data_34269 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure ; _BMRB_accession_number 34269 _BMRB_flat_file_name bmr34269.str _Entry_type original _Submission_date 2018-05-04 _Accession_date 2018-05-04 _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 Kotar A. . . 2 Rigo R. . . 3 Sissi C. . . 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" 193 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-08-13 update BMRB 'update entry citation' 2019-01-07 original author 'original release' stop_ _Original_release_date 2019-01-02 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30590801 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kotar A. . . 2 Rigo R. . . 3 Sissi C. . . 4 Plavec J. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 47 _Journal_issue 5 _Journal_ASTM NARHAD _Journal_ISSN 1362-4962 _Journal_CSD 0389 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2641 _Page_last 2653 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-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 6940.439 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGCGAGGAGGGGCGTGGCCG GC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DC 4 DG 5 DA 6 DG 7 DG 8 DA 9 DG 10 DG 11 DG 12 DG 13 DC 14 DG 15 DT 16 DG 17 DG 18 DC 19 DC 20 DG 21 DG 22 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 $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_5 _Saveframe_category sample _Sample_type solution _Details ; 0.5 mM 10% 13C, 10% 15N DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[10% 13C; 10% 15N]' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type solution _Details ; 0.4 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_7 _Saveframe_category sample _Sample_type solution _Details ; 0.4 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 100% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_8 _Saveframe_category sample _Sample_type solution _Details ; 0.5 mM DNA (5'-D(*GP*GP*CP*GP*AP*GP*GP*AP*GP*GP*GP*GP*CP*GP*TP*GP*GP*CP*CP*GP*GP*C)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name VNMR _Version 3.2A loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name AMBER _Version 14 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 Varian _Model 'Uniform NMR System' _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Uniform NMR System' _Field_strength 600 _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_8 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_8 save_ save_1D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H-15N HSQC' _Sample_label $sample_5 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_5 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_5 save_ save_2D_1H-1H_TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_7 save_ save_2D_1H-13C_HSQC_aromatic_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_6 save_ save_2D_1H-15N_HSQC_NH2_only_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC NH2 only' _Sample_label $sample_5 save_ save_2D_DQF-COSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_7 save_ save_2D_1H-1H_NOESY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_6 save_ save_2D_1H-1H_NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_6 save_ save_2D_1H-1H_NOESY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_7 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 7.4 . pH pressure 1 . atm temperature 310 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 7.8 . pD pressure 1 . atm temperature 310 . 