data_34034 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A two-quartet G-quadruplex formed by human telomere in KCl solution at neutral pH ; _BMRB_accession_number 34034 _BMRB_flat_file_name bmr34034.str _Entry_type original _Submission_date 2016-08-17 _Accession_date 2016-08-17 _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 Galer P. . . 2 Wang B. . . 3 Sket P. . . 4 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" 182 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-06-07 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 34035 'A two-quartet G-quadruplex formed by human telomere in KCl solution at pH 5.0' stop_ _Original_release_date 2017-07-31 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Ammonium ion as a probe to asses the kinetics of structural changes upon de/protonation of G-quadruplexes ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wang B. . . 2 Galer P. . . 3 Sket P. . . 4 Plavec J. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*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 'not present' _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(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')" _Molecular_mass 6958.484 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; TAGGGTTAGGGTTAGGGTTA GG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DA 3 3 DG 4 4 DG 5 5 DG 6 6 DT 7 7 DT 8 8 DA 9 9 DG 10 10 DG 11 11 DG 12 12 DT 13 13 DT 14 14 DA 15 15 DG 16 16 DG 17 17 DG 18 18 DT 19 19 DT 20 20 DA 21 21 DG 22 22 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 ; 1 mM 8% 13C; 8% 15N DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3'), 70 mM potassium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM '8% 13C; 8% 15N' 'potassium chloride' 70 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "1 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3'), 70 mM potassium chloride, 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'potassium chloride' 70 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details "1 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3'), 70 mM potassium chloride, 100% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'potassium chloride' 70 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_NH2_only_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC NH2 only' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_3 save_ save_2D_ROESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_3 save_ save_2D_NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_3 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' 70 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . 