data_34210 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 2'F-araG modified quadruplex with flipped G-tract and central tetrad ; _BMRB_accession_number 34210 _BMRB_flat_file_name bmr34210.str _Entry_type original _Submission_date 2017-11-30 _Accession_date 2017-11-30 _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 Dickerhoff J. . . 2 Weisz K. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 143 "13C chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-08-14 update BMRB 'update entry citation' 2018-04-20 original author 'original release' stop_ _Original_release_date 2018-04-18 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29460996 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dickerhoff J. . . 2 Weisz K. . . stop_ _Journal_abbreviation Chembiochem _Journal_volume 19 _Journal_issue 9 _Journal_ISSN 1439-7633 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 927 _Page_last 930 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*(GFL)P*GP*GP*AP*CP*GP*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 entity_1 _Molecular_mass 6990.482 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGATGGGACACAGGGGACG GG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DA 5 DT 6 DG 7 DG 8 DG 9 DA 10 DC 11 DA 12 DC 13 DA 14 DG 15 GFL 16 DG 17 DG 18 DA 19 DC 20 DG 21 DG 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_GFL _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE _BMRB_code GFL _PDB_code GFL _Standard_residue_derivative . _Molecular_mass 365.212 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O3P O3P O . 0 . ? P P P . 0 . ? O1P O1P O . 0 . ? O2P O2P O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? F F F . 0 . ? HO3P HO3P H . 0 . ? HO2P HO2P H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 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 SING O3P P ? ? SING O3P HO3P ? ? DOUB P O1P ? ? SING P O2P ? ? SING P O5' ? ? SING O2P HO2P ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' F ? ? SING C2' H2' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 HN1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N3 C4 ? ? 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 . 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 '0.37 mM DNA, 10 mM potassium phosphate, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.37 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.37 mM DNA, 10 mM potassium phosphate, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.37 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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_ save_software_2 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_3 _Saveframe_category software _Name Analysis _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_1 save_ save_2D_1H-13C_HSQC_aromatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_5 _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' 10 . mM pH 7 . pH pressure 1 . atm 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 C 13 'methyl protons' ppm 0.000 external indirect . . . 