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 TMS H 1 'methyl protons' ppm 0.0 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_ _Experiment_label '2D 1H-1H NOESY' '1D 1H-15N HSQC' '2D 1H-15N HSQC' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D 1H-13C HSQC aromatic' '2D 1H-15N HSQC NH2 only' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_8 $sample_5 $sample_7 $sample_6 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 12.134 0.001 1 2 1 1 DG H1' H 5.910 0.004 1 3 1 1 DG H2' H 2.850 0.001 1 4 1 1 DG H2'' H 2.909 0.000 1 5 1 1 DG H3' H 5.006 0.000 1 6 1 1 DG H4' H 4.361 0.000 1 7 1 1 DG H5' H 4.153 0.000 2 8 1 1 DG H5'' H 4.153 0.000 2 9 1 1 DG H8 H 7.087 0.004 1 10 2 2 DG H1 H 12.057 0.004 1 11 2 2 DG H1' H 5.630 0.004 1 12 2 2 DG H2' H 2.507 0.000 1 13 2 2 DG H2'' H 2.507 0.006 1 14 2 2 DG H3' H 5.013 0.000 1 15 2 2 DG H4' H 4.364 0.000 1 16 2 2 DG H5' H 4.149 0.000 2 17 2 2 DG H5'' H 4.149 0.000 2 18 2 2 DG H8 H 7.929 0.005 1 19 3 3 DC H1' H 6.235 0.004 1 20 3 3 DC H2' H 2.117 0.004 1 21 3 3 DC H2'' H 2.731 0.000 1 22 3 3 DC H4' H 4.358 0.000 1 23 3 3 DC H5 H 5.874 0.005 1 24 3 3 DC H5' H 4.108 0.000 2 25 3 3 DC H5'' H 4.108 0.000 2 26 3 3 DC H6 H 7.911 0.005 1 27 4 4 DG H1' H 5.740 0.004 1 28 4 4 DG H2' H 2.224 0.006 2 29 4 4 DG H2'' H 2.224 0.006 2 30 4 4 DG H3' H 4.860 0.000 1 31 4 4 DG H4' H 4.292 0.000 1 32 4 4 DG H5' H 4.131 0.000 2 33 4 4 DG H5'' H 4.131 0.000 2 34 4 4 DG H8 H 7.730 0.007 1 35 5 5 DA H1' H 6.189 0.002 1 36 5 5 DA H2 H 7.636 0.002 1 37 5 5 DA H2' H 2.656 0.006 2 38 5 5 DA H2'' H 2.656 0.006 2 39 5 5 DA H3' H 4.840 0.000 1 40 5 5 DA H5' H 4.173 0.000 2 41 5 5 DA H5'' H 4.173 0.000 2 42 5 5 DA H8 H 8.136 0.003 1 43 6 6 DG H1 H 11.831 0.002 1 44 6 6 DG H1' H 6.077 0.003 1 45 6 6 DG H2' H 3.380 0.007 1 46 6 6 DG H2'' H 2.907 0.003 1 47 6 6 DG H3' H 4.826 0.000 1 48 6 6 DG H4' H 4.329 0.000 1 49 6 6 DG H5' H 3.637 0.001 1 50 6 6 DG H5'' H 3.782 0.005 1 51 6 6 DG H8 H 7.382 0.001 1 52 7 7 DG H1 H 11.861 0.006 1 53 7 7 DG H1' H 6.254 0.007 1 54 7 7 DG H2' H 2.602 0.003 1 55 7 7 DG H2'' H 2.976 0.008 1 56 7 7 DG H3' H 5.211 0.002 1 57 7 7 DG H4' H 4.955 0.004 1 58 7 7 DG H5' H 4.339 0.000 2 59 7 7 DG H5'' H 4.339 0.000 2 60 7 7 DG H8 H 8.368 0.003 1 61 8 8 DA H1' H 6.592 0.001 1 62 8 8 DA H2 H 8.286 0.001 1 63 8 8 DA H2' H 3.043 0.006 2 64 8 8 DA H2'' H 3.043 0.006 2 65 8 8 DA H3' H 4.844 0.000 1 66 8 8 DA H4' H 4.494 0.000 1 67 8 8 DA H5' H 4.178 0.000 2 68 8 8 DA H5'' H 4.178 0.000 2 69 8 8 DA H8 H 8.574 0.001 1 70 9 9 DG H1' H 5.915 0.007 1 71 9 9 DG H2' H 1.882 0.003 2 72 9 9 DG H2'' H 1.882 0.003 2 73 9 9 DG H3' H 4.806 0.000 1 74 9 9 DG H4' H 4.356 0.000 1 75 9 9 DG H5' H 4.049 0.000 2 76 9 9 DG H5'' H 4.049 0.000 2 77 9 9 DG H8 H 7.919 0.002 1 78 10 10 DG H1 H 13.504 0.004 1 79 10 10 DG H1' H 5.891 0.007 1 80 10 10 DG H2' H 3.015 0.002 1 81 10 10 DG H2'' H 2.535 0.007 1 82 10 10 DG H3' H 5.082 0.002 1 83 10 10 DG H4' H 4.794 0.000 1 84 10 10 DG H5' H 4.219 0.000 1 85 10 10 DG H5'' H 4.233 0.000 1 86 10 10 DG H8 H 7.304 0.004 1 87 10 10 DG H21 H 6.815 0.000 2 88 10 10 DG H22 H 6.815 0.000 2 89 11 11 DG H1 H 11.202 0.001 1 90 11 11 DG H1' H 5.780 0.005 1 91 11 11 DG H2' H 2.673 0.002 1 92 11 11 DG H2'' H 3.048 0.000 