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 H 1 'methyl protons' ppm 0.000 external 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_3 stop_ loop_ _Experiment_label '1D 1H-15N HSQC' '2D 1H-15N HSQC NH2 only' '2D 1H-13C HSQC aromatic' '2D 1H-1H TOCSY' '2D NOESY' '2D ROESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 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 DT H1' H 6.078 0.002 1 2 1 1 DT H2' H 2.084 0.004 1 3 1 1 DT H2'' H 2.352 0.004 1 4 1 1 DT H3' H 4.678 0.002 1 5 1 1 DT H4' H 4.050 0.002 1 6 1 1 DT H6 H 7.425 0.001 1 7 1 1 DT H71 H 1.656 0.002 1 8 1 1 DT H72 H 1.656 0.002 1 9 1 1 DT H73 H 1.656 0.002 1 10 2 2 DA H1' H 6.316 0.001 1 11 2 2 DA H2 H 8.022 0.001 1 12 2 2 DA H2' H 2.757 0.000 1 13 2 2 DA H2'' H 2.811 0.001 1 14 2 2 DA H3' H 5.002 0.003 1 15 2 2 DA H4' H 4.391 0.001 1 16 2 2 DA H8 H 8.075 0.001 1 17 2 2 DA H61 H 6.790 0.001 2 18 3 3 DG H1 H 11.968 0.000 1 19 3 3 DG H1' H 6.012 0.001 1 20 3 3 DG H2' H 3.481 0.002 1 21 3 3 DG H2'' H 2.878 0.003 1 22 3 3 DG H3' H 5.008 0.007 1 23 3 3 DG H4' H 4.263 0.001 1 24 3 3 DG H5' H 4.058 0.000 2 25 3 3 DG H8 H 7.402 0.002 1 26 4 4 DG H1 H 11.966 0.001 1 27 4 4 DG H1' H 5.904 0.002 1 28 4 4 DG H2' H 2.320 0.001 1 29 4 4 DG H2'' H 2.513 0.004 1 30 4 4 DG H3' H 5.037 0.005 1 31 4 4 DG H4' H 4.443 0.002 1 32 4 4 DG H8 H 7.773 0.006 1 33 5 5 DG H1' H 5.909 0.002 1 34 5 5 DG H2' H 2.804 0.003 1 35 5 5 DG H2'' H 2.543 0.007 1 36 5 5 DG H3' H 5.056 0.004 1 37 5 5 DG H4' H 4.357 0.001 1 38 5 5 DG H5' H 4.621 0.000 2 39 5 5 DG H8 H 8.054 0.001 1 40 6 6 DT H1' H 5.965 0.001 1 41 6 6 DT H2' H 1.705 0.004 1 42 6 6 DT H2'' H 1.875 0.001 1 43 6 6 DT H3' H 4.560 0.004 1 44 6 6 DT H4' H 3.916 0.001 1 45 6 6 DT H6 H 7.537 0.001 1 46 6 6 DT H71 H 1.699 0.001 1 47 6 6 DT H72 H 1.699 0.001 1 48 6 6 DT H73 H 1.699 0.001 1 49 7 7 DT H1' H 5.646 0.001 1 50 7 7 DT H2' H 1.878 0.002 1 51 7 7 DT H2'' H 2.179 0.001 1 52 7 7 DT H3' H 4.524 0.002 1 53 7 7 DT H4' H 3.817 0.001 1 54 7 7 DT H5' H 3.309 0.000 2 55 7 7 DT H5'' H 3.536 0.000 2 56 7 7 DT H6 H 7.178 0.005 1 57 7 7 DT H71 H 1.411 0.001 1 58 7 7 DT H72 H 1.411 0.001 1 59 7 7 DT H73 H 1.411 0.001 1 60 8 8 DA H1' H 6.241 0.003 1 61 8 8 DA H2 H 7.976 0.001 1 62 8 8 DA H2' H 2.402 0.002 1 63 8 8 DA H2'' H 3.036 0.000 1 64 8 8 DA H3' H 4.828 0.001 1 65 8 8 DA H4' H 4.296 0.002 1 66 8 8 DA H8 H 8.186 0.001 1 67 8 8 DA H61 H 6.780 0.001 1 68 8 8 DA H62 H 6.830 0.001 1 69 9 9 DG H1 H 11.972 0.001 1 70 9 9 DG H1' H 5.753 0.001 1 71 9 9 DG H2' H 3.285 0.002 1 72 9 9 DG H2'' H 2.782 0.001 1 73 9 9 DG H3' H 4.967 0.001 1 74 9 9 DG H4' H 4.384 0.001 1 75 9 9 DG H5' H 4.285 0.000 2 76 9 9 DG H8 H 6.937 0.001 1 77 10 10 DG H1 H 12.053 0.001 1 78 10 10 DG H1' H 5.766 0.003 1 79 10 10 DG H2' H 2.227 0.002 1 80 10 10 DG H2'' H 2.423 0.003 1 81 10 10 DG H3' H 5.066 0.001 1 82 10 10 DG H4' H 4.291 0.003 1 83 10 10 DG H8 H 7.793 0.001 1 84 11 11 DG H1' H 6.018 0.001 1 85 11 11 DG H2' H 2.888 0.001 1 86 11 11 DG H2'' H 2.374 0.004 1 87 11 11 DG H3' H 5.037 0.004 1 88 11 11 DG H4' H 4.331 0.002 1 89 11 11 DG H5' H 4.207 0.000 2 90 11 11 DG H8 H 7.850 0.001 1 91 11 11 DG H21 H 6.270 0.001 2 92 12 12 DT H1' H 5.953 0.003 1 93 12 12 DT H2' H 1.865 0.001 1 94 12 12 DT