data_34297 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex ; _BMRB_accession_number 34297 _BMRB_flat_file_name bmr34297.str _Entry_type original _Submission_date 2018-07-04 _Accession_date 2018-07-04 _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 'Lenarcic Zivkovic' M. . . 2 Rozman J. . . 3 Plavec J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 156 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-31 update BMRB 'update entry citation' 2018-09-21 original author 'original release' stop_ _Original_release_date 2018-09-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30222243 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'Lenarcic Zivkovic' M. . . 2 Rozman J. . . 3 Plavec J. . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_volume 57 _Journal_issue 47 _Journal_ASTM ACIEAY _Journal_ISSN 1521-3773 _Journal_CSD 0179 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15395 _Page_last 15399 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*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 entity_1 _Molecular_mass 6410.127 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GGGTAGGGAGCGGGAGAGGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DT 5 DA 6 DG 7 DG 8 DG 9 DA 10 DG 11 DC 12 DG 13 DG 14 DG 15 DA 16 DG 17 DA 18 DG 19 DG 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 Human 9606 Eukaryota Metazoa Homo sapiens 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 "0.6 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.6 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "0.8 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3'), 100% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . 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 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aliphatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _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' 100 . mM pH 7.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 C 13 'methyl protons' ppm 0.000 external indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 external direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 external indirect . . . 0.10132912 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_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' 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 11.551 0.001 . 2 1 1 DG H1' H 6.051 0.002 . 3 1 1 DG H2' H 2.676 0.002 . 4 1 1 DG H2'' H 2.899 0.001 . 5 1 1 DG H3' H 4.951 0.002 . 6 1 1 DG H8 H 7.413 0.002 . 7 1 1 DG H21 H 10.207 0.002 . 8 1 1 DG H22 H 6.255 0.001 . 9 2 2 DG H1 H 11.921 0.001 . 10 2 2 DG H1' H 5.885 0.002 . 11 2 2 DG H2' H 2.267 0.001 . 12 2 2 DG H2'' H 2.423 0.003 . 13 2 2 DG H3' H 4.947 0.002 . 14 2 2 DG H4' H 4.443 0.001 . 15 2 2 DG H5' H 4.227 0.005 . 16 2 2 DG H5'' H 4.313 0.001 . 17 2 2 DG H8 H 7.779 0.003 . 18 3 3 DG H1 H 12.94 0.001 . 19 3 3 DG H1' H 5.9 0.004 . 20 3 3 DG H2' H 2.811 0.007 . 21 3 3 DG H2'' H 2.515 0.002 . 22 3 3 DG H3' H 4.986 0.002 . 23 3 3 DG H4' H 4.678 0.001 . 24 3 3 DG H5' H 4.223 0 . 25 3 3 DG H5'' H 4.315 0.001 . 26 3 3 DG H8 H 8.234 0.001 . 27 4 4 DT H1' H 5.773 0.003 . 28 4 4 DT H2' H 1.824 0.004 . 29 4 4 DT H2'' H 1.938 0.004 . 30 4 4 DT H3' H 4.371 0.001 . 31 4 4 DT H4' H 3.347 0.003 . 32 4 4 DT H6 H 7.166 0.005 . 33 4 4 DT H71 H 1.637 0.002 . 34 4 4 DT H72 H 1.637 0.002 . 35 4 4 DT H73 H 1.637 0.002 . 36 5 5 DA H1' H 6.385 0.002 . 37 5 5 DA H2 H 8.103 0.002 . 38 5 5 DA H2' H 2.646 0.003 . 39 5 5 DA H2'' H 3.187 0.003 . 40 5 5 DA H3' H 4.819 0.002 . 41 5 5 DA H4' H 4.377 0.003 . 42 5 5 DA H5' H 3.581 0.002 . 43 5 5 DA H5'' H 3.874 0.001 . 