1 93 11 11 DG H3' H 4.957 0.000 1 94 11 11 DG H4' H 4.368 0.000 1 95 11 11 DG H5' H 4.198 0.000 2 96 11 11 DG H5'' H 4.198 0.000 2 97 11 11 DG H8 H 7.135 0.001 1 98 12 12 DG H1 H 11.650 0.005 1 99 12 12 DG H1' H 6.134 0.006 1 100 12 12 DG H2' H 2.502 0.004 2 101 12 12 DG H2'' H 2.712 0.004 2 102 12 12 DG H3' H 4.826 0.000 1 103 12 12 DG H4' H 4.514 0.000 1 104 12 12 DG H5' H 4.111 0.000 2 105 12 12 DG H5'' H 4.111 0.000 2 106 12 12 DG H8 H 7.680 0.003 1 107 13 13 DC H1' H 6.353 0.002 1 108 13 13 DC H2' H 2.220 0.002 1 109 13 13 DC H2'' H 2.649 0.005 1 110 13 13 DC H3' H 4.892 0.000 1 111 13 13 DC H4' H 4.406 0.000 1 112 13 13 DC H5 H 6.164 0.007 1 113 13 13 DC H5' H 4.248 0.000 2 114 13 13 DC H5'' H 4.248 0.000 2 115 13 13 DC H6 H 8.050 0.006 1 116 14 14 DG H1' H 5.762 0.001 1 117 14 14 DG H2' H 2.290 0.005 2 118 14 14 DG H2'' H 2.290 0.005 2 119 14 14 DG H3' H 4.889 0.000 1 120 14 14 DG H4' H 4.258 0.000 1 121 14 14 DG H5' H 4.076 0.000 2 122 14 14 DG H5'' H 4.076 0.000 2 123 14 14 DG H8 H 7.663 0.004 1 124 15 15 DT H1' H 5.849 0.007 1 125 15 15 DT H2' H 2.112 0.000 1 126 15 15 DT H2'' H 2.513 0.003 1 127 15 15 DT H3' H 4.681 0.000 1 128 15 15 DT H4' H 4.046 0.000 1 129 15 15 DT H5' H 3.183 0.005 1 130 15 15 DT H5'' H 3.736 0.002 1 131 15 15 DT H6 H 7.292 0.004 1 132 15 15 DT H71 H 1.669 0.002 3 133 15 15 DT H72 H 1.669 0.001 3 134 15 15 DT H73 H 1.669 0.000 3 135 16 16 DG H1 H 12.028 0.002 1 136 16 16 DG H1' H 6.114 0.006 1 137 16 16 DG H2' H 2.940 0.003 1 138 16 16 DG H2'' H 3.474 0.001 1 139 16 16 DG H3' H 4.910 0.000 1 140 16 16 DG H4' H 4.512 0.000 1 141 16 16 DG H5' H 4.070 0.001 1 142 16 16 DG H5'' H 4.303 0.000 1 143 16 16 DG H8 H 7.528 0.001 1 144 17 17 DG H1 H 12.015 0.002 1 145 17 17 DG H1' H 5.777 0.003 1 146 17 17 DG H2' H 2.731 0.005 2 147 17 17 DG H2'' H 2.531 0.005 2 148 17 17 DG H3' H 5.036 0.000 1 149 17 17 DG H4' H 4.508 0.000 1 150 17 17 DG H5' H 4.296 0.000 2 151 17 17 DG H5'' H 4.296 0.000 2 152 17 17 DG H8 H 8.135 0.003 1 153 18 18 DC H1' H 6.299 0.004 1 154 18 18 DC H2' H 2.623 0.005 1 155 18 18 DC H2'' H 2.335 0.004 1 156 18 18 DC H3' H 4.823 0.000 1 157 18 18 DC H4' H 4.348 0.000 1 158 18 18 DC H5 H 5.531 0.005 1 159 18 18 DC H5' H 4.276 0.000 2 160 18 18 DC H5'' H 4.276 0.000 2 161 18 18 DC H6 H 7.802 0.004 1 162 18 18 DC H41 H 8.525 0.003 1 163 18 18 DC H42 H 6.289 0.005 1 164 19 19 DC H1' H 5.962 0.004 1 165 19 19 DC H2' H 1.879 0.002 1 166 19 19 DC H2'' H 2.338 0.000 1 167 19 19 DC H3' H 4.805 0.000 1 168 19 19 DC H4' H 4.257 0.000 1 169 19 19 DC H5 H 5.632 0.005 1 170 19 19 DC H5' H 4.100 0.000 2 171 19 19 DC H5'' H 4.100 0.000 2 172 19 19 DC H6 H 7.430 0.004 1 173 20 20 DG H1' H 5.732 0.004 1 174 20 20 DG H2' H 2.448 0.002 2 175 20 20 DG H2'' H 2.448 0.002 2 176 20 20 DG H3' H 4.840 0.000 1 177 20 20 DG H5' H 4.053 0.000 2 178 20 20 DG H5'' H 4.053 0.000 2 179 20 20 DG H8 H 7.681 0.002 1 180 21 21 DG H1' H 6.003 0.002 1 181 21 21 DG H2' H 2.668 0.002 1 182 21 21 DG H2'' H 2.532 0.003 1 183 21 21 DG H3' H 4.888 0.000 1 184 21 21 DG H4' H 4.215 0.000 1 185 21 21 DG H5' H 4.060 0.000 2 186 21 21 DG H5'' H 4.060 0.000 2 187 21 21 DG H8 H 7.836 0.001 1 188 22 22 DC H1' H 6.114 0.003 1 189 22 22 DC H2' H 2.323 0.007 2 190 22 22 DC H2'' H 2.323 0.007 2 191 22 22 DC H3' H 5.008 0.000 1 192 22 22 DC H5 H 5.823 0.004 1 193 22 22 DC H6 H 7.677 0.006 1 stop_ save_