data_34174 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 2'F-ANA-G modified quadruplex with a flipped tetrad ; _BMRB_accession_number 34174 _BMRB_flat_file_name bmr34174.str _Entry_type original _Submission_date 2017-08-27 _Accession_date 2017-08-27 _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" 164 "13C chemical shifts" 27 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-10-13 original BMRB . stop_ _Original_release_date 2017-10-09 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Nonconventional C-HF Hydrogen Bonds Support a Tetrad Flip in Modified G-Quadruplexes. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28976755 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dickerhoff J. . . 2 Weisz K. . . stop_ _Journal_abbreviation 'J. Phys. Chem. Lett.' _Journal_volume . _Journal_issue . _Journal_ISSN 1948-7185 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5148 _Page_last 5152 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'artificial quadruplex with propeller, diagonal, and lateral loop' _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 7026.464 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; XGGATXGGACACAGGGGACX GG ; loop_ _Residue_seq_code _Residue_label 1 GFL 2 DG 3 DG 4 DA 5 DT 6 GFL 7 DG 8 DG 9 DA 10 DC 11 DA 12 DC 13 DA 14 DG 15 DG 16 DG 17 DG 18 DA 19 DC 20 GFL 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 '0.58 mM DNA, 10 mM potassium phosphate, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.58 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.58 mM DNA, 10 mM potassium phosphate, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.58 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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_2 _Saveframe_category software _Name Analysis _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _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 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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _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_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aromatic_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 internal 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 DQF-COSY' '2D 1H-13C HSQC aromatic' '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 GFL H1' H 6.241 0.003 1 2 1 1 GFL H2' H 5.467 0.003 1 3 1 1 GFL H3' H 4.987 0.002 1 4 1 1 GFL H4' H 4.378 0.003 1 5 1 1 GFL H5'1 H 3.995 0.002 2 6 1 1 GFL H5'2 H 4.040 0.002 2 7 1 1 GFL H8 H 7.995 0.002 1 8 1 1 GFL C8 C 139.083 . 1 9 1 1 GFL HN1 H 11.828 0.004 1 10 2 2 DG H1 H 11.468 0.002 1 11 2 2 DG H1' H 6.133 0.004 1 12 2 2 DG H2' H 2.529 0.001 1 13 2 2 DG H2'' H 2.728 0.004 1 14 2 2 DG H3' H 5.007 0.001 1 15 2 2 DG H4' H 4.488 0.002 1 16 2 2 DG H8 H 7.668 0.001 1 17 2 2 DG C8 C 137.725 . 