data_34499 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 2'-F-riboguanosine and LNA modified hybrid type G-quadruplex with V-loop ; _BMRB_accession_number 34499 _BMRB_flat_file_name bmr34499.str _Entry_type original _Submission_date 2020-03-19 _Accession_date 2020-03-19 _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 Weisz K. . . 2 Haase L. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 113 "13C chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-08-31 original BMRB . stop_ _Original_release_date 2020-07-13 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Sugar pucker vs glycosidic torsion angle: Locking specific G-quadruplex topologies through LNA modifications ; _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 Weisz K. . . 2 Haase L. . . 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*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_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 7018.492 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGATGGGACACAXXGGACG 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 GF2 15 LCG 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_GF2 _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common "2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate)" _BMRB_code GF2 _PDB_code GF2 _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 F F F . 0 . ? P P P . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N7 N7 N . 0 . ? C8 C8 C . 0 . ? N9 N9 N . 0 . ? C1' C1' C . 0 . ? OP2 OP2 O . 0 . ? C2' C2' C . 0 . ? OP1 OP1 O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? OP3 OP3 O . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? HN2A HN2A H . 0 . ? H8 H8 H . 0 . ? H1' H1' H . 0 . ? HOP2 HOP2 H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'A H5'A 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 SING P O5' ? ? SING N1 C2 ? ? DOUB C2 N3 ? ? SING C2 N2 ? ? SING C4 N3 ? ? DOUB C5 C4 ? ? SING C6 N1 ? ? SING C6 C5 ? ? DOUB O6 C6 ? ? SING N7 C5 ? ? DOUB N7 C8 ? ? SING C8 N9 ? ? SING N9 C4 ? ? SING N9 C1' ? ? SING C1' O4' ? ? SING OP2 P ? ? SING C2' F ? ? SING C2' C1' ? ? DOUB OP1 P ? ? SING C3' C2' ? ? SING C3' C4' ? ? SING O3' C3' ? ? SING C4' O4' ? ? SING C5' C4' ? ? SING O5' C5' ? ? SING P OP3 ? ? SING N1 HN1 ? ? SING N2 HN2 ? ? SING N2 HN2A ? ? SING C8 H8 ? ? SING C1' H1' ? ? SING OP2 HOP2 ? ? SING C2' H2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C4' H4' ? ? SING C5' H5' ? ? SING C5' H5'A ? ? SING OP3 HOP3 ? ? stop_ save_ save_chem_comp_LCG _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' _BMRB_code LCG _PDB_code LCG _Standard_residue_derivative . _Molecular_mass 375.231 _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 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C3' C3' C . 0 . ? C6' C6' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? C4 C4 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C2' C2' C . 0 . ? O6 O6 O . 0 . ? C4' C4' C . 0 . ? C1' C1' C . 0 . ? C2 C2 C . 0 . ? N1 N1 N . 0 . ? O4' O4' O . 0 . ? OP2 OP2 O . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H3' H3' H . 0 . ? H6'1 H6'1 H . 0 . ? H6'2 H6'2 H . 0 . ? H8 H8 H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? H1 H1 H . 