data_30055 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIY G-Quadruplexes: Solution structure of d(GGTTTGGTTTTGGTTTGG) in sodium ; _BMRB_accession_number 30055 _BMRB_flat_file_name bmr30055.str _Entry_type original _Submission_date 2016-04-01 _Accession_date 2016-04-01 _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 Dvorkin S. A. . 2 'Webba da Silva' M. . . 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 2019-07-19 update BMRB 'update entry citation' 2017-04-06 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30045 'DIY G-Quadruplexes: d(GGGTTTGGGTTTTGGGAGGG)' 30056 'DIY G-Quadruplexes: d(GGTTTGGTTTTGGTTGG)' 30058 'DIY G-Quadruplexes: d(GGGGTTTGGGGTTTTGGGGAAGGGG)' stop_ _Original_release_date 2016-04-04 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Encoding canonical DNA quadruplex structure. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30182059 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dvorkin Scarlett A. . 2 Karsisiotis Andreas I. . 3 'Webba da Silva' Mateus . . stop_ _Journal_abbreviation 'Sci Adv' _Journal_name_full 'Science advances' _Journal_volume 4 _Journal_issue 8 _Journal_ISSN 2375-2548 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first eaat3007 _Page_last eaat3007 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*TP*GP*GP*TP*TP*TP*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 . _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(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*TP*GP*GP*TP*TP*TP*GP*G)-3')" _Molecular_mass 5630.618 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; GGTTTGGTTTTGGTTTGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DT 4 4 DT 5 5 DT 6 6 DG 7 7 DG 8 8 DT 9 9 DT 10 10 DT 11 11 DT 12 12 DG 13 13 DG 14 14 DT 15 15 DT 16 16 DT 17 17 DG 18 18 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 . 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 '2 mM no dna, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM none NaPi 100 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2 mM no dna, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM none NaPi 100 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VXRS _Field_strength 500 _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_2 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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' 100 0.1 mM pH 6.8 . pH pressure 1 . atm temperature 278.15 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details NONE 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 4.78 external indirect . . . 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_1 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_2 $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 DG H1 H 11.94 0.02 . 2 1 1 DG H1' H 5.85 0.02 . 3 1 1 DG H2' H 2.88 0.02 . 