue_label 1 DC 2 DT 3 DC 4 DG 5 DG 6 DC 7 DG 8 DC 9 DC 10 DA 11 DT 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' _Molecular_mass . _Mol_thiol_state 'not available' _Details . _Residue_count 12 _Mol_residue_sequence GATGGCGCCGAG loop_ _Residue_seq_code _Residue_label 1 DG 2 DA 3 DT 4 DG 5 DG 6 DC 7 DG 8 DC 9 DC 10 DG 11 DA 12 DG 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 $5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 'Escherichia coli' 562 Bacteria . Escherichia coli $5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 'Escherichia coli' 562 Bacteria . Escherichia coli 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 _Details $5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 'chemical synthesis' . . . . . "The unmodified oligodeoxynucleotides 5'-d(CTCGGCGCCATC)-3' and 5'-d(GATGGCGCCGAG)-3' were obtained from the Midland Certified Reagent Company, and had been purified by anion exchange chromatography." $5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 'chemical synthesis' . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.7 mM Oligodeoxynucleotide duplex, 0.1 M NaCl, 10 mM phosphate buffer, and 50 uM Na2EDTA (pH 7.0), 99.996% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 0.7 mM . $5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 0.7 mM . 'potassium phosphate' 10 mM . 'sodium chloride' 100 mM . D2O 99.996 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.7 mM Oligodeoxynucleotide duplex, 0.1 M NaCl, 10 mM phosphate buffer, and 50 uM Na2EDTA (pH 7.0), 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3' 0.7 mM . $5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3' 0.7 mM . 'potassium phosphate' 10 mM . 'sodium chloride' 100 mM . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 95.0 loop_ _Vendor _Address _Electronic_address Biosym/MSI . . stop_ loop_ _Task processing stop_ _Details . save_ save_CORMA _Saveframe_category software _Name CORMA _Version 5.2 loop_ _Vendor _Address _Electronic_address Keepers . . stop_ loop_ _Task 'iterative matrix relaxation' stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.1 loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task refinement stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version 5.2 loop_ _Vendor _Address _Electronic_address Borgias . . stop_ loop_ _Task 'iterative matrix relaxation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model CPTCI _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'TXI-Z, CP' _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model TXI _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_Magnitude_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Magnitude COSY' _Sample_label $sample_1 save_ save_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label $sample_1 save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_P-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name P-COSY _Sample_label $sample_1 save_ save_2D_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 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' 0.1 . M pH 7.0 . pH pressure 1 . atm temperature 288 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.1 . M pH 7.0 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.1 . M pH 7.