0.25144953 water H 1 protons ppm 4.78 internal 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-13C HSQC aromatic' '2D DQF-COSY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 $sample_2 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 11.657 0.005 1 2 1 1 DG H1' H 6.078 0.002 1 3 1 1 DG H2' H 2.651 0.003 1 4 1 1 DG H2'' H 3.185 0.001 1 5 1 1 DG H3' H 5.028 0.002 1 6 1 1 DG H8 H 7.298 0.001 1 7 1 1 DG C8 C 140.750 . 1 8 2 2 DG H1 H 11.615 0.001 1 9 2 2 DG H1' H 5.855 0.002 1 10 2 2 DG H2' H 2.577 0.001 1 11 2 2 DG H2'' H 2.680 0.001 1 12 2 2 DG H3' H 5.135 0.001 1 13 2 2 DG H8 H 7.951 0.001 1 14 2 2 DG C8 C 138.283 . 1 15 3 3 DG H1 H 11.467 0.003 1 16 3 3 DG H1' H 6.331 0.002 1 17 3 3 DG H2' H 2.857 0.002 1 18 3 3 DG H2'' H 2.640 0.001 1 19 3 3 DG H3' H 4.962 0.001 1 20 3 3 DG H4' H 4.476 . 1 21 3 3 DG H8 H 7.897 0.001 1 22 3 3 DG C8 C 136.696 . 1 23 4 4 DA H1' H 6.398 0.002 1 24 4 4 DA H2 H 7.965 0.002 1 25 4 4 DA H2' H 2.635 0.007 1 26 4 4 DA H2'' H 2.693 0.003 1 27 4 4 DA H3' H 5.053 0.002 1 28 4 4 DA H4' H 4.476 . 1 29 4 4 DA H8 H 8.306 0.0 1 30 4 4 DA C2 C 155.078 . 1 31 4 4 DA C8 C 141.959 . 1 32 5 5 DT H1' H 6.039 0.001 1 33 5 5 DT H2' H 2.102 0.004 1 34 5 5 DT H2'' H 2.638 0.001 1 35 5 5 DT H3' H 4.901 0.001 1 36 5 5 DT H6 H 7.270 0.001 1 37 5 5 DT H71 H 1.112 0.003 1 38 5 5 DT H72 H 1.112 0.003 1 39 5 5 DT H73 H 1.112 0.003 1 40 5 5 DT C6 C 137.923 . 1 41 6 6 DG H1 H 11.409 0.003 1 42 6 6 DG H1' H 6.156 0.002 1 43 6 6 DG H2' H 3.615 0.002 1 44 6 6 DG H2'' H 3.167 0.001 1 45 6 6 DG H3' H 4.878 0.002 1 46 6 6 DG H8 H 7.343 0.001 1 47 6 6 DG C8 C 141.656 . 1 48 7 7 DG H1 H 11.278 0.0 1 49 7 7 DG H1' H 5.803 0.003 1 50 7 7 DG H2' H 2.677 0.004 1 51 7 7 DG H2'' H 2.520 0.003 1 52 7 7 DG H3' H 5.035 0.001 1 53 7 7 DG H8 H 7.266 0.0 1 54 7 7 DG C8 C 140.166 . 1 55 8 8 DG H1 H 11.277 0.001 1 56 8 8 DG H1' H 5.840 0.001 1 57 8 8 DG H2' H 2.208 0.001 1 58 8 8 DG H2'' H 2.445 0.002 1 59 8 8 DG H3' H 4.976 . 1 60 8 8 DG H8 H 7.702 0.002 1 61 8 8 DG C8 C 137.713 . 1 62 9 9 DA H1' H 6.028 0.001 1 63 9 9 DA H2 H 7.728 0.0 1 64 9 9 DA H2' H 2.671 0.002 1 65 9 9 DA H2'' H 2.552 0.002 1 66 9 9 DA H3' H 4.955 0.002 1 67 9 9 DA H8 H 8.013 0.002 1 68 9 9 DA C2 C 154.783 . 1 69 9 9 DA C8 C 141.509 . 1 70 10 10 DC H1' H 5.926 0.002 1 71 10 10 DC H2' H 1.762 0.004 1 72 10 10 DC H2'' H 2.170 0.002 1 73 10 10 DC H3' H 4.605 0.003 1 74 10 10 DC H5 H 5.923 0.002 1 75 10 10 DC H6 H 7.613 0.002 1 76 10 10 DC C6 C 143.495 . 1 77 11 11 DA H1' H 5.736 0.001 1 78 11 11 DA H2 H 7.640 0.001 1 79 11 11 DA H2' H 2.407 0.001 1 80 11 11 DA H2'' H 1.988 . 