data_34390 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A quadruplex hybrid structure with lpp loop orientation and 5 syn residues ; _BMRB_accession_number 34390 _BMRB_flat_file_name bmr34390.str _Entry_type original _Submission_date 2019-04-03 _Accession_date 2019-04-03 _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 Karg B. . . 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" 139 "13C chemical shifts" 25 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-10-17 original BMRB . stop_ _Original_release_date 2019-10-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31134741 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Karg B. . . 2 Mohr S. . . 3 Weisz K. . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed. Engl.' _Journal_volume 58 _Journal_issue 32 _Journal_ASTM ACIEAY _Journal_ISSN 1521-3773 _Journal_CSD 0179 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11068 _Page_last 11071 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA (25-MER)' _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 8050.834 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GCGTGGGTCAGGGTXGGTXG GACGC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DT 5 DG 6 DG 7 DG 8 DT 9 DC 10 DA 11 DG 12 DG 13 DG 14 DT 15 BGM 16 DG 17 DG 18 DT 19 BGM 20 DG 21 DG 22 DA 23 DC 24 DG 25 DC 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 '0.8 mM MYC4t-5s, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.8 mM MYC4t-5s, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version 3 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'CcpNmr Analysis' _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name Xplor-NIH _Version . 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 . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . 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 NEO' _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_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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' 10 . mM pH 7 . pH* pressure 1 . atm temperature 303 . 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 4.73 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' 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 5.933 0.001 1 2 1 1 DG H2' H 2.515 0.006 2 3 1 1 DG H2'' H 2.692 0.003 2 4 1 1 DG H8 H 7.904 0.002 1 5 1 1 DG C8 C 138.796 . 1 6 2 2 DC H1' H 5.600 0.002 1 7 2 2 DC H2' H 1.960 0.005 2 8 2 2 DC H2'' H 2.302 0.006 2 9 2 2 DC H5 H 5.313 0.002 1 10 2 2 DC H6 H 7.288 0.005 1 11 2 2 DC H41 H 8.329 0.006 1 12 2 2 DC H42 H 6.432 0.005 1 13 2 2 DC C6 C 142.750 . 1 14 3 3 DG H1 H 12.846 0.003 1 15 3 3 DG H1' H 5.928 0.002 1 16 3 3 DG H2' H 2.604 0.006 2 17 3 3 DG H2'' H 2.364 0.005 2 18 3 3 DG H8 H 7.726 0.001 1 19 3 3 DG C8 C 138.479 . 