4 1 1 DG H2'' H 2.79 0.02 . 5 1 1 DG H3' H 4.99 0.02 . 6 1 1 DG H4' H 4.36 0.02 . 7 1 1 DG H8 H 7.33 0.02 . 8 1 1 DG H21 H 10.71 0.02 . 9 1 1 DG H22 H 6.29 0.02 . 10 2 2 DG H1 H 12.25 0.02 . 11 2 2 DG H1' H 6.01 0.02 . 12 2 2 DG H2' H 2.69 0.02 . 13 2 2 DG H2'' H 2.68 0.02 . 14 2 2 DG H3' H 5.09 0.02 . 15 2 2 DG H4' H 4.34 0.02 . 16 2 2 DG H5' H 4.21 0.02 . 17 2 2 DG H5'' H 4.19 0.02 . 18 2 2 DG H8 H 8.16 0.02 . 19 2 2 DG H21 H 10.39 0.02 . 20 2 2 DG H22 H 6.83 0.02 . 21 3 3 DT H1' H 6.45 0.02 . 22 3 3 DT H2' H 2.63 0.02 . 23 3 3 DT H2'' H 2.51 0.02 . 24 3 3 DT H3' H 4.42 0.02 . 25 3 3 DT H4' H 4.10 0.02 . 26 3 3 DT H5' H 4.10 0.02 . 27 3 3 DT H5'' H 4.11 0.02 . 28 3 3 DT H6 H 7.96 0.02 . 29 3 3 DT H71 H 2.00 0.02 . 30 3 3 DT H72 H 2.00 0.02 . 31 3 3 DT H73 H 2.00 0.02 . 32 4 4 DT H1' H 5.99 0.02 . 33 4 4 DT H2' H 2.12 0.02 . 34 4 4 DT H2'' H 1.97 0.02 . 35 4 4 DT H3' H 4.55 0.02 . 36 4 4 DT H4' H 4.10 0.02 . 37 4 4 DT H5' H 3.92 0.02 . 38 4 4 DT H5'' H 3.92 0.02 . 39 4 4 DT H6 H 7.30 0.02 . 40 4 4 DT H71 H 1.57 0.02 . 41 4 4 DT H72 H 1.57 0.02 . 42 4 4 DT H73 H 1.57 0.02 . 43 5 5 DT H1' H 5.95 0.02 . 44 5 5 DT H2' H 2.38 0.02 . 45 5 5 DT H2'' H 2.38 0.02 . 46 5 5 DT H3 H 10.85 0.02 . 47 5 5 DT H3' H 4.78 0.02 . 48 5 5 DT H4' H 3.79 0.02 . 49 5 5 DT H5' H 3.57 0.02 . 50 5 5 DT H5'' H 2.95 0.02 . 51 5 5 DT H6 H 7.19 0.02 . 52 5 5 DT H71 H 1.60 0.02 . 53 5 5 DT H72 H 1.60 0.02 . 54 5 5 DT H73 H 1.60 0.02 . 55 6 6 DG H1 H 11.93 0.02 . 56 6 6 DG H1' H 6.03 0.02 . 57 6 6 DG H2' H 3.33 0.02 . 58 6 6 DG H2'' H 3.32 0.02 . 59 6 6 DG H3' H 4.24 0.02 . 60 6 6 DG H4' H 4.17 0.02 . 61 6 6 DG H5' H 4.10 0.02 . 62 6 6 DG H5'' H 3.79 0.02 . 63 6 6 DG H8 H 7.55 0.02 . 64 6 6 DG H21 H 9.90 0.02 . 65 6 6 DG H22 H 7.03 0.02 . 66 7 7 DG H1 H 11.72 0.02 . 67 7 7 DG H1' H 5.95 0.02 . 68 7 7 DG H2' H 2.76 0.02 . 69 7 7 DG H2'' H 2.66 0.02 . 70 7 7 DG H3' H 4.99 0.02 . 71 7 7 DG H4' H 4.47 0.02 . 72 7 7 DG H8 H 8.10 0.02 . 73 7 7 DG H21 H 9.5 0.08 . 74 7 7 DG H22 H 6.9 0.08 . 75 8 8 DT H1' H 5.53 0.02 . 76 8 8 DT H2' H 2.27 0.02 . 77 8 8 DT H2'' H 1.53 0.02 . 78 8 8 DT H3 H 10.65 0.02 . 79 8 8 DT H3' H 4.45 0.02 . 80 8 8 DT H4' H 4.03 0.02 . 81 8 8 DT H5' H 3.51 0.02 . 82 8 8 DT H5'' H 3.62 0.02 . 83 8 8 DT H6 H 7.06 0.02 . 84 8 8 DT H71 H 1.77 0.02 . 85 8 8 DT H72 H 1.77 0.02 . 86 8 8 DT H73 H 1.77 0.02 . 87 9 9 DT H1' H 5.49 0.02 . 88 9 9 DT H2' H 1.93 0.02 . 89 9 9 DT H2'' H 2.02 0.02 . 90 9 9 DT H3 H 10.20 0.02 . 91 9 9 DT H3' H 4.54 0.02 . 92 9 9 DT H4' H 4.54 0.02 . 93 9 9 DT H5' H 3.63 0.02 . 94 9 9 DT H5'' H 3.52 0.02 . 95 9 9 DT H6 H 7.26 0.02 . 96 9 9 DT H71 H 1.58 0.02 . 97 9 9 DT H72 H 1.58 0.02 . 98 9 9 DT H73 H 1.58 0.02 . 99 10 10 DT H1' H 5.43 0.02 . 100 10 10 DT H2' H 2.34 0.02 . 101 10 10 DT H2'' H 2.06 0.02 . 102 10 10 DT H3 H 9.90 0.02 . 103 10 10 DT H3' H 4.71 0.02 . 