1 81 11 11 DA H3' H 4.410 0.003 1 82 11 11 DA H8 H 7.846 0.001 1 83 11 11 DA C2 C 154.676 . 1 84 11 11 DA C8 C 141.422 . 1 85 12 12 DC H1' H 5.533 0.001 1 86 12 12 DC H2' H 1.678 0.001 1 87 12 12 DC H2'' H 1.977 0.004 1 88 12 12 DC H3' H 4.414 0.005 1 89 12 12 DC H4' H 3.531 0.005 1 90 12 12 DC H5 H 5.130 0.002 1 91 12 12 DC H5' H 3.241 0.003 1 92 12 12 DC H6 H 7.027 0.0 1 93 13 13 DA H1' H 5.993 0.001 1 94 13 13 DA H2 H 7.654 0.002 1 95 13 13 DA H2' H 2.420 0.002 1 96 13 13 DA H2'' H 2.719 0.001 1 97 13 13 DA H3' H 4.764 0.002 1 98 13 13 DA H4' H 4.159 0.001 1 99 13 13 DA H5' H 3.526 0.0 1 100 13 13 DA H5'' H 3.810 0.003 1 101 13 13 DA H8 H 7.981 0.001 1 102 13 13 DA C8 C 141.444 . 1 103 14 14 DG H1 H 11.399 0.003 1 104 14 14 DG H1' H 6.018 0.003 1 105 14 14 DG H2' H 3.401 0.003 1 106 14 14 DG H2'' H 2.971 0.0 1 107 14 14 DG H3' H 4.939 0.0 1 108 14 14 DG H8 H 7.408 0.001 1 109 14 14 DG C8 C 141.868 . 1 110 15 15 GFL H1' H 5.827 0.004 1 111 15 15 GFL H2' H 5.110 0.002 1 112 15 15 GFL H3' H 4.979 . 1 113 15 15 GFL H8 H 7.665 0.002 1 114 15 15 GFL C8 C 140.774 . 1 115 15 15 GFL HN1 H 11.852 0.0 1 116 16 16 DG H1 H 11.520 0.001 1 117 16 16 DG H1' H 5.905 0.004 1 118 16 16 DG H2' H 1.894 0.004 1 119 16 16 DG H2'' H 2.444 0.004 1 120 16 16 DG H3' H 4.905 0.003 1 121 16 16 DG H8 H 7.279 0.001 1 122 16 16 DG C8 C 136.720 . 1 123 17 17 DG H1' H 6.075 0.001 1 124 17 17 DG H2' H 2.665 0.002 1 125 17 17 DG H2'' H 2.374 0.004 1 126 17 17 DG H3' H 4.849 0.007 1 127 17 17 DG H8 H 7.938 0.001 1 128 17 17 DG C8 C 138.311 . 1 129 18 18 DA H1' H 5.889 0.002 1 130 18 18 DA H2 H 7.270 . 1 131 18 18 DA H2' H 2.404 0.002 1 132 18 18 DA H2'' H 2.295 0.001 1 133 18 18 DA H3' H 4.768 0.007 1 134 18 18 DA H4' H 3.722 0.003 1 135 18 18 DA H5' H 3.761 0.001 2 136 18 18 DA H5'' H 3.878 0.003 2 137 18 18 DA H8 H 8.082 0.001 1 138 18 18 DA C8 C 142.229 . 1 139 19 19 DC H1' H 5.898 . 1 140 19 19 DC H2' H 1.906 0.004 1 141 19 19 DC H2'' H 2.431 0.005 1 142 19 19 DC H3' H 4.610 0.003 1 143 19 19 DC H4' H 4.148 . 1 144 19 19 DC H5 H 5.818 0.002 1 145 19 19 DC H6 H 7.370 0.002 1 146 19 19 DC C6 C 142.967 . 1 147 20 20 DG H1 H 11.571 0.0 1 148 20 20 DG H1' H 6.077 0.0 1 149 20 20 DG H2' H 3.738 0.0 1 150 20 20 DG H2'' H 3.190 0.001 1 151 20 20 DG H3' H 4.689 . 1 152 20 20 DG H8 H 7.171 0.001 1 153 20 20 DG C8 C 141.227 . 1 154 21 21 DG H1 H 11.526 0.003 1 155 21 21 DG H1' H 5.768 0.001 1 156 21 21 DG H2' H 2.490 0.0 1 157 21 21 DG H2'' H 2.490 0.0 1 158 21 21 DG H3' H 5.051 0.004 1 159 21 21 DG H8 H 7.403 0.001 1 160 21 21 DG C8 C 140.774 . 1 161 22 22 DG H1 H 11.702 0.0 1 162 22 22 DG H1' H 6.191 0.003 1 163 22 22 DG H2' H 2.575 0.003 1 164 22 22 DG H2'' H 2.285 0.001 1 165 22 22 DG H3' H 4.677 0.002 1 166 22 22 DG H8 H 7.994 0.001 1 167 22 22 DG C8 C 138.638 . 1 stop_ save_