data_18625 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of the Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'. ; _BMRB_accession_number 18625 _BMRB_flat_file_name bmr18625.str _Entry_type original _Submission_date 2012-07-31 _Accession_date 2012-07-31 _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 Rettig Michael . . 2 Germann Markus W. . 3 Wilson 'W. David' . . 4 Wang Shuo . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 200 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 update BMRB 'update entry citation' 2013-01-22 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18626 "Self-Complementary 10 mer DNA Duplex 5'-GGATATATCC-3' in Complex with Netropsin" stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Molecular basis for sequence-dependent induced DNA bending.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23355266 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rettig Michael . . 2 Germann Markus W. . 3 Wang Shuo . . 4 Wilson 'W. David' . . stop_ _Journal_abbreviation Chembiochem _Journal_name_full 'Chembiochem : a European journal of chemical biology' _Journal_volume 14 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 323 _Page_last 331 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'GGATATATCC, 1' $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 'GGATATATCC, 2' $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')_ _Molecular_mass 3044.042 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GGATATATCC loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DA 4 DT 5 DA 6 DT 7 DA 8 DT 9 DC 10 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 $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') . . . . . . 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_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1_D2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 0.9 mM 'natural abundance' stop_ save_ save_sample_1_H2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 0.9 mM 'natural abundance' stop_ save_ save_sample_1_Pf1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3') 1.2 mM 'natural abundance' 'Pf1 phage' 11 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'QXI probe' save_ save_500 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details 'TXI cryoprobe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1_D2O save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1_H2O save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1_D2O save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1_Pf1 save_ save_2D_1H-13C_HSQC_aliphatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1_Pf1 save_ save_2D_1H-13C_HSQC_aromatic_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1_Pf1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _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 temperature 278 . K pH 7 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 water H 1 protons ppm 5 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 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1_D2O $sample_1_H2O stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGATATATCC, 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 DG H1 H 12.86 . 