0 . ? HOP2 HOP2 H . 0 . ? H21 H21 H . 0 . ? H22 H22 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 O5' ? ? SING P OP2 ? ? SING P OP3 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C3' C2' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C6' C4' ? ? SING C6' O2' ? ? SING C6' H6'1 ? ? SING C6' H6'2 ? ? SING N9 C8 ? ? SING N9 C4 ? ? SING N9 C1' ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? DOUB C4 C5 ? ? SING C4 N3 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING C2' C1' ? ? SING C2' O2' ? ? SING C2' H2' ? ? SING C4' O4' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2 N1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N1 H1 ? ? SING OP2 HOP2 ? ? SING N2 H21 ? ? SING N2 H22 ? ? 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 . 32630 . . synthetic construct 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 '0.4 mM F14L15, 90% H2O/10% D2O; 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' 'potassium phosphate buffer' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.4 mM F14L15, 100% D2O; 10 mM potassium phosphate buffer at pH 7, i.e. 6.13 mM KH2PO4 and 3.87 mM K2HPO4.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' 'potassium phosphate buffer' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version 4.0.4 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'CcpNmr Analysis' _Version 2.4.2 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.49 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name Amber _Version 16 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE NEO' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_1H_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_DQF-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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' 15 . mM pH 7 . pH pressure 1 . atm temperature 308 . 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' 15 . mM pH 7 . pH pressure 1 . atm temperature 313 . 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 4.67 na 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 '1D 1H' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D DQF-COSY' 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 unit_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 11.827 0.002 1 2 1 1 DG H1' H 5.809 0.002 1 3 1 1 DG H2' H 2.550 0.004 1 4 1 1 DG H2'' H 2.662 0.002 1 5 1 1 DG H3' H 4.907 0.001 1 6 1 1 DG H8 H 7.238 0.002 1 7 1 1 DG C8 C 140.972 . 1 8 2 2 DG H1 H 11.652 0.002 1 9 2 2 DG H1' H 5.877 0.003 1 10 2 2 DG H2' H 2.422 0.003 1 11 2 2 DG H2'' H 2.593 0.002 1 12 2 2 DG H3' H 4.987 0.0 1 13 2 2 DG H8 H 7.489 0.001 1 14 2 2 DG C8 C 137.183 . 1 15 3 3 DG H1' H 5.861 0.004 1 16 3 3 DG H2' H 2.578 0.008 2 17 3 3 DG H2'' H 2.515 0.004 2 18 3 3 DG H3' H 4.835 0.003 1 19 3 3 DG H8 H 7.942 0.002 1 20 3 3 DG C8 C 139.470 . 1 21 4 4 DA H1' H 6.021 0.002 1 22 4 4 DA H2 H 7.790 0.0 1 23 4 4 DA H2' H 2.375 0.006 1 24 4 4 DA H2'' H 2.375 0.006 1 25 4 4 DA H3' H 4.737 0.004 1 26 4 4 DA H8 H 7.976 0.001 1 27 4 4 DA C8 C 141.758 . 1 28 5 5 DT H1' H 5.852 0.004 1 29 5 5 DT H2' H 1.892 0.002 1 30 5 5 DT H2'' H 2.301 0.002 1 31 5 5 DT H3' H 4.632 0.004 1 32 5 5 DT H6 H 7.240 0.002 1 33 5 5 DT H71 H 1.527 0.003 1 34 5 5 DT H72 H 1.527 0.003 1 35 5 5 DT H73 H 1.527 0.003 1 36 5 5 DT C6 C 139.167 . 