1 18 3 3 DG H1 H 11.220 0.004 1 19 3 3 DG H1' H 6.145 0.003 1 20 3 3 DG H2' H 2.634 0.002 1 21 3 3 DG H2'' H 2.554 0.002 1 22 3 3 DG H3' H 5.006 0.002 1 23 3 3 DG H8 H 7.680 0.001 1 24 3 3 DG C8 C 137.483 . 1 25 4 4 DA H1' H 6.603 0.002 1 26 4 4 DA H2 H 8.322 0.001 1 27 4 4 DA H2' H 2.920 0.002 1 28 4 4 DA H2'' H 2.920 0.002 1 29 4 4 DA H3' H 4.899 0.003 1 30 4 4 DA H4' H 4.608 0.001 1 31 4 4 DA H5' H 4.067 0.004 1 32 4 4 DA H5'' H 4.113 0.004 1 33 4 4 DA H8 H 8.567 0.001 1 34 4 4 DA C2 C 155.452 . 1 35 4 4 DA C8 C 142.642 . 1 36 5 5 DT H1' H 6.539 0.002 1 37 5 5 DT H2' H 2.611 0.003 1 38 5 5 DT H2'' H 2.680 0.004 1 39 5 5 DT H3' H 5.017 0.002 1 40 5 5 DT H4' H 4.468 0.001 1 41 5 5 DT H6 H 7.870 0.001 1 42 5 5 DT H71 H 2.048 0.003 1 43 5 5 DT H72 H 2.048 0.003 1 44 5 5 DT H73 H 2.048 0.003 1 45 5 5 DT C6 C 140.377 . 1 46 6 6 GFL H1' H 6.143 0.002 1 47 6 6 GFL H2' H 5.364 0.002 1 48 6 6 GFL H3' H 5.029 0.003 1 49 6 6 GFL H4' H 4.351 0.004 1 50 6 6 GFL H5'1 H 4.157 0.004 1 51 6 6 GFL H5'2 H 3.890 0.002 1 52 6 6 GFL H8 H 7.847 0.001 1 53 6 6 GFL C8 C 140.305 . 1 54 6 6 GFL HN1 H 11.671 0.002 1 55 7 7 DG H1 H 11.348 0.002 1 56 7 7 DG H1' H 5.921 0.001 1 57 7 7 DG H2' H 2.603 0.002 1 58 7 7 DG H2'' H 2.701 0.003 1 59 7 7 DG H3' H 5.072 0.003 1 60 7 7 DG H4' H 4.387 0.001 1 61 7 7 DG H5' H 4.272 . 2 62 7 7 DG H5'' H 4.215 . 2 63 7 7 DG H8 H 7.648 0.001 1 64 7 7 DG C8 C 137.216 . 1 65 8 8 DG H1 H 11.095 0.003 1 66 8 8 DG H1' H 5.880 0.002 1 67 8 8 DG H2' H 2.153 0.003 1 68 8 8 DG H2'' H 2.393 0.003 1 69 8 8 DG H3' H 4.958 0.003 1 70 8 8 DG H4' H 4.414 0.002 1 71 8 8 DG H8 H 7.505 0.002 1 72 8 8 DG C8 C 136.762 . 1 73 9 9 DA H1' H 6.037 0.003 1 74 9 9 DA H2 H 7.733 0.003 1 75 9 9 DA H2' H 2.684 0.003 1 76 9 9 DA H2'' H 2.542 0.004 1 77 9 9 DA H3' H 4.961 0.003 1 78 9 9 DA H4' H 4.418 0.003 1 79 9 9 DA H8 H 8.067 0.002 1 80 9 9 DA C2 C 154.740 . 1 81 9 9 DA C8 C 141.656 . 1 82 10 10 DC H1' H 5.831 0.003 1 83 10 10 DC H2' H 1.789 0.005 1 84 10 10 DC H2'' H 2.172 0.002 1 85 10 10 DC H3' H 4.595 0.005 1 86 10 10 DC H4' H 4.080 0.0 1 87 10 10 DC H5 H 5.896 0.001 1 88 10 10 DC H6 H 7.583 0.001 1 89 10 10 DC C6 C 143.474 . 1 90 11 11 DA H1' H 5.750 0.002 1 91 11 11 DA H2 H 7.681 0.001 1 92 11 11 DA H2' H 2.401 0.003 1 93 11 11 DA H2'' H 2.089 0.007 1 94 11 11 DA H3' H 4.458 0.006 1 95 11 11 DA H4' H 3.934 0.003 1 96 11 11 DA H8 H 7.853 0.001 1 97 11 11 DA C2 C 154.557 . 1 98 11 11 DA C8 C 141.587 . 1 99 12 12 DC H1' H 5.502 0.004 1 100 12 12 DC H2' H 1.704 0.001 1 101 12 12 DC H2'' H 1.998 0.004 1 102 12 12 DC H3' H 4.395 0.003 1 103 12 12 DC H4' H 3.553 0.002 1 104 12 12 DC H5 H 5.180 0.002 1 105 12 12 DC H5' H 3.352 0.001 2 106 12 12 DC H5'' H 3.540 0.0 2 107 12 12 DC H6 H 7.022 0.001 1 108 12 12 DC C6 C 143.606 . 