1 2 1 1 DG H1' H 5.633 . 1 3 1 1 DG H2' H 2.528 . 1 4 1 1 DG H2'' H 2.712 . 1 5 1 1 DG H3' H 4.815 . 1 6 1 1 DG H4' H 4.176 . 1 7 1 1 DG H5' H 3.647 . 1 8 1 1 DG H5'' H 3.647 . 1 9 1 1 DG H8 H 7.841 . 1 10 2 2 DG H1 H 12.80 . 1 11 2 2 DG H1' H 5.63 . 1 12 2 2 DG H2' H 2.694 . 1 13 2 2 DG H2'' H 2.783 . 1 14 2 2 DG H3' H 5.019 . 1 15 2 2 DG H4' H 4.378 . 1 16 2 2 DG H5' H 4.063 . 2 17 2 2 DG H5'' H 4.147 . 2 18 2 2 DG H8 H 7.831 . 1 19 3 3 DA H1' H 6.276 . 1 20 3 3 DA H2 H 7.787 . 1 21 3 3 DA H2' H 2.655 . 1 22 3 3 DA H2'' H 2.979 . 1 23 3 3 DA H3' H 5.033 . 1 24 3 3 DA H4' H 4.497 . 1 25 3 3 DA H5' H 4.238 . 2 26 3 3 DA H8 H 8.245 . 1 27 3 3 DA H61 H 7.598 . 1 28 3 3 DA H62 H 6.028 . 1 29 4 4 DT H1' H 5.709 . 1 30 4 4 DT H2' H 2.125 . 1 31 4 4 DT H2'' H 2.542 . 1 32 4 4 DT H3 H 13.24 . 1 33 4 4 DT H3' H 4.896 . 1 34 4 4 DT H4' H 4.224 . 1 35 4 4 DT H5' H 4.16 . 2 36 4 4 DT H5'' H 4.293 . 2 37 4 4 DT H6 H 7.165 . 1 38 4 4 DT H71 H 1.392 . 1 39 4 4 DT H72 H 1.392 . 1 40 4 4 DT H73 H 1.392 . 1 41 5 5 DA H1' H 6.224 . 1 42 5 5 DA H2 H 7.005 . 1 43 5 5 DA H2' H 2.60 . 1 44 5 5 DA H2'' H 2.955 . 1 45 5 5 DA H3' H 5.004 . 1 46 5 5 DA H4' H 4.44 . 1 47 5 5 DA H8 H 8.251 . 1 48 5 5 DA H61 H 7.442 . 1 49 5 5 DA H62 H 6.215 . 1 50 6 6 DT H1' H 5.75 . 1 51 6 6 DT H2' H 2.152 . 1 52 6 6 DT H2'' H 2.558 . 1 53 6 6 DT H3 H 13.22 . 1 54 6 6 DT H3' H 4.905 . 1 55 6 6 DT H4' H 4.251 . 1 56 6 6 DT H5' H 4.195 . 2 57 6 6 DT H5'' H 4.306 . 2 58 6 6 DT H6 H 7.188 . 1 59 6 6 DT H71 H 1.336 . 1 60 6 6 DT H72 H 1.336 . 1 61 6 6 DT H73 H 1.336 . 1 62 7 7 DA H1' H 6.223 . 1 63 7 7 DA H2 H 7.155 . 1 64 7 7 DA H2' H 2.612 . 1 65 7 7 DA H2'' H 2.938 . 1 66 7 7 DA H3' H 5.002 . 1 67 7 7 DA H4' H 4.435 . 1 68 7 7 DA H8 H 8.249 . 1 69 7 7 DA H61 H 7.477 . 1 70 7 7 DA H62 H 6.23 . 1 71 8 8 DT H1' H 5.963 . 1 72 8 8 DT H2' H 2.082 . 1 73 8 8 DT H2'' H 2.503 . 1 74 8 8 DT H3 H 13.64 . 1 75 8 8 DT H3' H 4.872 . 1 76 8 8 DT H4' H 4.23 . 1 77 8 8 DT H5' H 4.156 . 2 78 8 8 DT H5'' H 4.312 . 2 79 8 8 DT H6 H 7.21 . 1 80 8 8 DT H71 H 1.266 . 1 81 8 8 DT H72 H 1.266 . 1 82 8 8 DT H73 H 1.266 . 1 83 9 9 DC H1' H 6.004 . 1 84 9 9 DC H2' H 2.179 . 1 85 9 9 DC H2'' H 2.469 . 1 86 9 9 DC H3' H 4.818 . 1 87 9 9 DC H4' H 4.157 . 1 88 9 9 DC H5 H 5.601 . 1 89 9 9 DC H6 H 7.558 . 1 90 9 9 DC H41 H 8.402 . 1 91 9 9 DC H42 H 6.933 . 1 92 10 10 DC H1' H 6.211 . 1 93 10 10 DC H2' H 2.251 . 1 94 10 10 DC H2'' H 2.251 . 1 95 10 10 DC H3' H 4.559 . 1 96 10 10 DC H4' H 4.012 . 1 97 10 10 DC H5 H 5.671 . 1 98 10 10 DC H6 H 7.609 . 1 99 10 10 DC H41 H 8.293 . 1 100 10 10 DC H42 H 7.193 . 