data_30045 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIY G-Quadruplexes: Solution structure of d(GGGTTTGGGTTTTGGGAGGG) in sodium ; _BMRB_accession_number 30045 _BMRB_flat_file_name bmr30045.str _Entry_type original _Submission_date 2016-03-27 _Accession_date 2016-03-27 _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 Dvorkin S. A. . 2 Karsisiotis A. I. . 3 'Webba da Silva' M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 210 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-19 update BMRB 'update entry citation' 2017-03-30 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30055 'DIY G-Quadruplexes: d(GGTTTGGTTTTGGTTTGG)' 30056 'DIY G-Quadruplexes: d(GGTTTGGTTTTGGTTGG)' 30058 'DIY G-Quadruplexes: d(GGGGTTTGGGGTTTTGGGGAAGGGG)' stop_ _Original_release_date 2016-03-31 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Encoding canonical DNA quadruplex structure. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30182059 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dvorkin Scarlett A. . 2 Karsisiotis Andreas I. . 3 'Webba da Silva' Mateus . . stop_ _Journal_abbreviation 'Sci Adv' _Journal_name_full 'Science advances' _Journal_volume 4 _Journal_issue 8 _Journal_ISSN 2375-2548 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first eaat3007 _Page_last eaat3007 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3')" _Molecular_mass 6348.070 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GGGTTTGGGTTTTGGGAGGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DT 5 5 DT 6 6 DT 7 7 DG 8 8 DG 9 9 DG 10 10 DT 11 11 DT 12 12 DT 13 13 DT 14 14 DG 15 15 DG 16 16 DG 17 17 DA 18 18 DG 19 19 DG 20 20 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 $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM DNA, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM none H2O 93 % 'natural abundance' D2O 7 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1 mM DNA, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM none D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_H,H_jr-NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'H,H jr-NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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' 20 0.02 mM pH 6.8 0.2 pD pressure 1 0.2 atm temperature 293.15 0.2 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'internal chemical shift referencing' 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 indirect . . . 0.25144953 DSS proton 1 'methyl protons' ppm 0.0 internal indirect . . . 0.25144953 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label 'H,H jr-NOESY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 12.161 0.02 . 2 1 1 DG H1' H 5.761 0.02 . 3 1 1 DG H2' H 2.824 0.02 . 4 1 1 DG H2'' H 2.824 0.02 . 5 1 1 DG H3' H 4.871 0.02 . 6 1 1 DG H4' H 4.156 0.02 . 7 1 1 DG H8 H 7.358 0.02 . 8 1 1 DG H21 H 11.039 0.02 . 9 1 1 DG H22 H 6.408 0.02 . 10 2 2 DG H1 H 12.182 0.02 . 11 2 2 DG H1' H 5.566 0.02 . 12 2 2 DG H2' H 2.568 0.02 . 13 2 2 DG H2'' H 2.505 0.02 . 