104 10 10 DT H4' H 4.43 0.02 . 105 10 10 DT H5' H 3.99 0.02 . 106 10 10 DT H5'' H 3.98 0.02 . 107 10 10 DT H6 H 7.18 0.02 . 108 10 10 DT H71 H 1.54 0.02 . 109 10 10 DT H72 H 1.54 0.02 . 110 10 10 DT H73 H 1.54 0.02 . 111 11 11 DT H1' H 6.25 0.02 . 112 11 11 DT H2' H 2.40 0.02 . 113 11 11 DT H2'' H 2.11 0.02 . 114 11 11 DT H3 H 10.79 0.02 . 115 11 11 DT H3' H 4.55 0.02 . 116 11 11 DT H5' H 3.19 0.02 . 117 11 11 DT H5'' H 2.91 0.02 . 118 11 11 DT H6 H 7.57 0.02 . 119 11 11 DT H71 H 1.72 0.02 . 120 11 11 DT H72 H 1.72 0.02 . 121 11 11 DT H73 H 1.72 0.02 . 122 12 12 DG H1 H 11.82 0.02 . 123 12 12 DG H1' H 6.12 0.02 . 124 12 12 DG H2' H 3.18 0.02 . 125 12 12 DG H2'' H 3.42 0.02 . 126 12 12 DG H3' H 4.96 0.02 . 127 12 12 DG H4' H 4.72 0.02 . 128 12 12 DG H5' H 4.13 0.02 . 129 12 12 DG H5'' H 4.14 0.02 . 130 12 12 DG H8 H 7.90 0.02 . 131 12 12 DG H21 H 9.53 0.02 . 132 12 12 DG H22 H 7.59 0.02 . 133 13 13 DG H1 H 11.79 0.02 . 134 13 13 DG H1' H 6.18 0.02 . 135 13 13 DG H2' H 2.55 0.02 . 136 13 13 DG H2'' H 2.62 0.02 . 137 13 13 DG H3' H 5.18 0.02 . 138 13 13 DG H4' H 4.44 0.02 . 139 13 13 DG H5' H 4.13 0.02 . 140 13 13 DG H5'' H 4.14 0.02 . 141 13 13 DG H8 H 7.68 0.02 . 142 13 13 DG H21 H 9.64 0.02 . 143 13 13 DG H22 H 6.68 0.02 . 144 14 14 DT H1' H 6.04 0.02 . 145 14 14 DT H2' H 2.50 0.02 . 146 14 14 DT H2'' H 2.40 0.02 . 147 14 14 DT H3 H 11.15 0.02 . 148 14 14 DT H3' H 4.93 0.02 . 149 14 14 DT H4' H 4.19 0.02 . 150 14 14 DT H6 H 7.43 0.02 . 151 14 14 DT H71 H 1.44 0.02 . 152 14 14 DT H72 H 1.44 0.02 . 153 14 14 DT H73 H 1.44 0.02 . 154 15 15 DT H1' H 6.07 0.02 . 155 15 15 DT H2' H 2.52 0.02 . 156 15 15 DT H2'' H 2.18 0.02 . 157 15 15 DT H3 H 11.29 0.02 . 158 15 15 DT H3' H 4.82 0.02 . 159 15 15 DT H4' H 4.28 0.02 . 160 15 15 DT H5' H 3.97 0.02 . 161 15 15 DT H5'' H 3.96 0.02 . 162 15 15 DT H6 H 7.50 0.02 . 163 15 15 DT H71 H 1.65 0.02 . 164 15 15 DT H72 H 1.65 0.02 . 165 15 15 DT H73 H 1.65 0.02 . 166 16 16 DT H1' H 6.37 0.02 . 167 16 16 DT H2' H 2.50 0.02 . 168 16 16 DT H2'' H 2.23 0.02 . 169 16 16 DT H3 H 9.81 0.02 . 170 16 16 DT H3' H 4.88 0.02 . 171 16 16 DT H4' H 4.51 0.02 . 172 16 16 DT H5' H 4.27 0.02 . 173 16 16 DT H5'' H 4.14 0.02 . 174 16 16 DT H6 H 7.91 0.02 . 175 16 16 DT H71 H 2.08 0.02 . 176 16 16 DT H72 H 2.08 0.02 . 177 16 16 DT H73 H 2.08 0.02 . 178 17 17 DG H1 H 11.52 0.02 . 179 17 17 DG H1' H 5.99 0.02 . 180 17 17 DG H2' H 3.58 0.02 . 181 17 17 DG H2'' H 3.59 0.02 . 182 17 17 DG H3' H 4.97 0.02 . 183 17 17 DG H4' H 4.44 0.02 . 184 17 17 DG H5' H 4.32 0.02 . 185 17 17 DG H5'' H 4.31 0.02 . 186 17 17 DG H8 H 7.25 0.02 . 187 17 17 DG H21 H 9.24 0.02 . 188 17 17 DG H22 H 7.06 0.02 . 189 18 18 DG H1 H 11.74 0.02 . 190 18 18 DG H1' H 6.38 0.02 . 191 18 18 DG H2' H 2.52 0.02 . 192 18 18 DG H2'' H 2.78 0.02 . 193 18 18 DG H8 H 8.28 0.02 . stop_ save_