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details '4.866 ppm for HDO was used for calibration at 288.15K' 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 4.866 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 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 'subunit 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 1 DC H5 H 5.90 . . 2 1 1 DC H6 H 7.87 . . 3 1 1 DC H1' H 5.75 . . 4 1 1 DC H2' H 2.56 . . 5 1 1 DC H3' H 4.63 . . 6 1 1 DC H4' H 4.07 . . 7 1 1 DC H5' H 3.77 . . 8 1 1 DC H2'' H 2.22 . . 9 1 1 DC H5'' H 4.41 . . 10 2 2 DT H6 H 7.64 . . 11 2 2 DT H1' H 6.07 . . 12 2 2 DT H2' H 2.21 . . 13 2 2 DT H3' H 4.89 . . 14 2 2 DT H4' H 4.25 . . 15 2 2 DT H5' H 4.04 . . 16 2 2 DT H2'' H 2.53 . . 17 2 2 DT H5'' H 4.61 . . 18 3 3 DC H5 H 5.69 . . 19 3 3 DC H6 H 7.46 . . 20 3 3 DC H1' H 5.56 . . 21 3 3 DC H2' H 1.99 . . 22 3 3 DC H3' H 4.83 . . 23 3 3 DC H4' H 4.83 . . 24 3 3 DC H5' H 4.09 . . 25 3 3 DC H2'' H 2.35 . . 26 3 3 DC H5'' H 4.05 . . 27 4 4 DG H8 H 7.86 . . 28 4 4 DG H1' H 5.49 . . 29 4 4 DG H2' H 2.43 . . 30 4 4 DG H3' H 4.95 . . 31 4 4 DG H4' H 4.30 . . 32 4 4 DG H5' H 4.09 . . 33 4 4 DG H2'' H 2.41 . . 34 4 4 DG H5'' H 4.01 . . 35 5 5 DG H8 H 7.73 . . 36 5 5 DG H1' H 5.77 . . 37 5 5 DG H2' H 2.68 . . 38 5 5 DG H3' H 4.94 . . 39 5 5 DG H4' H 4.35 . . 40 5 5 DG H5' H 4.14 . . 41 5 5 DG H2'' H 2.50 . . 42 5 5 DG H5'' H 4.31 . . 43 6 6 DC H5 H 5.24 . . 44 6 6 DC H6 H 7.22 . . 45 6 6 DC H1' H 5.55 . . 46 6 6 DC H2' H 1.90 . . 47 6 6 DC H3' H 4.94 . . 48 6 6 DC H4' H 4.36 . . 49 6 6 DC H5' H 4.09 . . 50 6 6 DC H2'' H 2.32 . . 51 6 6 DC H5'' H 4.15 . . 52 7 7 DG H8 H 7.85 . . 53 7 7 DG H1' H 5.76 . . 54 7 7 DG H2' H 2.68 . . 55 7 7 DG H3' H 4.97 . . 56 7 7 DG H4' H 4.31 . . 57 7 7 DG H5' H 4.06 . . 58 7 7 DG H2'' H 2.58 . . 59 7 7 DG H5'' H 3.98 . . 60 8 8 DC H5 H 5.26 . . 61 8 8 DC H6 H 7.32 . . 62 8 8 DC H1' H 5.81 . . 63 8 8 DC H2' H 2.01 . . 64 8 8 DC H3' H 4.93 . . 65 8 8 DC H4' H 4.15 . . 66 8 8 DC H5' H 4.33 . . 67 8 8 DC H2'' H 2.41 . . 68 8 8 DC H5'' H 4.07 . . 69 9 9 DC H5 H 5.57 . . 70 9 9 DC H6 H 7.49 . . 71 9 9 DC H1' H 5.33 . . 72 9 9 DC H2' H 2.09 . . 73 9 9 DC H3' H 4.87 . . 74 9 9 DC H4' H 4.09 . . 75 9 9 DC H5' H 4.06 . . 76 9 9 DC H2'' H 2.39 . . 77 9 9 DC H5'' H 4.04 . . 78 10 10 DA H2 H 7.73 . . 79 10 10 DA H8 H 8.32 . . 80 10 10 DA H1' H 6.20 . . 81 10 10 DA H2' H 2.93 . . 82 10 10 DA H3' H 5.01 . . 83 10 10 DA H4' H 4.14 . . 84 10 10 DA H5' H 4.41 . . 85 10 10 DA H2'' H 2.62 . . 86 10 10 DA H5'' H 4.07 . . 87 11 11 DT H6 H 7.18 . . 88 11 11 DT H1' H 5.89 . . 89 11 11 DT H2' H 1.97 . . 90 11 11 DT H3' H 4.99 . . 91 11 11 DT H4' H 4.26 . . 92 11 11 DT H5' H 4.11 . . 93 11 11 DT H2'' H 2.40 . . 94 11 11 DT H5'' H 4.13 . . 95 12 12 DC H5 H 5.58 . . 96 12 12 DC H6 H 7.52 . . 