14 2 2 DG H3' H 5.151 0.02 . 15 2 2 DG H4' H 4.195 0.02 . 16 2 2 DG H5' H 4.117 0.02 . 17 2 2 DG H5'' H 4.198 0.02 . 18 2 2 DG H8 H 8.15 0.02 . 19 2 2 DG H21 H 10.125 0.02 . 20 2 2 DG H22 H 6.997 0.02 . 21 3 3 DG H1 H 11.414 0.02 . 22 3 3 DG H1' H 6.311 0.02 . 23 3 3 DG H2' H 2.789 0.02 . 24 3 3 DG H2'' H 2.789 0.02 . 25 3 3 DG H3' H 5.708 0.02 . 26 3 3 DG H4' H 4.451 0.02 . 27 3 3 DG H5' H 4.289 0.02 . 28 3 3 DG H5'' H 4.71 0.02 . 29 3 3 DG H8 H 7.827 0.02 . 30 3 3 DG H21 H 10.363 0.02 . 31 3 3 DG H22 H 6.594 0.02 . 32 4 4 DT H1' H 5.147 0.02 . 33 4 4 DT H2' H 1.408 0.02 . 34 4 4 DT H2'' H 2.1 0.02 . 35 4 4 DT H3' H 4.383 0.02 . 36 4 4 DT H4' H 3.775 0.02 . 37 4 4 DT H5' H 3.627 0.02 . 38 4 4 DT H5'' H 3.627 0.02 . 39 4 4 DT H6 H 6.673 0.02 . 40 4 4 DT H71 H 1.46 0.02 . 41 4 4 DT H72 H 1.46 0.02 . 42 4 4 DT H73 H 1.46 0.02 . 43 5 5 DT H1' H 6.105 0.02 . 44 5 5 DT H2' H 2.328 0.02 . 45 5 5 DT H2'' H 2.328 0.02 . 46 5 5 DT H3' H 4.657 0.02 . 47 5 5 DT H4' H 4.106 0.02 . 48 5 5 DT H5' H 4.029 0.02 . 49 5 5 DT H5'' H 3.901 0.02 . 50 5 5 DT H6 H 7.495 0.02 . 51 5 5 DT H71 H 1.814 0.02 . 52 5 5 DT H72 H 1.814 0.02 . 53 5 5 DT H73 H 1.814 0.02 . 54 6 6 DT H1' H 5.802 0.02 . 55 6 6 DT H2' H 1.658 0.02 . 56 6 6 DT H2'' H 1.949 0.02 . 57 6 6 DT H3' H 4.486 0.02 . 58 6 6 DT H4' H 3.869 0.02 . 59 6 6 DT H5' H 3.693 0.02 . 60 6 6 DT H5'' H 3.693 0.02 . 61 6 6 DT H6 H 6.675 0.02 . 62 6 6 DT H71 H 0.694 0.02 . 63 6 6 DT H72 H 0.694 0.02 . 64 6 6 DT H73 H 0.694 0.02 . 65 7 7 DG H1 H 10.905 0.02 . 66 7 7 DG H1' H 5.78 0.02 . 67 7 7 DG H2' H 3.267 0.02 . 68 7 7 DG H2'' H 2.596 0.02 . 69 7 7 DG H3' H 4.575 0.02 . 70 7 7 DG H4' H 4.142 0.02 . 71 7 7 DG H8 H 8.091 0.02 . 72 7 7 DG H21 H 9.879 0.02 . 73 7 7 DG H22 H 7.186 0.02 . 74 8 8 DG H1 H 11.521 0.02 . 75 8 8 DG H1' H 5.851 0.02 . 76 8 8 DG H2' H 2.617 0.02 . 77 8 8 DG H2'' H 2.617 0.02 . 78 8 8 DG H3' H 4.959 0.02 . 79 8 8 DG H4' H 4.189 0.02 . 80 8 8 DG H5' H 4.102 0.02 . 81 8 8 DG H5'' H 4.102 0.02 . 82 8 8 DG H8 H 7.535 0.02 . 83 8 8 DG H21 H 9.928 0.02 . 84 8 8 DG H22 H 6.931 0.02 . 85 9 9 DG H1 H 11.368 0.02 . 86 9 9 DG H1' H 5.855 0.02 . 87 9 9 DG H2' H 2.477 0.02 . 88 9 9 DG H2'' H 2.625 0.02 . 89 9 9 DG H3' H 4.886 0.02 . 90 9 9 DG H4' H 4.423 0.02 . 91 9 9 DG H5' H 4.421 0.02 . 92 9 9 DG H5'' H 3.988 0.02 . 93 9 9 DG H8 H 7.949 0.02 . 94 9 9 DG H21 H 10.205 0.02 . 95 9 9 DG H22 H 6.205 0.02 . 96 10 10 DT H1' H 5.362 0.02 . 97 10 10 DT H2' H 1.117 0.02 . 98 10 10 DT H2'' H 2.005 0.02 . 99 10 10 DT H3' H 4.401 0.02 . 100 10 10 DT H4' H 3.814 0.02 . 101 10 10 DT H5' H 3.341 0.02 . 102 10 10 DT H5'' H 3.344 0.02 . 103 10 10 DT H6 H 6.881 0.02 . 104 10 10 DT H71 H 1.69 0.02 . 105 10 10 DT H72 H 1.69 0.02 . 106 10 10 DT H73 H 1.69 0.02 . 107 11 11 DT H1' H 5.306 0.02 . 108 11 11 DT H2' H 2.084 0.02 . 109 11 11 DT H2'' H 1.852 0.02 . 110 11 11 DT H3' H 4.497 0.02 . 111 11 11 DT H4' H 3.498 0.02 . 112 11 11 DT H5' H 3.447 0.02 . 113 11 11 DT H5'' H 3.495 0.02 . 114 11 11 DT H6 H 7.183 0.02 . 115 11 11 DT H71 H 1.486 0.02 . 116 11 11 DT H72 H 1.486 0.02 . 