data_34135 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; M2 G-quadruplex dilute solution ; _BMRB_accession_number 34135 _BMRB_flat_file_name bmr34135.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" 182 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-04-06 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 34136 'M2 G-quadruplex 20 wt% ethylene glycol' 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, 1 mM 0 M2, 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 VNMRJ _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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_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_ save_sample_conditions_2 _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 DQF-COSY' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' 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 5.839 0.002 1 2 1 1 DT H2' H 1.704 0.003 1 3 1 1 DT H2'' H 2.155 0.003 1 4 1 1 DT H3' H 4.506 0.001 1 5 1 1 DT H4' H 3.940 0.001 1 6 1 1 DT H5' H 3.504 0.001 2 7 1 1 DT H5'' H 3.504 0.001 2 8 1 1 DT H6 H 7.180 0.000 1 9 1 1 DT H71 H 1.607 0.004 2 10 1 1 DT H72 H 1.607 0.004 2 11 1 1 DT H73 H 1.607 0.004 2 12 2 2 DA H1' H 5.857 0.006 1 13 2 2 DA H2 H 7.885 0.001 1 14 2 2 DA H2' H 2.487 0.002 1 15 2 2 DA H2'' H 2.672 0.001 1 16 2 2 DA H3' H 4.900 0.010 1 17 2 2 DA H4' H 4.180 0.001 1 18 2 2 DA H5' H 3.744 0.002 1 19 2 2 DA H5'' H 3.930 0.004 1 20 2 2 DA H8 H 8.040 0.001 1 21 3 3 DG H1 H 11.689 0.002 1 22 3 3 DG H1' H 6.133 0.002 1 23 3 3 DG H2' H 2.848 0.002 1 24 3 3 DG H2'' H 3.056 0.000 1 25 3 3 DG H3' H 5.054 0.005 1 26 3 3 DG H4' H 4.534 0.001 1 27 3 3 DG H5' H 4.165 0.003 1 28 3 3 DG H5'' H 4.222 0.002 1 29 3 3 DG H8 H 8.110 0.001 1 30 4 4 DG H1 H 11.563 0.002 1 31 4 4 DG H1' H 6.127 0.001 1 32 4 4 DG H2' H 2.682 0.003 1 33 4 4 DG H2'' H 2.790 0.002 1 34 4 4 DG H3' H 4.988 0.003 1 35 4 4 DG H4' H 4.531 0.001 1 36 4 4 DG H5' H 4.346 0.003 2 37 4 4 DG H5'' H 4.346 0.003 2 38 4 4 DG H8 H 7.781 0.002 1 39 5 5 DG H1 H 11.352 0.002 1 40 5 5 DG H1' H 6.291 0.001 1 41 5 5 DG H2' H 2.521 0.003 1 42 5 5 DG H2'' H 2.478 0.004 1 43 5 5 DG H3' H 4.966 0.002 1 44 5 5 DG H4' H 4.171 0.002 1 45 5 5 DG H5' H 4.010 0.006 1 46 5 5 DG H5'' H 3.614 0.005 1 47 5 5 DG H8 H 7.705 0.001 1 48 6 6 DA H1' H 6.572 0.002 1 49 6 6 DA H2 H 8.400 0.002 1 50 6 6 DA H2' H 3.061 0.006 1 51 6 6 DA H2'' H 2.948 0.001 1 52 6 6 DA H3' H 5.066 0.004 1 53 6 6 DA H4' H 4.533 0.004 1 54 6 6 DA H5'' H 4.167 0.003 1 55 6 6 DA H8 H 8.626 0.001 1 56 7 7 DC H1' H 6.402 0.000 1 57 7 7 DC H2' H 2.450 0.000 1 58 7 7 DC H2'' H 2.708 0.001 1 59 7 7 DC H3' H 4.970 0.003 1 60 7 7 DC H4' H 4.492 0.002 1 61 7 7 DC H5 H 6.104 0.000 1 62 7 7 DC H5' H 4.305 0.001 1 63 7 7 DC H6 H 7.958 0.003 1 64 8 8 DG H1 H 11.925 0.001 1 65 8 8 DG H1' H 6.165 0.001 1 66 8 8 DG H2' H 2.484 0.002 1 67 8 8 DG H2'' H 3.052 0.002 1 68 8 8 DG H3' H 4.861 0.002 1 69 8 8 DG H4' H 4.430 0.004 1 70 8 8 DG H5' H 3.616 0.002 1 71 8 8 DG H5'' H 4.047 0.003 1 72 8 8 DG H8 H 7.955 0.001 1 73 9 9 DG H1 H 11.448 0.006 1 74 9 9 DG H1' H 6.277 0.001 1 75 9 9 DG H2' H 2.810 0.001 1 76 9 9 DG H2'' H 3.004 0.001 1 77 9 9 DG H3' H 5.112 0.001 1 78 9 9 DG H4' H 4.613 0.005 1 79 9 9 DG H5' H 4.330 0.005 2 80 9 9 DG H5'' H 4.330 0.005 2 81 9 9 DG H8 H 8.020 0.000 1 82 10 10 DG H1 H 11.264 0.003 