data_19017 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of an intramolecular propeller-type G-quadruplex containing a single bulge ; _BMRB_accession_number 19017 _BMRB_flat_file_name bmr19017.str _Entry_type original _Submission_date 2013-02-08 _Accession_date 2013-02-08 _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 'Thachappilly Mukundan' Vineeth . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 183 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-07 update BMRB 'update entry citation' 2013-05-30 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Bulges in g-quadruplexes: broadening the definition of g-quadruplex-forming sequences.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23521617 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mukundan 'Vineeth Thachappilly' . . 2 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 135 _Journal_issue 13 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5017 _Page_last 5028 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Bulges in G-quadruplexes' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_1 $DNA_1 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_1 _Molecular_mass 6034.914 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence TTGTGGTGGGTGGGTGGGT loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DT 3 3 DG 4 4 DT 5 5 DG 6 6 DG 7 7 DT 8 8 DG 9 9 DG 10 10 DG 11 11 DT 12 12 DG 13 13 DG 14 14 DG 15 15 DT 16 16 DG 17 17 DG 18 18 DG 19 19 DT 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_1 . . . . . . 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_1 '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_1 . mM 0.1 2.0 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' 'Potassium Ion' 60 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_JR-HMBC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C JR-HMBC' _Sample_label $sample_1 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' 0.05 . M pH 7.0 . pH pressure 1 . atm temperature 298 . K 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 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-13C HSQC' '2D 1H-1H NOESY' '2D 1H-13C JR-HMBC' 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 DNA_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 DT H1' H 5.724 0.01 1 2 1 1 DT H2' H 1.935 0.01 1 3 1 1 DT H2'' H 2.278 0.01 1 4 1 1 DT H3' H 4.514 0.01 1 5 1 1 DT H4' H 4.162 0.01 1 6 1 1 DT H5' H 3.436 0.01 2 7 1 1 DT H5'' H 3.454 0.01 2 8 1 1 DT H6 H 7.216 0.01 1 9 1 1 DT H71 H 1.612 0.01 1 10 1 1 DT H72 H 1.612 0.01 1 11 1 1 DT H73 H 1.612 0.01 1 12 2 2 DT H1' H 5.750 0.01 1 13 2 2 DT H2' H 1.738 