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1_D2O $sample_1_H2O stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGATATATCC, 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 11 1 DG H1 H 12.86 . 1 2 11 1 DG H1' H 5.633 . 1 3 11 1 DG H2' H 2.528 . 1 4 11 1 DG H2'' H 2.712 . 1 5 11 1 DG H3' H 4.815 . 1 6 11 1 DG H4' H 4.176 . 1 7 11 1 DG H5' H 3.647 . 1 8 11 1 DG H5'' H 3.647 . 1 9 11 1 DG H8 H 7.841 . 1 10 12 2 DG H1 H 12.80 . 1 11 12 2 DG H1' H 5.63 . 1 12 12 2 DG H2' H 2.694 . 1 13 12 2 DG H2'' H 2.783 . 1 14 12 2 DG H3' H 5.019 . 1 15 12 2 DG H4' H 4.378 . 1 16 12 2 DG H5' H 4.063 . 2 17 12 2 DG H5'' H 4.147 . 2 18 12 2 DG H8 H 7.831 . 1 19 13 3 DA H1' H 6.276 . 1 20 13 3 DA H2 H 7.787 . 1 21 13 3 DA H2' H 2.655 . 1 22 13 3 DA H2'' H 2.979 . 1 23 13 3 DA H3' H 5.033 . 1 24 13 3 DA H4' H 4.497 . 1 25 13 3 DA H5' H 4.238 . 2 26 13 3 DA H8 H 8.245 . 1 27 13 3 DA H61 H 7.598 . 1 28 13 3 DA H62 H 6.028 . 1 29 14 4 DT H1' H 5.709 . 1 30 14 4 DT H2' H 2.125 . 1 31 14 4 DT H2'' H 2.542 . 1 32 14 4 DT H3 H 13.24 . 1 33 14 4 DT H3' H 4.896 . 1 34 14 4 DT H4' H 4.224 . 1 35 14 4 DT H5' H 4.16 . 2 36 14 4 DT H5'' H 4.293 . 2 37 14 4 DT H6 H 7.165 . 1 38 14 4 DT H71 H 1.392 . 1 39 14 4 DT H72 H 1.392 . 1 40 14 4 DT H73 H 1.392 . 1 41 15 5 DA H1' H 6.224 . 1 42 15 5 DA H2 H 7.005 . 1 43 15 5 DA H2' H 2.60 . 1 44 15 5 DA H2'' H 2.955 . 1 45 15 5 DA H3' H 5.004 . 1 46 15 5 DA H4' H 4.44 . 1 47 15 5 DA H8 H 8.251 . 1 48 15 5 DA H61 H 7.442 . 1 49 15 5 DA H62 H 6.215 . 1 50 16 6 DT H1' H 5.75 . 1 51 16 6 DT H2' H 2.152 . 1 52 16 6 DT H2'' H 2.558 . 1 53 16 6 DT H3 H 13.22 . 1 54 16 6 DT H3' H 4.905 . 1 55 16 6 DT H4' H 4.251 . 1 56 16 6 DT H5' H 4.195 . 2 57 16 6 DT H5'' H 4.306 . 2 58 16 6 DT H6 H 7.188 . 1 59 16 6 DT H71 H 1.336 . 1 60 16 6 DT H72 H 1.336 . 1 61 16 6 DT H73 H 1.336 . 1 62 17 7 DA H1' H 6.223 . 1 63 17 7 DA H2 H 7.155 . 1 64 17 7 DA H2' H 2.612 . 1 65 17 7 DA H2'' H 2.938 . 1 66 17 7 DA H3' H 5.002 . 1 67 17 7 DA H4' H 4.435 . 1 68 17 7 DA H8 H 8.249 . 1 69 17 7 DA H61 H 7.477 . 1 70 17 7 DA H62 H 6.23 . 1 71 18 8 DT H1' H 5.963 . 1 72 18 8 DT H2' H 2.082 . 1 73 18 8 DT H2'' H 2.503 . 1 74 18 8 DT H3 H 13.64 . 1 75 18 8 DT H3' H 4.872 . 1 76 18 8 DT H4' H 4.23 . 1 77 18 8 DT H5' H 4.156 . 2 78 18 8 DT H5'' H 4.312 . 2 79 18 8 DT H6 H 7.21 . 1 80 18 8 DT H71 H 1.266 . 1 81 18 8 DT H72 H 1.266 . 1 82 18 8 DT H73 H 1.266 . 1 83 19 9 DC H1' H 6.004 . 1 84 19 9 DC H2' H 2.179 . 1 85 19 9 DC H2'' H 2.469 . 1 86 19 9 DC H3' H 4.818 . 1 87 19 9 DC H4' H 4.157 . 1 88 19 9 DC H5 H 5.601 . 1 89 19 9 DC H6 H 7.558 . 1 90 19 9 DC H41 H 8.402 . 1 91 19 9 DC H42 H 6.933 . 1 92 20 10 DC H1' H 6.211 . 1 93 20 10 DC H2' H 2.251 . 1 94 20 10 DC H2'' H 2.251 . 1 95 20 10 DC H3' H 4.559 . 1 96 20 10 DC H4' H 4.012 . 1 97 20 10 DC H5 H 5.671 . 1 98 20 10 DC H6 H 7.609 . 1 99 20 10 DC H41 H 8.293 . 1 100 20 10 DC H42 H 7.193 . 1 stop_ save_