1 37 6 6 DG H1 H 11.530 0.001 1 38 6 6 DG H1' H 5.959 0.002 1 39 6 6 DG H2' H 3.442 0.002 1 40 6 6 DG H2'' H 2.873 0.002 1 41 6 6 DG H3' H 4.860 0.004 1 42 6 6 DG H8 H 7.269 0.002 1 43 6 6 DG C8 C 142.013 . 1 44 7 7 DG H1 H 11.750 0.003 1 45 7 7 DG H1' H 5.980 0.002 1 46 7 7 DG H2' H 2.623 0.002 1 47 7 7 DG H2'' H 2.875 0.001 1 48 7 7 DG H3' H 5.035 0.009 1 49 7 7 DG H8 H 8.018 0.001 1 50 7 7 DG C8 C 138.376 . 1 51 8 8 DG H1 H 11.300 0.002 1 52 8 8 DG H1' H 5.963 0.004 1 53 8 8 DG H2' H 2.007 0.002 1 54 8 8 DG H2'' H 2.465 . 1 55 8 8 DG H3' H 4.902 0.003 1 56 8 8 DG H8 H 7.407 0.001 1 57 8 8 DG C8 C 137.627 . 1 58 10 10 DC H5 H 5.983 . 1 59 10 10 DC H6 H 7.648 0.003 1 60 10 10 DC C6 C 143.768 . 1 61 12 12 DC H1' H 5.768 0.0 1 62 12 12 DC H2' H 1.947 0.01 1 63 12 12 DC H2'' H 2.155 0.003 1 64 12 12 DC H5 H 5.630 . 1 65 12 12 DC H6 H 7.417 0.001 1 66 12 12 DC C6 C 143.649 . 1 67 13 13 DA H1' H 5.837 0.001 1 68 13 13 DA H2 H 7.583 0.002 1 69 13 13 DA H2' H 2.047 0.008 2 70 13 13 DA H2'' H 2.416 0.005 2 71 13 13 DA H3' H 4.799 . 1 72 13 13 DA H8 H 7.889 0.001 1 73 13 13 DA C2 C 154.070 . 1 74 13 13 DA C8 C 141.445 . 1 75 14 14 GF2 H1' H 6.028 0.001 1 76 14 14 GF2 H2' H 5.414 0.001 1 77 14 14 GF2 H3' H 6.082 . 1 78 14 14 GF2 H8 H 7.188 0.003 1 79 14 14 GF2 C8 C 140.447 . 1 80 14 14 GF2 HN1 H 10.913 0.002 1 81 15 15 LCG H1 H 11.299 0.001 1 82 15 15 LCG H1' H 5.951 0.0 1 83 15 15 LCG H2' H 5.207 0.001 1 84 15 15 LCG H3' H 4.873 0.003 1 85 15 15 LCG H8 H 7.333 0.002 1 86 15 15 LCG C8 C 136.129 . 1 87 16 16 DG H1 H 11.724 0.002 1 88 16 16 DG H1' H 6.065 0.004 1 89 16 16 DG H2' H 3.212 0.001 1 90 16 16 DG H2'' H 2.406 0.001 1 91 16 16 DG H3' H 4.769 0.003 1 92 16 16 DG H8 H 7.651 0.002 1 93 16 16 DG C8 C 138.302 . 1 94 17 17 DG H1 H 11.065 0.002 1 95 17 17 DG H1' H 6.282 0.0 1 96 17 17 DG H2' H 2.507 0.006 1 97 17 17 DG H2'' H 2.561 0.001 1 98 17 17 DG H3' H 4.996 . 1 99 17 17 DG H8 H 7.795 0.004 1 100 17 17 DG C8 C 138.109 . 1 101 18 18 DA H1' H 6.546 0.001 1 102 18 18 DA H2 H 8.317 0.001 1 103 18 18 DA H2' H 3.176 0.001 1 104 18 18 DA H2'' H 2.881 0.002 1 105 18 18 DA H3' H 4.892 . 1 106 18 18 DA H8 H 8.554 0.002 1 107 18 18 DA C8 C 143.313 . 1 108 19 19 DC H1' H 6.358 0.004 1 109 19 19 DC H2' H 2.445 0.004 1 110 19 19 DC H2'' H 2.642 0.001 1 111 19 19 DC H5 H 6.091 . 1 112 19 19 DC H6 H 7.949 0.001 1 113 19 19 DC C6 C 145.052 . 1 114 20 20 DG H1 H 11.941 0.004 1 115 20 20 DG H1' H 5.985 0.002 1 116 20 20 DG H2' H 2.982 0.004 1 117 20 20 DG H2'' H 2.982 0.004 1 118 20 20 DG H3' H 4.815 0.002 1 119 20 20 DG H8 H 7.339 0.001 1 120 20 20 DG C8 C 141.750 . 1 121 21 21 DG H1 H 11.555 0.003 1 122 21 21 DG H1' H 6.078 0.002 1 123 21 21 DG H2' H 2.824 0.005 1 124 21 21 DG H2'' H 2.870 0.003 1 125 21 21 DG H3' H 5.094 0.002 1 126 21 21 DG H8 H 8.095 0.002 1 127 21 21 DG C8 C 138.652 . 1 128 22 22 DG H1 H 11.387 0.001 1 129 22 22 DG H1' H 6.439 0.001 1 130 22 22 DG H2' H 2.637 0.002 1 131 22 22 DG H2'' H 2.537 . 1 132 22 22 DG H3' H 4.740 0.001 1 133 22 22 DG H8 H 7.789 0.002 1 134 22 22 DG C8 C 138.088 . 1 stop_ save_