0.01 1 14 2 2 DT H2'' H 2.265 0.01 1 15 2 2 DT H3' H 4.558 0.01 1 16 2 2 DT H4' H 3.452 0.01 1 17 2 2 DT H5' H 3.240 0.01 2 18 2 2 DT H5'' H 3.587 0.01 2 19 2 2 DT H6 H 7.252 0.01 1 20 2 2 DT H71 H 1.570 0.01 1 21 2 2 DT H72 H 1.570 0.01 1 22 2 2 DT H73 H 1.570 0.01 1 23 3 3 DG H1 H 11.984 0.01 1 24 3 3 DG H1' H 6.263 0.01 1 25 3 3 DG H2' H 3.139 0.01 1 26 3 3 DG H2'' H 3.685 0.01 1 27 3 3 DG H3' H 5.114 0.01 1 28 3 3 DG H4' H 4.397 0.01 1 29 3 3 DG H5' H 3.930 0.01 2 30 3 3 DG H5'' H 4.032 0.01 2 31 3 3 DG H8 H 8.096 0.01 1 32 4 4 DT H1' H 6.443 0.01 1 33 4 4 DT H2' H 2.577 0.01 1 34 4 4 DT H2'' H 2.689 0.01 1 35 4 4 DT H3' H 4.976 0.01 1 36 4 4 DT H4' H 4.434 0.01 1 37 4 4 DT H5' H 4.223 0.01 2 38 4 4 DT H5'' H 4.275 0.01 2 39 4 4 DT H6 H 7.728 0.01 1 40 4 4 DT H71 H 1.965 0.01 1 41 4 4 DT H72 H 1.965 0.01 1 42 4 4 DT H73 H 1.965 0.01 1 43 5 5 DG H1 H 11.525 0.01 1 44 5 5 DG H1' H 6.268 0.01 1 45 5 5 DG H2' H 2.869 0.01 1 46 5 5 DG H2'' H 2.955 0.01 1 47 5 5 DG H3' H 4.902 0.01 1 48 5 5 DG H4' H 4.566 0.01 1 49 5 5 DG H5' H 4.313 0.01 2 50 5 5 DG H5'' H 4.386 0.01 2 51 5 5 DG H8 H 7.566 0.01 1 52 6 6 DG H1 H 11.382 0.01 1 53 6 6 DG H1' H 6.487 0.01 1 54 6 6 DG H2' H 2.670 0.01 1 55 6 6 DG H2'' H 2.601 0.01 1 56 6 6 DG H3' H 5.109 0.01 1 57 6 6 DG H4' H 4.690 0.01 1 58 6 6 DG H5' H 4.296 0.01 2 59 6 6 DG H5'' H 4.392 0.01 2 60 6 6 DG H8 H 7.891 0.01 1 61 7 7 DT H1' H 6.551 0.01 1 62 7 7 DT H2' H 2.686 0.01 1 63 7 7 DT H2'' H 2.485 0.01 1 64 7 7 DT H3' H 5.149 0.01 1 65 7 7 DT H4' H 4.676 0.01 1 66 7 7 DT H5' H 4.318 0.01 2 67 7 7 DT H5'' H 4.374 0.01 2 68 7 7 DT H6 H 7.878 0.01 1 69 7 7 DT H71 H 1.993 0.01 1 70 7 7 DT H72 H 1.993 0.01 1 71 7 7 DT H73 H 1.993 0.01 1 72 8 8 DG H1 H 11.883 0.01 1 73 8 8 DG H1' H 6.132 0.01 1 74 8 8 DG H2' H 2.455 0.01 1 75 8 8 DG H2'' H 2.966 0.01 1 76 8 8 DG H3' H 5.156 0.01 1 77 8 8 DG H4' H 4.458 0.01 1 78 8 8 DG H5' H 4.280 0.01 2 79 8 8 DG H5'' H 4.358 0.01 2 80 8 8 DG H8 H 8.023 0.01 1 81 9 9 DG H1 H 11.507 0.01 1 82 9 9 DG H1' H 6.221 0.01 1 83 9 9 DG H2' H 2.963 0.01 1 84 9 9 DG H2'' H 2.693 0.01 1 85 9 9 DG H3' H 5.106 0.01 1 86 9 9 DG H4' H 4.595 0.01 1 87 9 9 DG H5' H 4.278 0.01 2 88 9 9 DG H8 H 7.998 0.01 1 89 10 10 DG H1 H 11.382 0.01 1 90 10 10 DG H1' H 6.494 0.01 1 91 10 10 DG H2' H 2.712 0.01 1 92 10 10 DG H2'' H 2.604 0.01 1 93 10 10 DG H3' H 5.134 0.01 1 94 10 10 DG H4' H 4.673 0.01 1 95 10 10 DG H5' H 4.329 0.01 2 96 10 10 DG H5'' H 4.444 0.01 2 97 10 10 DG H8 H 7.862 0.01 1 98 11 11 DT H1' H 6.541 0.01 1 99 11 11 DT H2' H 2.680 0.01 1 100 11 11 DT H2'' H 2.489 0.01 1 101 11 11 DT H3' H 5.153 0.01 1 102 11 11 DT H4' H 