H2'' H 2.306 0.002 1 95 12 12 DT H3' H 4.738 0.002 1 96 12 12 DT H4' H 4.209 0.001 1 97 12 12 DT H5' H 4.080 0.000 2 98 12 12 DT H6 H 7.524 0.001 1 99 12 12 DT H71 H 1.780 0.001 1 100 12 12 DT H72 H 1.780 0.001 1 101 12 12 DT H73 H 1.780 0.001 1 102 13 13 DT H1' H 5.679 0.001 1 103 13 13 DT H2' H 1.279 0.001 1 104 13 13 DT H2'' H 1.717 0.001 1 105 13 13 DT H3' H 4.543 0.001 1 106 13 13 DT H4' H 3.919 0.000 1 107 13 13 DT H5' H 3.823 0.000 2 108 13 13 DT H6 H 6.945 0.002 1 109 13 13 DT H71 H 1.127 0.000 1 110 13 13 DT H72 H 1.127 0.000 1 111 13 13 DT H73 H 1.127 0.000 1 112 14 14 DA H1' H 5.869 0.003 1 113 14 14 DA H2 H 7.222 0.002 1 114 14 14 DA H2' H 2.080 0.003 1 115 14 14 DA H2'' H 2.222 0.002 1 116 14 14 DA H3' H 4.757 0.002 1 117 14 14 DA H4' H 4.161 0.002 1 118 14 14 DA H8 H 7.657 0.001 1 119 15 15 DG H1' H 5.861 0.000 1 120 15 15 DG H2' H 2.820 0.002 1 121 15 15 DG H2'' H 2.675 0.003 1 122 15 15 DG H3' H 5.050 0.003 1 123 15 15 DG H4' H 4.513 0.000 1 124 15 15 DG H8 H 7.958 0.002 1 125 15 15 DG H21 H 5.850 0.001 2 126 16 16 DG H1 H 11.545 0.000 1 127 16 16 DG H1' H 5.738 0.001 1 128 16 16 DG H2' H 3.342 0.001 1 129 16 16 DG H2'' H 2.729 0.007 1 130 16 16 DG H3' H 5.003 0.003 1 131 16 16 DG H4' H 4.362 0.002 1 132 16 16 DG H8 H 6.889 0.003 1 133 17 17 DG H1 H 11.707 0.001 1 134 17 17 DG H1' H 5.855 0.002 1 135 17 17 DG H2' H 2.522 0.002 1 136 17 17 DG H2'' H 2.616 0.004 1 137 17 17 DG H3' H 5.156 0.003 1 138 17 17 DG H4' H 4.261 0.002 1 139 17 17 DG H8 H 7.120 0.003 1 140 18 18 DT H1' H 6.402 0.001 1 141 18 18 DT H2' H 2.435 0.002 1 142 18 18 DT H2'' H 2.549 0.003 1 143 18 18 DT H3' H 5.005 0.002 1 144 18 18 DT H4' H 4.530 0.001 1 145 18 18 DT H5' H 4.228 0.000 2 146 18 18 DT H5'' H 4.379 0.000 2 147 18 18 DT H6 H 7.972 0.001 1 148 18 18 DT H71 H 2.071 0.000 1 149 18 18 DT H72 H 2.071 0.000 1 150 18 18 DT H73 H 2.071 0.000 1 151 19 19 DT H1' H 5.891 0.001 1 152 19 19 DT H2' H 1.415 0.004 1 153 19 19 DT H2'' H 2.037 0.003 1 154 19 19 DT H3' H 4.822 0.002 1 155 19 19 DT H4' H 4.269 0.001 1 156 19 19 DT H6 H 7.490 0.006 1 157 19 19 DT H71 H 1.757 0.000 1 158 19 19 DT H72 H 1.757 0.000 1 159 19 19 DT H73 H 1.757 0.000 1 160 20 20 DA H1' H 6.280 0.001 1 161 20 20 DA H2 H 8.375 0.002 1 162 20 20 DA H2' H 2.875 0.002 1 163 20 20 DA H2'' H 2.736 0.001 1 164 20 20 DA H3' H 5.071 0.001 1 165 20 20 DA H4' H 4.421 0.004 1 166 20 20 DA H5' H 4.068 0.000 2 167 20 20 DA H8 H 8.248 0.000 1 168 20 20 DA H61 H 6.790 0.001 2 169 21 21 DG H1 H 11.776 0.000 1 170 21 21 DG H1' H 5.880 0.004 1 171 21 21 DG H2' H 3.428 0.003 1 172 21 21 DG H2'' H 2.791 0.002 1 173 21 21 DG H3' H 5.022 0.001 1 174 21 21 DG H4' H 4.199 0.000 1 175 21 21 DG H8 H 7.273 0.003 1 176 22 22 DG H1 H 11.573 0.000 1 177 22 22 DG H1' H 5.977 0.008 1 178 22 22 DG H2' H 2.419 0.004 1 179 22 22 DG H2'' H 2.469 0.002 1 180 22 22 DG H3' H 4.745 0.002 1 181 22 22 DG H4' H 4.202 0.004 1 182 22 22 DG H8 H 7.385 0.005 1 stop_ save_