1 109 13 13 DA H1' H 5.792 0.003 1 110 13 13 DA H2 H 7.755 0.001 1 111 13 13 DA H2' H 2.359 0.002 1 112 13 13 DA H2'' H 2.671 0.001 1 113 13 13 DA H3' H 4.758 0.003 1 114 13 13 DA H4' H 4.105 0.005 1 115 13 13 DA H5' H 3.784 0.003 2 116 13 13 DA H5'' H 3.431 0.001 2 117 13 13 DA H8 H 7.895 0.002 1 118 13 13 DA C2 C 154.400 . 1 119 13 13 DA C8 C 141.340 . 1 120 14 14 DG H1 H 11.224 0.002 1 121 14 14 DG H1' H 6.029 0.002 1 122 14 14 DG H2' H 3.520 0.003 1 123 14 14 DG H2'' H 3.006 0.002 1 124 14 14 DG H3' H 4.889 0.004 1 125 14 14 DG H4' H 4.344 0.001 1 126 14 14 DG H8 H 7.221 0.001 1 127 14 14 DG C8 C 141.395 . 1 128 15 15 DG H1 H 11.431 0.003 1 129 15 15 DG H1' H 5.823 0.003 1 130 15 15 DG H2' H 2.848 0.001 1 131 15 15 DG H2'' H 2.893 0.002 1 132 15 15 DG H3' H 4.996 0.002 1 133 15 15 DG H4' H 4.285 0.002 1 134 15 15 DG H8 H 7.341 0.002 1 135 15 15 DG C8 C 140.707 . 1 136 16 16 DG H1 H 11.016 0.002 1 137 16 16 DG H1' H 5.780 0.001 1 138 16 16 DG H2' H 2.518 0.002 1 139 16 16 DG H2'' H 2.267 0.003 1 140 16 16 DG H3' H 4.916 0.002 1 141 16 16 DG H4' H 4.293 0.003 1 142 16 16 DG H8 H 7.488 0.001 1 143 16 16 DG C8 C 141.271 . 1 144 17 17 DG H1' H 6.155 0.002 1 145 17 17 DG H2' H 2.960 0.004 1 146 17 17 DG H2'' H 2.784 0.003 1 147 17 17 DG H3' H 5.111 0.002 1 148 17 17 DG H8 H 7.893 0.003 1 149 17 17 DG C8 C 139.059 . 1 150 18 18 DA H1' H 6.045 0.002 1 151 18 18 DA H2 H 7.679 0.003 1 152 18 18 DA H2' H 2.455 0.002 1 153 18 18 DA H2'' H 2.361 0.002 1 154 18 18 DA H3' H 5.181 0.003 1 155 18 18 DA H8 H 7.985 0.001 1 156 18 18 DA C2 C 154.841 . 1 157 18 18 DA C8 C 141.755 . 1 158 19 19 DC H1' H 5.602 0.002 1 159 19 19 DC H2' H 2.034 0.002 1 160 19 19 DC H2'' H 2.493 0.003 1 161 19 19 DC H3' H 4.695 0.003 1 162 19 19 DC H4' H 4.523 0.003 1 163 19 19 DC H5 H 5.737 0.002 1 164 19 19 DC H5' H 3.881 0.004 1 165 19 19 DC H5'' H 3.698 0.009 1 166 19 19 DC H6 H 7.617 0.002 1 167 19 19 DC C6 C 143.722 . 1 168 20 20 GFL H1' H 5.895 0.0 1 169 20 20 GFL H2' H 5.459 0.001 1 170 20 20 GFL H3' H 4.723 0.004 1 171 20 20 GFL H4' H 4.306 0.004 1 172 20 20 GFL H8 H 8.012 0.001 1 173 20 20 GFL C8 C 140.913 . 1 174 20 20 GFL HN1 H 11.638 0.002 1 175 21 21 DG H1 H 11.483 0.004 1 176 21 21 DG H1' H 5.970 0.004 1 177 21 21 DG H2' H 2.652 0.004 1 178 21 21 DG H2'' H 2.753 0.001 1 179 21 21 DG H3' H 5.118 0.001 1 180 21 21 DG H4' H 4.471 0.002 1 181 21 21 DG H8 H 7.846 0.002 1 182 21 21 DG C8 C 137.888 . 1 183 22 22 DG H1 H 11.359 0.002 1 184 22 22 DG H1' H 6.286 0.001 1 185 22 22 DG H2' H 2.573 0.0 1 186 22 22 DG H2'' H 2.393 0.001 1 187 22 22 DG H3' H 4.674 0.002 1 188 22 22 DG H4' H 4.323 0.003 1 189 22 22 DG H5' H 4.233 0.003 1 190 22 22 DG H8 H 7.843 0.001 1 191 22 22 DG C8 C 137.513 . 1 stop_ save_