data_34168 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; G-quadruplex structure of DNA oligonucleotide containing GGGGCC repeats linked to ALS and FTD ; _BMRB_accession_number 34168 _BMRB_flat_file_name bmr34168.str _Entry_type original _Submission_date 2017-08-09 _Accession_date 2017-08-09 _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 Brcic J. . . 2 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" 176 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-08-24 original BMRB . stop_ _Original_release_date 2018-08-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; G-quadruplex structure of DNA oligonucleotide with GGGGCC repeats, linked to ALS and FTD ; _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 Brcic J. . . 2 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(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*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 7036.323 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGGCCGGGGCCGGGGCCGG XG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DG 5 DC 6 DC 7 DG 8 DG 9 DG 10 DG 11 DC 12 DC 13 DG 14 DG 15 DG 16 DG 17 DC 18 DC 19 DG 20 DG 21 BGM 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_BGM _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE _BMRB_code BGM _PDB_code BGM _Standard_residue_derivative . _Molecular_mass 426.117 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C4 C4 C . 0 . ? N3 N3 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? BR BR BR . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H1 H1 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 BR ? ? SING N7 C5 ? ? DOUB C5 C4 ? ? SING C5 C6 ? ? SING C4 N3 ? ? DOUB N3 C2 ? ? SING C2 N2 ? ? SING C2 N1 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING N1 C6 ? ? SING N1 H1 ? ? DOUB C6 O6 ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING OP3 HOP3 ? ? stop_ 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 ; 1.0 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' 'potassium chloride' 30 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 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' 30 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details ; 0.3 mM one guanine in the sequence labeled 5% 15N and 13 C DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), \ 30 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.3 mM 'one guanine in the sequence labeled 5% 15N and 13 C' 'potassium chloride' 30 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 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 processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model VNMRS _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model VNMRS _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_2 save_ save_2D_1H-13C_HSQC_aromatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_2 save_ save_1D_15N-edited_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 15N-edited HSQC' _Sample_label $sample_3 save_ save_1D_13C-edited_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 13C-edited HSQC' _Sample_label $sample_3 save_ save_2D_1H-1H_NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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' 53 . mM pH 5.8 . 