data_34136 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; M2 G-quadruplex 20 wt% ethylene glycol ; _BMRB_accession_number 34136 _BMRB_flat_file_name bmr34136.str _Entry_type original _Submission_date 2017-05-11 _Accession_date 2017-05-11 _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 Trajkovski M. . . 2 Plavec J. . . 3 Endoh T. . . 4 Tateishi-Karimata H. . . 5 Sugimoto N. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 184 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-04-06 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 34135 'M2 G-quadruplex dilute solution' 34137 'M2 G-quadruplex 10 wt% PEG8000' stop_ _Original_release_date 2018-04-03 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; M2 G-quadruplex ; _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 Trajkovski M. . . 2 Plavec J. . . 3 Endoh T. . . 4 Tateishi-Karimata H. . . 5 Sugimoto N. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume . _Journal_issue . _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 . _Page_last . _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*TP*AP*GP*GP*GP*AP*CP*GP*GP*GP*CP*GP*GP*GP*CP*AP*GP*GP*GP*T)-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 6321.064 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; TAGGGACGGGCGGGCAGGGT ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DG 4 DG 5 DG 6 DA 7 DC 8 DG 9 DG 10 DG 11 DC 12 DG 13 DG 14 DG 15 DC 16 DA 17 DG 18 DG 19 DG 20 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 $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 '0.2 mM 0 M2 20EG, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.2 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 AMBER _Version 14 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model "Agilent-Varian 'Uniform NMR System' 1" _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model "Agilent-Varian 'Uniform NMR System' 2" _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_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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' 120 . mM pH 7.0 . pH pressure 1 . bar 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 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' '2D 1H-1H TOCSY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 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 5.857 0.001 1 2 1 1 DT H2' H 1.704 0.003 1 3 1 1 DT H2'' H 2.172 0.003 1 4 1 1 DT H3' H 4.519 0.002 1 5 1 1 DT H4' H 3.942 0.002 1 6 1 1 DT H5' H 3.515 0.001 2 7 1 1 DT H5'' H 3.515 0.001 2 8 1 1 DT H6 H 7.205 0.001 1 9 1 1 DT H71 H 1.618 0.003 2 10 1 1 DT H72 H 1.618 0.003 2 11 1 1 DT H73 H 1.618 0.003 2 12 2 2 DA H1' H 5.896 0.004 1 13 2 2 DA H2 H 7.888 0.001 1 14 2 2 DA H2' H 