117 11 11 DT H73 H 1.486 0.02 . 118 12 12 DT H1' H 5.404 0.02 . 119 12 12 DT H2' H 1.565 0.02 . 120 12 12 DT H2'' H 2.218 0.02 . 121 12 12 DT H3' H 4.649 0.02 . 122 12 12 DT H4' H 4.398 0.02 . 123 12 12 DT H5' H 2.657 0.02 . 124 12 12 DT H5'' H 4.264 0.02 . 125 12 12 DT H6 H 7.076 0.02 . 126 12 12 DT H71 H 1.424 0.02 . 127 12 12 DT H72 H 1.424 0.02 . 128 12 12 DT H73 H 1.424 0.02 . 129 13 13 DT H1' H 6.21 0.02 . 130 13 13 DT H2' H 2.019 0.02 . 131 13 13 DT H2'' H 2.312 0.02 . 132 13 13 DT H3' H 4.473 0.02 . 133 13 13 DT H4' H 3.044 0.02 . 134 13 13 DT H5' H 2.731 0.02 . 135 13 13 DT H5'' H 3.044 0.02 . 136 13 13 DT H6 H 7.569 0.02 . 137 13 13 DT H71 H 1.673 0.02 . 138 13 13 DT H72 H 1.673 0.02 . 139 13 13 DT H73 H 1.673 0.02 . 140 14 14 DG H1 H 11.939 0.02 . 141 14 14 DG H1' H 6.09 0.02 . 142 14 14 DG H2' H 3.419 0.02 . 143 14 14 DG H2'' H 2.895 0.02 . 144 14 14 DG H3' H 4.849 0.02 . 145 14 14 DG H4' H 4.254 0.02 . 146 14 14 DG H5' H 4.06 0.02 . 147 14 14 DG H5'' H 4.04 0.02 . 148 14 14 DG H8 H 7.438 0.02 . 149 14 14 DG H21 H 9.491 0.02 . 150 14 14 DG H22 H 7.514 0.02 . 151 15 15 DG H1 H 11.313 0.02 . 152 15 15 DG H1' H 6.074 0.02 . 153 15 15 DG H2' H 2.599 0.02 . 154 15 15 DG H2'' H 2.792 0.02 . 155 15 15 DG H3' H 5.097 0.02 . 156 15 15 DG H4' H 4.425 0.02 . 157 15 15 DG H8 H 7.511 0.02 . 158 15 15 DG H21 H 9.813 0.02 . 159 15 15 DG H22 H 6.614 0.02 . 160 16 16 DG H1 H 11.152 0.02 . 161 16 16 DG H1' H 6.246 0.02 . 162 16 16 DG H2' H 2.954 0.02 . 163 16 16 DG H2'' H 2.69 0.02 . 164 16 16 DG H3' H 5.026 0.02 . 165 16 16 DG H4' H 4.244 0.02 . 166 16 16 DG H5' H 3.777 0.02 . 167 16 16 DG H5'' H 3.629 0.02 . 168 16 16 DG H8 H 7.866 0.02 . 169 16 16 DG H21 H 9.976 0.02 . 170 16 16 DG H22 H 6.414 0.02 . 171 17 17 DA H1' H 5.927 0.02 . 172 17 17 DA H2 H 7.664 0.02 . 173 17 17 DA H2' H 1.959 0.02 . 174 17 17 DA H2'' H 2.76 0.02 . 175 17 17 DA H3' H 4.882 0.02 . 176 17 17 DA H4' H 4.295 0.02 . 177 17 17 DA H5' H 4.161 0.02 . 178 17 17 DA H5'' H 4.161 0.02 . 179 17 17 DA H8 H 7.446 0.02 . 180 18 18 DG H1 H 11.326 0.02 . 181 18 18 DG H1' H 5.992 0.02 . 182 18 18 DG H2' H 2.516 0.02 . 183 18 18 DG H2'' H 2.784 0.02 . 184 18 18 DG H3' H 4.891 0.02 . 185 18 18 DG H4' H 4.386 0.02 . 186 18 18 DG H5' H 4.015 0.02 . 187 18 18 DG H5'' H 4.015 0.02 . 188 18 18 DG H8 H 7.887 0.02 . 189 18 18 DG H21 H 10.416 0.02 . 190 18 18 DG H22 H 5.848 0.02 . 191 19 19 DG H1 H 10.893 0.02 . 192 19 19 DG H1' H 5.995 0.02 . 193 19 19 DG H2' H 3.544 0.02 . 194 19 19 DG H2'' H 2.825 0.02 . 195 19 19 DG H3' H 5.035 0.02 . 196 19 19 DG H4' H 4.267 0.02 . 197 19 19 DG H5' H 4.159 0.02 . 198 19 19 DG H5'' H 4.251 0.02 . 199 19 19 DG H8 H 7.32 0.02 . 200 19 19 DG H21 H 8.673 0.02 . 201 19 19 DG H22 H 6.641 0.02 . 202 20 20 DG H1 H 11.628 0.02 . 203 20 20 DG H1' H 6.283 0.02 . 204 20 20 DG H2' H 2.703 0.02 . 205 20 20 DG H2'' H 2.418 0.02 . 206 20 20 DG H3' H 4.252 0.02 . 207 20 20 DG H4' H 4.165 0.02 . 208 20 20 DG H8 H 8.263 0.02 . 209 20 20 DG H21 H 9.292 0.02 . 210 20 20 DG H22 H 6.999 0.02 . stop_ save_