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 0.000 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_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '1D 15N-edited HSQC' '1D 13C-edited HSQC' 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 DG H1 H 11.675 0.007 1 2 1 1 DG H1' H 6.097 0.011 1 3 1 1 DG H2' H 2.735 0.011 1 4 1 1 DG H2'' H 3.144 0.014 1 5 1 1 DG H3' H 4.963 0.009 1 6 1 1 DG H4' H 4.366 0.010 1 7 1 1 DG H8 H 7.454 0.008 1 8 2 2 DG H1 H 11.731 0.005 1 9 2 2 DG H1' H 6.173 0.011 1 10 2 2 DG H2' H 2.599 0.012 1 11 2 2 DG H2'' H 2.788 0.018 1 12 2 2 DG H3' H 5.067 0.009 1 13 2 2 DG H4' H 4.465 0.007 1 14 2 2 DG H8 H 7.994 0.004 1 15 3 3 DG H1 H 11.123 0.004 1 16 3 3 DG H1' H 5.970 0.011 1 17 3 3 DG H2' H 3.137 0.012 1 18 3 3 DG H2'' H 2.769 0.015 1 19 3 3 DG H3' H 5.062 0.010 1 20 3 3 DG H4' H 4.523 0.010 1 21 3 3 DG H8 H 7.254 0.031 1 22 3 3 DG H21 H 8.820 0.004 1 23 3 3 DG H22 H 6.296 0.004 1 24 4 4 DG H1 H 11.642 0.005 1 25 4 4 DG H1' H 5.998 0.009 1 26 4 4 DG H2' H 2.580 0.012 1 27 4 4 DG H2'' H 2.701 0.014 1 28 4 4 DG H3' H 4.972 0.011 1 29 4 4 DG H4' H 4.443 0.017 1 30 4 4 DG H8 H 8.033 0.008 1 31 4 4 DG H21 H 9.896 0.001 1 32 4 4 DG H22 H 6.354 0.002 1 33 5 5 DC H1' H 5.343 0.011 1 34 5 5 DC H2' H 1.707 0.011 1 35 5 5 DC H2'' H 2.209 0.007 1 36 5 5 DC H3' H 4.538 0.014 1 37 5 5 DC H4' H 4.112 0.040 1 38 5 5 DC H5' H 4.200 0.007 1 39 5 5 DC H5'' H 3.896 0.016 1 40 5 5 DC H6 H 7.404 0.039 1 41 6 6 DC H1' H 5.472 0.007 1 42 6 6 DC H2' H 1.719 0.014 1 43 6 6 DC H2'' H 2.476 0.019 1 44 6 6 DC H3' H 4.548 0.009 1 45 6 6 DC H5 H 5.312 0.014 1 46 6 6 DC H5' H 3.539 0.021 1 47 6 6 DC H5'' H 3.499 0.030 1 48 6 6 DC H6 H 7.303 0.009 1 49 7 7 DG H1 H 11.647 0.008 1 50 7 7 DG H1' H 6.060 0.010 1 51 7 7 DG H2' H 3.437 0.013 1 52 7 7 DG H2'' H 2.987 0.015 1 53 7 7 DG H3' H 4.743 0.015 1 54 7 7 DG H4' H 4.425 0.022 1 55 7 7 DG H8 H 7.480 0.008 1 56 8 8 DG H1 H 11.732 0.008 1 57 8 8 DG H1' H 6.197 0.010 1 58 8 8 DG H2' H 2.481 0.014 1 59 8 8 DG H2'' H 2.741 0.014 1 60 8 8 DG H3' H 4.977 0.008 1 61 8 8 DG H4' H 4.513 0.006 1 62 8 8 DG H8 H 7.761 0.002 1 63 9 9 DG H1 H 11.134 0.003 1 64 9 9 DG H1' H 5.906 0.010 1 65 9 9 DG H2' H 3.135 0.011 1 66 9 9 DG H2'' H 2.698 0.012 1 67 9 9 DG H3' H 5.070 0.009 1 68 9 9 DG H4' H 4.503 0.008 1 69 9 9 DG H8 H 7.251 0.006 1 70 9 9 DG H21 H 8.682 0.011 1 71 9 9 DG H22 H 6.411 0.004 1 72 10 10 DG H1 H 11.519 0.007 1 73 10 10 DG H1' H 5.932 0.012 1 74 10 10 DG H2' H 2.886 0.011 1 75 10 10 DG H2'' H 2.329 0.008 1 76 10 10 DG H3' H 5.065 0.009 1 77 10 10 DG H4' H 4.424 0.009 1 78 10 10 DG H8 H 8.263 0.003 1 79 11 11 DC H1' H 5.914 0.016 1 80 11 11 DC H2' H 1.923 0.013 1 81 11 11 DC H2'' H 2.375 0.017 1 82 11 11 DC H3' H 4.735 0.014 1 83 11 11 DC H4' H 4.245 0.010 1 84 11 11 DC H5 H 6.012 0.018 1 85 11 11 DC H6 H 