44 5 5 DA H8 H 8.078 0.003 . 45 6 6 DG H1 H 11.639 0.003 . 46 6 6 DG H1' H 5.827 0.001 . 47 6 6 DG H2' H 3.126 0.003 . 48 6 6 DG H2'' H 2.811 0.005 . 49 6 6 DG H4' H 4.461 0.004 . 50 6 6 DG H8 H 6.776 0.002 . 51 7 7 DG H1 H 11.84 0.001 . 52 7 7 DG H1' H 5.54 0.002 . 53 7 7 DG H2' H 2.669 0.001 . 54 7 7 DG H2'' H 2.469 0.002 . 55 7 7 DG H3' H 4.934 0.001 . 56 7 7 DG H4' H 4.412 0.002 . 57 7 7 DG H5' H 4.271 0.003 . 58 7 7 DG H5'' H 4.214 0.004 . 59 7 7 DG H8 H 8.158 0.002 . 60 7 7 DG H21 H 9.841 0 . 61 7 7 DG H22 H 6.077 0 . 62 8 8 DG H1 H 10.701 0.001 . 63 8 8 DG H1' H 5.964 0.005 . 64 8 8 DG H2' H 2.077 0.004 . 65 8 8 DG H2'' H 2.47 0.003 . 66 8 8 DG H3' H 4.949 0.001 . 67 8 8 DG H4' H 4.191 0.001 . 68 8 8 DG H8 H 7.421 0.002 . 69 8 8 DG H22 H 5.74 0.004 . 70 9 9 DA H2 H 7.696 0.004 . 71 9 9 DA H8 H 8.101 0.002 . 72 10 10 DG H1' H 5.576 0.003 . 73 10 10 DG H2' H 2.432 0.002 . 74 10 10 DG H2'' H 2.168 0.002 . 75 10 10 DG H4' H 4.672 0.002 . 76 10 10 DG H5' H 3.797 0.003 . 77 10 10 DG H5'' H 3.742 0.007 . 78 10 10 DG H8 H 7.734 0.003 . 79 11 11 DC H1' H 5.947 0.001 . 80 11 11 DC H2' H 2.37 0.006 . 81 11 11 DC H2'' H 1.98 0.003 . 82 11 11 DC H4' H 4.439 0.004 . 83 11 11 DC H5 H 5.565 0.002 . 84 11 11 DC H5' H 3.656 0.002 . 85 11 11 DC H5'' H 3.769 0.004 . 86 11 11 DC H6 H 7.142 0.003 . 87 12 12 DG H2' H 2.213 0.002 . 88 12 12 DG H2'' H 2.913 0.002 . 89 12 12 DG H5' H 3.889 0.003 . 90 12 12 DG H5'' H 4.022 0.006 . 91 12 12 DG H8 H 7.709 0.002 . 92 13 13 DG H1 H 11.783 0.003 . 93 13 13 DG H1' H 5.982 0.002 . 94 13 13 DG H2' H 3.156 0.003 . 95 13 13 DG H2'' H 2.836 0.005 . 96 13 13 DG H3' H 4.825 0.003 . 97 13 13 DG H4' H 4.466 0.004 . 98 13 13 DG H8 H 7.346 0.002 . 99 13 13 DG H21 H 9.824 0 . 100 14 14 DG H1 H 11.642 0.003 . 101 14 14 DG H1' H 6.257 0.001 . 102 14 14 DG H2' H 2.839 0.003 . 103 14 14 DG H2'' H 2.839 0.004 . 104 14 14 DG H3' H 5.059 0 . 105 14 14 DG H4' H 4.491 0.001 . 106 14 14 DG H8 H 7.184 0.004 . 107 15 15 DA H1' H 6.494 0.003 . 108 15 15 DA H2 H 7.862 0 . 109 15 15 DA H2' H 2.831 0.001 . 110 15 15 DA H2'' H 2.831 0.001 . 111 15 15 DA H4' H 4.527 0.001 . 112 15 15 DA H5' H 4.452 0.004 . 113 15 15 DA H5'' H 4.365 0.002 . 114 15 15 DA H8 H 8.312 0.003 . 115 16 16 DG H1' H 5.984 0.001 . 116 16 16 DG H2' H 2.466 0.002 . 117 16 16 DG H2'' H 2.759 0.002 . 118 16 16 DG H3' H 5.05 0.002 . 119 16 16 DG H4' H 4.456 0.002 . 120 16 16 DG H8 H 8.1 0.001 . 121 17 17 DA H1' H 5.973 0.002 . 122 17 17 DA H2 H 8.178 0.003 . 123 17 17 DA H2' H 2.842 0.001 . 124 17 17 DA H3' H 5.096 0.004 . 125 17 17 DA H4' H 4.492 0.001 . 126 17 17 DA H5' H 4.093 0.002 . 127 17 17 DA H5'' H 4.232 0.007 . 128 17 17 DA H8 H 8.322 0.002 . 129 18 18 DG H1 H 11.784 0.001 . 130 18 18 DG H1' H 6.141 0.002 . 131 18 18 DG H2' H 3.597 0.001 . 132 18 18 DG H2'' H 3.02 0.001 . 133 18 18 DG H3' H 5.052 0.002 . 134 18 18 DG H4' H 4.492 0 . 135 18 18 DG H8 H 7.546 0.002 . 136 18 18 DG H21 H 8.747 0 . 137 19 19 DG H1 H 11.509 0.001 . 138 19 19 DG H1' H 5.957 0.003 . 139 19 19 DG H2' H 2.775 0.006 . 140 19 19 DG H2'' H 2.774 0.006 . 141 19 19 DG H3' H 5.122 0 . 142 19 19 DG H4' H 4.499 0.006 . 143 19 19 DG H5' H 4.29 0.005 . 144 19 19 DG H5'' H 4.356 0.002 . 145 19 19 DG H8 H 8.35 0.002 . 146 19 19 DG H21 H 9.8 0.005 . 147 19 19 DG H22 H 6.304 0 . 148 20 20 DG H1 H 10.88 0.003 . 149 20 20 DG H1' H 6.412 0.001 . 150 20 20 DG H2' H 2.567 0.003 . 151 20 20 DG H2'' H 2.461 0.002 . 152 20 20 DG H3' H 4.712 0.002 . 153 20 20 DG H4' H 4.42 0.002 . 154 20 20 DG H5' H 4.264 0.001 . 155 20 20 DG H5'' H 4.335 0.005 . 156 20 20 DG H8 H 7.705 0.002 . stop_ save_