4.637 0.01 1 103 11 11 DT H5' H 4.315 0.01 2 104 11 11 DT H5'' H 4.374 0.01 2 105 11 11 DT H6 H 7.877 0.01 1 106 11 11 DT H71 H 1.993 0.01 1 107 11 11 DT H72 H 1.993 0.01 1 108 11 11 DT H73 H 1.993 0.01 1 109 12 12 DG H1 H 11.821 0.01 1 110 12 12 DG H1' H 6.186 0.01 1 111 12 12 DG H2' H 2.534 0.01 1 112 12 12 DG H2'' H 2.991 0.01 1 113 12 12 DG H3' H 5.164 0.01 1 114 12 12 DG H4' H 4.464 0.01 1 115 12 12 DG H5' H 4.283 0.01 2 116 12 12 DG H5'' H 4.356 0.01 2 117 12 12 DG H8 H 8.016 0.01 1 118 13 13 DG H1 H 11.454 0.01 1 119 13 13 DG H1' H 6.225 0.01 1 120 13 13 DG H2' H 2.689 0.01 1 121 13 13 DG H2'' H 2.924 0.01 1 122 13 13 DG H3' H 5.104 0.01 1 123 13 13 DG H4' H 4.586 0.01 1 124 13 13 DG H5' H 4.282 0.01 2 125 13 13 DG H5'' H 4.347 0.01 2 126 13 13 DG H8 H 7.974 0.01 1 127 14 14 DG H1 H 11.182 0.01 1 128 14 14 DG H1' H 6.494 0.01 1 129 14 14 DG H2' H 2.700 0.01 1 130 14 14 DG H2'' H 2.612 0.01 1 131 14 14 DG H3' H 5.133 0.01 1 132 14 14 DG H4' H 4.669 0.01 1 133 14 14 DG H5' H 4.332 0.01 2 134 14 14 DG H5'' H 4.433 0.01 2 135 14 14 DG H8 H 7.828 0.01 1 136 15 15 DT H1' H 6.549 0.01 1 137 15 15 DT H2' H 2.682 0.01 1 138 15 15 DT H2'' H 2.489 0.01 1 139 15 15 DT H3' H 5.148 0.01 1 140 15 15 DT H4' H 4.643 0.01 1 141 15 15 DT H5' H 4.300 0.01 2 142 15 15 DT H5'' H 4.387 0.01 2 143 15 15 DT H6 H 7.876 0.01 1 144 15 15 DT H71 H 1.993 0.01 1 145 15 15 DT H72 H 1.993 0.01 1 146 15 15 DT H73 H 1.993 0.01 1 147 16 16 DG H1 H 11.639 0.01 1 148 16 16 DG H1' H 6.133 0.01 1 149 16 16 DG H2' H 2.411 0.01 1 150 16 16 DG H2'' H 2.878 0.01 1 151 16 16 DG H3' H 5.158 0.01 1 152 16 16 DG H4' H 4.469 0.01 1 153 16 16 DG H5' H 4.283 0.01 2 154 16 16 DG H5'' H 4.347 0.01 2 155 16 16 DG H8 H 7.963 0.01 1 156 17 17 DG H1 H 11.709 0.01 1 157 17 17 DG H1' H 6.096 0.01 1 158 17 17 DG H2' H 2.759 0.01 1 159 17 17 DG H2'' H 2.749 0.01 1 160 17 17 DG H3' H 5.099 0.01 1 161 17 17 DG H4' H 4.548 0.01 1 162 17 17 DG H5' H 4.285 0.01 2 163 17 17 DG H5'' H 4.227 0.01 2 164 17 17 DG H8 H 8.045 0.01 1 165 18 18 DG H1 H 11.321 0.01 1 166 18 18 DG H1' H 6.302 0.01 1 167 18 18 DG H2' H 2.614 0.01 1 168 18 18 DG H2'' H 2.776 0.01 1 169 18 18 DG H3' H 4.874 0.01 1 170 18 18 DG H4' H 4.510 0.01 1 171 18 18 DG H5' H 4.308 0.01 2 172 18 18 DG H8 H 7.695 0.01 1 173 19 19 DT H1' H 5.980 0.01 1 174 19 19 DT H2' H 2.101 0.01 1 175 19 19 DT H2'' H 2.148 0.01 1 176 19 19 DT H3' H 4.454 0.01 1 177 19 19 DT H4' H 4.014 0.01 1 178 19 19 DT H5' H 4.084 0.01 2 179 19 19 DT H5'' H 4.230 0.01 2 180 19 19 DT H6 H 7.281 0.01 1 181 19 19 DT H71 H 1.592 0.01 1 182 19 19 DT H72 H 1.592 0.01 1 183 19 19 DT H73 H 1.592 0.01 1 stop_ save_