7.968 0.012 1 86 12 12 DC H1' H 5.908 0.014 1 87 12 12 DC H2' H 1.929 0.010 1 88 12 12 DC H2'' H 2.535 0.012 1 89 12 12 DC H3' H 4.752 0.017 1 90 12 12 DC H4' H 4.188 0.008 1 91 12 12 DC H5 H 4.515 0.030 1 92 12 12 DC H5' H 3.979 0.008 1 93 12 12 DC H5'' H 3.900 0.007 1 94 12 12 DC H6 H 7.079 0.017 1 95 13 13 DG H1 H 11.157 0.003 1 96 13 13 DG H1' H 6.095 0.019 1 97 13 13 DG H2' H 3.399 0.012 1 98 13 13 DG H2'' H 2.975 0.013 1 99 13 13 DG H3' H 4.867 0.005 1 100 13 13 DG H4' H 4.422 0.003 1 101 13 13 DG H8 H 7.455 0.009 1 102 13 13 DG H21 H 9.391 0.004 1 103 13 13 DG H22 H 6.789 0.004 1 104 14 14 DG H1 H 11.317 0.017 1 105 14 14 DG H1' H 6.167 0.014 1 106 14 14 DG H2' H 2.521 0.014 1 107 14 14 DG H2'' H 2.739 0.014 1 108 14 14 DG H3' H 5.000 0.015 1 109 14 14 DG H4' H 4.460 0.009 1 110 14 14 DG H8 H 7.848 0.003 1 111 14 14 DG H22 H 6.757 0.004 1 112 15 15 DG H1 H 11.242 0.003 1 113 15 15 DG H1' H 5.973 0.010 1 114 15 15 DG H2' H 3.135 0.010 1 115 15 15 DG H2'' H 2.773 0.019 1 116 15 15 DG H3' H 5.061 0.009 1 117 15 15 DG H4' H 4.525 0.011 1 118 15 15 DG H8 H 7.356 0.020 1 119 15 15 DG H21 H 8.811 0.004 1 120 15 15 DG H22 H 6.280 0.004 1 121 16 16 DG H1 H 11.640 0.004 1 122 16 16 DG H1' H 5.999 0.008 1 123 16 16 DG H2' H 2.579 0.013 1 124 16 16 DG H2'' H 2.701 0.013 1 125 16 16 DG H3' H 4.973 0.011 1 126 16 16 DG H4' H 4.441 0.016 1 127 16 16 DG H8 H 8.033 0.007 1 128 16 16 DG H21 H 9.898 0.001 1 129 16 16 DG H22 H 6.354 0.002 1 130 17 17 DC H1' H 5.383 0.282 1 131 17 17 DC H2' H 1.709 0.014 1 132 17 17 DC H2'' H 2.210 0.007 1 133 17 17 DC H3' H 4.539 0.011 1 134 17 17 DC H4' H 4.354 0.863 1 135 17 17 DC H5' H 4.196 0.024 1 136 17 17 DC H5'' H 3.897 0.016 1 137 17 17 DC H6 H 7.409 0.041 1 138 18 18 DC H1' H 5.470 0.009 1 139 18 18 DC H2' H 1.714 0.012 1 140 18 18 DC H2'' H 2.480 0.018 1 141 18 18 DC H3' H 4.549 0.006 1 142 18 18 DC H5 H 5.315 0.011 1 143 18 18 DC H5' H 3.535 0.021 1 144 18 18 DC H5'' H 3.503 0.032 1 145 18 18 DC H6 H 7.146 0.692 1 146 19 19 DG H1 H 11.645 0.008 1 147 19 19 DG H1' H 6.058 0.010 1 148 19 19 DG H2' H 3.446 0.012 1 149 19 19 DG H2'' H 2.996 0.017 1 150 19 19 DG H3' H 4.744 0.014 1 151 19 19 DG H4' H 4.425 0.022 1 152 19 19 DG H8 H 7.505 0.059 1 153 20 20 DG H1 H 11.776 0.006 1 154 20 20 DG H1' H 6.184 0.011 1 155 20 20 DG H2' H 2.540 0.017 1 156 20 20 DG H2'' H 2.732 0.014 1 157 20 20 DG H3' H 4.985 0.011 1 158 20 20 DG H4' H 4.514 0.006 1 159 20 20 DG H8 H 7.796 0.044 1 160 21 21 BGM H1 H 11.489 0.005 1 161 21 21 BGM H1' H 6.098 0.009 1 162 21 21 BGM H2' H 3.344 0.014 1 163 21 21 BGM H2'' H 2.712 0.013 1 164 21 21 BGM H3' H 5.087 0.011 1 165 21 21 BGM H4' H 4.461 0.035 1 166 21 21 BGM H21 H 8.844 0.005 1 167 21 21 BGM H22 H 6.506 0.003 1 168 22 22 DG H1 H 11.806 0.061 1 169 22 22 DG H1' H 6.109 0.010 1 170 22 22 DG H2' H 2.603 0.011 1 171 22 22 DG H2'' H 2.310 0.014 1 172 22 22 DG H3' H 4.761 0.100 1 173 22 22 DG H4' H 4.189 0.007 1 174 22 22 DG H8 H 8.136 0.002 1 175 22 22 DG H21 H 8.852 0.002 1 176 22 22 DG H22 H 6.506 0.002 1 stop_ save_