2.529 0.002 1 15 2 2 DA H2'' H 2.701 0.004 1 16 2 2 DA H3' H 4.911 0.010 1 17 2 2 DA H4' H 4.207 0.002 1 18 2 2 DA H5' H 3.777 0.003 1 19 2 2 DA H5'' H 3.936 0.000 1 20 2 2 DA H8 H 8.061 0.007 1 21 3 3 DG H1 H 11.685 0.002 1 22 3 3 DG H1' H 6.119 0.002 1 23 3 3 DG H2' H 2.817 0.004 1 24 3 3 DG H2'' H 3.040 0.001 1 25 3 3 DG H3' H 5.049 0.002 1 26 3 3 DG H4' H 4.515 0.003 1 27 3 3 DG H5' H 4.176 0.006 1 28 3 3 DG H5'' H 4.198 0.001 1 29 3 3 DG H8 H 8.098 0.002 1 30 4 4 DG H1 H 11.572 0.001 1 31 4 4 DG H1' H 6.132 0.001 1 32 4 4 DG H2' H 2.678 0.003 1 33 4 4 DG H2'' H 2.805 0.004 1 34 4 4 DG H3' H 4.991 0.004 1 35 4 4 DG H4' H 4.521 0.004 1 36 4 4 DG H5' H 4.342 0.002 2 37 4 4 DG H5'' H 4.342 0.002 2 38 4 4 DG H8 H 7.772 0.001 1 39 5 5 DG H1 H 11.349 0.008 1 40 5 5 DG H1' H 6.289 0.004 1 41 5 5 DG H2' H 2.552 0.001 1 42 5 5 DG H2'' H 2.471 0.002 1 43 5 5 DG H3' H 4.979 0.002 1 44 5 5 DG H4' H 4.200 0.004 1 45 5 5 DG H5' H 4.033 0.007 1 46 5 5 DG H5'' H 3.681 0.001 1 47 5 5 DG H8 H 7.727 0.002 1 48 6 6 DA H1' H 6.575 0.005 1 49 6 6 DA H2 H 8.400 0.003 1 50 6 6 DA H2' H 3.061 0.002 1 51 6 6 DA H2'' H 2.945 0.004 1 52 6 6 DA H3' H 5.063 0.005 1 53 6 6 DA H4' H 4.526 0.003 1 54 6 6 DA H5' H 4.305 0.000 1 55 6 6 DA H5'' H 4.199 0.007 1 56 6 6 DA H8 H 8.634 0.000 1 57 7 7 DC H1' H 6.407 0.001 1 58 7 7 DC H2' H 2.463 0.005 1 59 7 7 DC H2'' H 2.696 0.001 1 60 7 7 DC H3' H 4.981 0.000 1 61 7 7 DC H4' H 4.483 0.018 1 62 7 7 DC H5 H 6.114 0.000 1 63 7 7 DC H5' H 4.298 0.004 2 64 7 7 DC H5'' H 4.298 0.004 2 65 7 7 DC H6 H 7.975 0.001 1 66 8 8 DG H1 H 11.934 0.003 1 67 8 8 DG H1' H 6.167 0.002 1 68 8 8 DG H2' H 2.485 0.008 1 69 8 8 DG H2'' H 3.060 0.002 1 70 8 8 DG H3' H 4.862 0.009 1 71 8 8 DG H4' H 4.425 0.004 1 72 8 8 DG H5' H 3.616 0.004 1 73 8 8 DG H5'' H 4.041 0.003 1 74 8 8 DG H8 H 7.950 0.001 1 75 9 9 DG H1 H 11.459 0.004 1 76 9 9 DG H1' H 6.280 0.002 1 77 9 9 DG H2' H 2.798 0.004 1 78 9 9 DG H2'' H 3.011 0.004 1 79 9 9 DG H3' H 5.107 0.001 1 80 9 9 DG H4' H 4.590 0.006 1 81 9 9 DG H5' H 4.327 0.004 1 82 9 9 DG H5'' H 4.327 0.004 1 83 9 9 DG H8 H 8.010 0.001 1 84 10 10 DG H1 H 11.269 0.006 1 85 10 10 DG H1' H 6.460 0.001 1 86 10 10 DG H2' H 2.745 0.001 1 87 10 10 DG H2'' H 2.557 0.000 1 88 10 10 DG H3' H 5.133 0.004 1 89 10 10 DG H4' H 4.650 0.001 1 90 10 10 DG H5' H 4.333 0.001 1 91 10 10 DG H5'' H 4.417 0.002 1 92 10 10 DG H8 H 7.869 0.001 1 93 11 11 DC H1' H 6.506 0.003 1 94 11 11 DC H2' H 2.441 0.001 1 95 11 11 DC H2'' H 2.761 0.001 1 96 11 11 DC H3' H 5.114 0.001 1 97 11 11 DC H4' H 4.624 0.005 1 98 11 11 DC H5 H 6.196 0.000 1 99 11 11 DC H5' H 4.399 0.004 2 100 11 11 DC H5'' H 4.399 0.004 2 101 11 11 DC H6 H 8.036 0.003 1 102 12 12 DG H1 H 11.948 0.000 1 103 12 12 