97 12 12 DC H1' H 6.13 . . 98 12 12 DC H2' H 2.22 . . 99 12 12 DC H3' H 4.52 . . 100 12 12 DC H4' H 4.15 . . 101 12 12 DC H5' H 3.99 . . 102 12 12 DC H2'' H 2.22 . . 103 12 12 DC H5'' H 4.52 . . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 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 'subunit 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 13 1 DG H8 H 7.89 . . 2 13 1 DG H1' H 5.56 . . 3 13 1 DG H2' H 2.55 . . 4 13 1 DG H3' H 4.82 . . 5 13 1 DG H4' H 3.66 . . 6 13 1 DG H5' H 4.52 . . 7 13 1 DG H2'' H 2.73 . . 8 13 1 DG H5'' H 4.43 . . 9 14 2 DA H2 H 7.92 . . 10 14 2 DA H8 H 8.30 . . 11 14 2 DA H1' H 6.20 . . 12 14 2 DA H2' H 2.72 . . 13 14 2 DA H3' H 5.03 . . 14 14 2 DA H4' H 4.11 . . 15 14 2 DA H5' H 4.55 . . 16 14 2 DA H2'' H 2.95 . . 17 14 2 DA H5'' H 4.10 . . 18 15 3 DT H6 H 7.08 . . 19 15 3 DT H1' H 5.61 . . 20 15 3 DT H2' H 1.90 . . 21 15 3 DT H3' H 4.82 . . 22 15 3 DT H4' H 4.31 . . 23 15 3 DT H5' H 4.12 . . 24 15 3 DT H2'' H 2.34 . . 25 15 3 DT H5'' H 4.23 . . 26 16 4 DG H8 H 7.79 . . 27 16 4 DG H1' H 5.54 . . 28 16 4 DG H2' H 2.60 . . 29 16 4 DG H3' H 4.87 . . 30 16 4 DG H4' H 4.31 . . 31 16 4 DG H5' H 4.34 . . 32 16 4 DG H2'' H 2.67 . . 33 16 4 DG H5'' H 4.14 . . 34 17 5 DG H8 H 7.71 . . 35 17 5 DG H1' H 5.67 . . 36 17 5 DG H2' H 2.65 . . 37 17 5 DG H3' H 4.94 . . 38 17 5 DG H4' H 4.36 . . 39 17 5 DG H5' H 4.14 . . 40 17 5 DG H2'' H 2.51 . . 41 17 5 DG H5'' H 4.31 . . 42 18 6 DC H5 H 5.24 . . 43 18 6 DC H6 H 7.23 . . 44 18 6 DC H1' H 5.56 . . 45 18 6 DC H2' H 1.91 . . 46 18 6 DC H3' H 4.94 . . 47 18 6 DC H4' H 4.36 . . 48 18 6 DC H5' H 4.08 . . 49 18 6 DC H2'' H 2.33 . . 50 18 6 DC H5'' H 4.15 . . 51 19 7 DG H8 H 7.86 . . 52 19 7 DG H1' H 5.76 . . 53 19 7 DG H2' H 2.67 . . 54 19 7 DG H3' H 4.96 . . 55 19 7 DG H4' H 4.30 . . 56 19 7 DG H5' H 4.05 . . 57 19 7 DG H2'' H 2.60 . . 58 19 7 DG H5'' H 3.97 . . 59 20 8 DC H5 H 5.29 . . 60 20 8 DC H6 H 7.33 . . 61 20 8 DC H1' H 5.83 . . 62 20 8 DC H2' H 2.01 . . 63 20 8 DC H3' H 4.93 . . 64 20 8 DC H4' H 4.15 . . 65 20 8 DC H5' H 4.33 . . 66 20 8 DC H2'' H 2.41 . . 67 20 8 DC H5'' H 4.07 . . 68 21 9 DC H5 H 5.56 . . 69 21 9 DC H6 H 7.38 . . 70 21 9 DC H1' H 5.35 . . 71 21 9 DC H2' H 1.91 . . 72 21 9 DC H3' H 4.87 . . 73 21 9 DC H4' H 4.39 . . 74 21 9 DC H5' H 4.01 . . 75 21 9 DC H2'' H 2.25 . . 76 21 9 DC H5'' H 4.01 . . 77 22 10 DG H8 H 7.89 . . 78 22 10 DG H1' H 5.34 . . 79 22 10 DG H2' H 2.66 . . 80 22 10 DG H3' H 4.96 . . 81 22 10 DG H4' H 4.27 . . 82 22 10 DG H5' H 3.93 . . 83 22 10 DG H2'' H 2.71 . . 84 23 11 DA H2 H 7.80 . . 85 23 11 DA H8 H 8.09 . . 86 23 11 DA H1' H 6.09 . . 87 23 11 DA H2' H 2.63 . . 88 23 11 DA H3' H 5.00 . . 89 23 11 DA H4' H 4.25 . . 90 23 11 DA H5' H 4.40 . . 91 23 11 DA H2'' H 2.82 . . 92 23 11 DA H5'' H 4.12 . . 93 24 12 DG H8 H 7.60 . . 94 24 12 DG H1' H 5.88 . . 95 24 12 DG H2' H 2.35 . . 96 24 12 DG H3' H 5.01 . . 97 24 12 DG H4' H 4.58 . . 98 24 12 DG H5' H 4.11 . . 99 24 12 DG H2'' H 2.22 . . 100 24 12 DG H5'' H 4.22 . . stop_ save_