1 83 10 10 DG H1' H 6.464 0.002 1 84 10 10 DG H2' H 2.732 0.001 1 85 10 10 DG H2'' H 2.571 0.002 1 86 10 10 DG H3' H 5.132 0.002 1 87 10 10 DG H4' H 4.656 0.002 1 88 10 10 DG H5' H 4.331 0.002 1 89 10 10 DG H5'' H 4.422 0.005 1 90 10 10 DG H8 H 7.864 0.001 1 91 11 11 DC H1' H 6.509 0.003 1 92 11 11 DC H2' H 2.447 0.003 1 93 11 11 DC H2'' H 2.767 0.001 1 94 11 11 DC H3' H 5.115 0.002 1 95 11 11 DC H4' H 4.641 0.001 1 96 11 11 DC H5 H 6.192 0.000 1 97 11 11 DC H5' H 4.393 0.002 2 98 11 11 DC H5'' H 4.393 0.002 2 99 11 11 DC H6 H 8.025 0.003 1 100 12 12 DG H1 H 11.950 0.001 1 101 12 12 DG H1' H 6.228 0.004 1 102 12 12 DG H2' H 2.567 0.001 1 103 12 12 DG H2'' H 2.997 0.001 1 104 12 12 DG H3' H 5.202 0.002 1 105 12 12 DG H4' H 4.515 0.001 1 106 12 12 DG H5' H 4.382 0.002 1 107 12 12 DG H5'' H 4.271 0.003 1 108 12 12 DG H8 H 8.109 0.000 1 109 13 13 DG H1 H 11.493 0.002 1 110 13 13 DG H1' H 6.191 0.002 1 111 13 13 DG H2' H 2.720 0.001 1 112 13 13 DG H2'' H 2.885 0.002 1 113 13 13 DG H3' H 5.106 0.004 1 114 13 13 DG H4' H 4.476 0.003 1 115 13 13 DG H5' H 4.260 0.001 1 116 13 13 DG H5'' H 4.312 0.007 1 117 13 13 DG H8 H 7.989 0.001 1 118 14 14 DG H1 H 11.078 0.004 1 119 14 14 DG H1' H 6.418 0.001 1 120 14 14 DG H2' H 2.664 0.004 1 121 14 14 DG H2'' H 2.520 0.001 1 122 14 14 DG H3' H 5.009 0.005 1 123 14 14 DG H4' H 4.507 0.008 1 124 14 14 DG H5' H 4.295 0.004 2 125 14 14 DG H5'' H 4.295 0.004 2 126 14 14 DG H8 H 7.833 0.001 1 127 15 15 DC H1' H 6.226 0.000 1 128 15 15 DC H2' H 2.158 0.001 1 129 15 15 DC H2'' H 2.520 0.008 1 130 15 15 DC H3' H 4.720 0.002 1 131 15 15 DC H4' H 3.901 0.002 1 132 15 15 DC H5 H 6.129 0.000 1 133 15 15 DC H5' H 3.728 0.002 2 134 15 15 DC H5'' H 3.728 0.002 2 135 15 15 DC H6 H 7.807 0.003 1 136 16 16 DA H1' H 6.699 0.002 1 137 16 16 DA H2 H 8.384 0.001 1 138 16 16 DA H2' H 3.128 0.001 1 139 16 16 DA H2'' H 2.986 0.002 1 140 16 16 DA H3' H 5.204 0.002 1 141 16 16 DA H4' H 4.606 0.004 1 142 16 16 DA H5' H 4.226 0.002 1 143 16 16 DA H5'' H 4.313 0.004 1 144 16 16 DA H8 H 8.530 0.001 1 145 17 17 DG H1 H 11.417 0.008 1 146 17 17 DG H1' H 6.108 0.001 1 147 17 17 DG H2' H 2.589 0.001 1 148 17 17 DG H2'' H 2.850 0.002 1 149 17 17 DG H3' H 5.030 0.004 1 150 17 17 DG H4' H 4.499 0.005 1 151 17 17 DG H5' H 4.301 0.000 1 152 17 17 DG H5'' H 4.213 0.003 1 153 17 17 DG H8 H 8.103 0.001 1 154 18 18 DG H1 H 11.346 0.006 1 155 18 18 DG H1' H 6.094 0.002 1 156 18 18 DG H2' H 2.749 0.002 1 157 18 18 DG H2'' H 2.779 0.001 1 158 18 18 DG H3' H 5.054 0.002 1 159 18 18 DG H4' H 4.532 0.003 1 160 18 18 DG H5' H 4.229 0.005 2 161 18 18 DG H5'' H 4.229 0.005 2 162 18 18 DG H8 H 7.884 0.002 1 163 19 19 DG H1 H 11.180 0.007 1 164 19 19 DG H1' H 6.227 0.003 1 165 19 19 DG H2' H 2.621 0.001 1 166 19 19 DG H2'' H 2.795 0.003 1 167 19 19 DG H3' H 4.942 0.006 1 168 19 19 DG H4' H 4.537 0.002 1 169 19 19 DG H5' H 4.313 0.001 1 170 19 19 DG H5'' H 4.266 0.001 1 171 19 19 DG H8 H 7.736 0.000 1 172 20 20 DT H1' H 5.929 0.002 1 173 20 20 DT H2' H 2.094 0.004 2 174 20 20 DT H2'' H 2.094 0.004 2 175 20 20 DT H3' H 4.451 0.002 1 176 20 20 DT H4' H 3.987 0.003 1 177 20 20 DT H5' H 4.257 0.005 1 178 20 20 DT H5'' H 4.090 0.002 1 179 20 20 DT H6 H 7.157 0.002 1 180 20 20 DT H71 H 1.531 0.001 2 181 20 20 DT H72 H 1.531 0.001 2 182 20 20 DT H73 H 1.531 0.001 2 stop_ save_