DG H1' H 6.225 0.002 1 104 12 12 DG H2' H 2.567 0.002 1 105 12 12 DG H2'' H 2.995 0.005 1 106 12 12 DG H3' H 5.202 0.001 1 107 12 12 DG H4' H 4.508 0.001 1 108 12 12 DG H5' H 4.373 0.002 1 109 12 12 DG H5'' H 4.252 0.006 1 110 12 12 DG H8 H 8.104 0.001 1 111 13 13 DG H1 H 11.506 0.004 1 112 13 13 DG H1' H 6.190 0.006 1 113 13 13 DG H2' H 2.715 0.001 1 114 13 13 DG H2'' H 2.891 0.001 1 115 13 13 DG H3' H 5.102 0.001 1 116 13 13 DG H4' H 4.452 0.002 1 117 13 13 DG H5' H 4.255 0.006 1 118 13 13 DG H5'' H 4.308 0.006 1 119 13 13 DG H8 H 7.975 0.002 1 120 14 14 DG H1 H 11.110 0.002 1 121 14 14 DG H1' H 6.406 0.006 1 122 14 14 DG H2' H 2.682 0.012 1 123 14 14 DG H2'' H 2.509 0.003 1 124 14 14 DG H3' H 5.012 0.006 1 125 14 14 DG H4' H 4.522 0.004 1 126 14 14 DG H5' H 4.294 0.003 2 127 14 14 DG H5'' H 4.294 0.003 2 128 14 14 DG H8 H 7.841 0.001 1 129 15 15 DC H1' H 6.248 0.001 1 130 15 15 DC H2' H 2.181 0.002 1 131 15 15 DC H2'' H 2.529 0.004 1 132 15 15 DC H3' H 4.726 0.006 1 133 15 15 DC H4' H 3.912 0.003 1 134 15 15 DC H5 H 6.129 0.000 1 135 15 15 DC H5' H 3.752 0.004 2 136 15 15 DC H5'' H 3.752 0.004 2 137 15 15 DC H6 H 7.837 0.001 1 138 16 16 DA H1' H 6.697 0.002 1 139 16 16 DA H2 H 8.384 0.001 1 140 16 16 DA H2' H 3.128 0.004 1 141 16 16 DA H2'' H 2.975 0.002 1 142 16 16 DA H3' H 5.199 0.003 1 143 16 16 DA H4' H 4.599 0.004 1 144 16 16 DA H5' H 4.221 0.003 1 145 16 16 DA H5'' H 4.307 0.007 1 146 16 16 DA H8 H 8.558 0.001 1 147 17 17 DG H1 H 11.455 0.007 1 148 17 17 DG H1' H 6.107 0.002 1 149 17 17 DG H2' H 2.597 0.003 1 150 17 17 DG H2'' H 2.866 0.005 1 151 17 17 DG H3' H 5.034 0.003 1 152 17 17 DG H4' H 4.494 0.008 1 153 17 17 DG H5' H 4.309 0.013 1 154 17 17 DG H5'' H 4.218 0.011 1 155 17 17 DG H8 H 8.092 0.001 1 156 18 18 DG H1 H 11.356 0.006 1 157 18 18 DG H1' H 6.110 0.002 1 158 18 18 DG H2' H 2.733 0.003 1 159 18 18 DG H2'' H 2.803 0.004 1 160 18 18 DG H3' H 5.056 0.003 1 161 18 18 DG H4' H 4.529 0.002 1 162 18 18 DG H5' H 4.229 0.004 2 163 18 18 DG H5'' H 4.229 0.004 2 164 18 18 DG H8 H 7.882 0.001 1 165 19 19 DG H1 H 11.176 0.003 1 166 19 19 DG H1' H 6.241 0.003 1 167 19 19 DG H2' H 2.614 0.001 1 168 19 19 DG H2'' H 2.747 0.002 1 169 19 19 DG H3' H 4.968 0.001 1 170 19 19 DG H4' H 4.526 0.002 1 171 19 19 DG H5' H 4.316 0.001 1 172 19 19 DG H5'' H 4.245 0.004 1 173 19 19 DG H8 H 7.745 0.002 1 174 20 20 DT H1' H 6.001 0.001 1 175 20 20 DT H2' H 2.141 0.001 2 176 20 20 DT H2'' H 2.141 0.001 2 177 20 20 DT H3' H 4.476 0.002 1 178 20 20 DT H4' H 4.015 0.003 1 179 20 20 DT H5' H 4.246 0.005 1 180 20 20 DT H5'' H 4.085 0.003 1 181 20 20 DT H6 H 7.265 0.002 1 182 20 20 DT H71 H 1.609 0.003 2 183 20 20 DT H72 H 1.609 0.003 2 184 20 20 DT H73 H 1.609 0.003 2 stop_ save_