1 20 4 4 DT H1' H 5.880 0.002 1 21 4 4 DT H2' H 2.873 0.009 2 22 4 4 DT H2'' H 2.036 0.005 2 23 4 4 DT H3 H 13.390 0.002 1 24 4 4 DT H6 H 6.950 0.002 1 25 4 4 DT H71 H 1.082 0.004 1 26 4 4 DT H72 H 1.082 0.004 1 27 4 4 DT H73 H 1.082 0.004 1 28 4 4 DT C6 C 138.074 . 1 29 5 5 DG H1 H 11.147 0.007 1 30 5 5 DG H1' H 5.984 0.003 1 31 5 5 DG H2' H 2.686 0.005 2 32 5 5 DG H2'' H 2.950 0.008 2 33 5 5 DG H8 H 7.297 0.002 1 34 5 5 DG C8 C 142.168 . 1 35 6 6 DG H1 H 11.190 0.002 1 36 6 6 DG H1' H 5.743 0.001 1 37 6 6 DG H2' H 2.812 0.006 2 38 6 6 DG H2'' H 2.611 0.004 2 39 6 6 DG H8 H 7.144 0.004 1 40 6 6 DG C8 C 140.901 . 1 41 7 7 DG H1 H 11.009 0.002 1 42 7 7 DG H1' H 6.024 0.003 1 43 7 7 DG H2' H 2.607 0.002 1 44 7 7 DG H2'' H 2.607 0.002 1 45 7 7 DG H8 H 7.777 0.005 1 46 7 7 DG C8 C 137.992 . 1 47 8 8 DT H1' H 6.301 0.003 1 48 8 8 DT H2' H 2.371 0.005 2 49 8 8 DT H2'' H 2.561 0.006 2 50 8 8 DT H6 H 7.800 0.002 1 51 8 8 DT H71 H 1.956 0.002 1 52 8 8 DT H72 H 1.956 0.002 1 53 8 8 DT H73 H 1.956 0.002 1 54 8 8 DT C6 C 140.332 . 1 55 9 9 DC H1' H 5.892 0.005 1 56 9 9 DC H2' H 1.057 0.008 2 57 9 9 DC H2'' H 1.844 0.004 2 58 9 9 DC H5 H 5.720 0.002 1 59 9 9 DC H6 H 7.318 0.003 1 60 9 9 DC C6 C 143.052 . 1 61 10 10 DA H1' H 5.896 0.004 1 62 10 10 DA H2 H 7.686 0.004 1 63 10 10 DA H2' H 2.592 0.001 2 64 10 10 DA H2'' H 2.741 0.001 2 65 10 10 DA H3' H 4.946 0.002 1 66 10 10 DA H8 H 7.956 0.002 1 67 10 10 DA C2 C 155.190 . 1 68 10 10 DA C8 C 141.208 . 1 69 11 11 DG H1 H 10.986 0.005 1 70 11 11 DG H1' H 6.112 0.004 1 71 11 11 DG H2' H 3.440 0.004 2 72 11 11 DG H2'' H 3.024 0.002 2 73 11 11 DG H8 H 7.492 0.002 1 74 11 11 DG C8 C 142.471 . 1 75 12 12 DG H1 H 11.675 0.005 1 76 12 12 DG H1' H 6.091 0.01 1 77 12 12 DG H2' H 3.019 0.004 2 78 12 12 DG H2'' H 2.584 0.005 2 79 12 12 DG H8 H 7.950 0.002 1 80 12 12 DG C8 C 138.547 . 1 81 13 13 DG H1 H 11.230 0.002 1 82 13 13 DG H1' H 6.529 0.004 1 83 13 13 DG H2' H 2.741 0.002 1 84 13 13 DG H2'' H 2.741 0.002 1 85 13 13 DG H8 H 7.758 0.002 1 86 13 13 DG C8 C 138.997 . 1 87 14 14 DT H1' H 6.542 0.001 1 88 14 14 DT H2' H 2.444 0.002 2 89 14 14 DT H2'' H 2.787 0.006 2 90 14 14 DT H6 H 7.938 0.003 1 91 14 14 DT H71 H 2.030 . 1 92 14 14 DT H72 H 2.030 . 1 93 14 14 DT H73 H 2.030 . 1 94 14 14 DT C6 C 139.963 . 1 95 15 15 BGM H1 H 11.888 0.002 1 96 15 15 BGM H1' H 6.182 0.001 1 97 15 15 BGM H2' H 3.287 0.002 2 98 15 15 BGM H2'' H 3.169 0.001 2 99 16 16 DG H1 H 11.545 0.001 1 100 16 16 DG H1' H 6.053 0.001 1 101 16 16 DG H2' H 2.947 0.001 2 102 16 16 DG H2'' H 2.611 0.003 2 103 16 16 DG H3' H 5.138 . 1 104 16 16 DG H8 H 8.227 0.003 1 105 16 16 DG C8 C 139.372 . 1 106 17 17 DG H1 H 11.240 0.002 1 107 17 17 DG H1' H 6.559 0.001 1 108 17 17 DG H2' H 2.714 0.0 1 109 17 17 DG H8 H 7.883 0.001 1 110 17 17 DG C8 C 138.236 . 1 111 18 18 DT H1' H 6.542 0.001 1 112 18 18 DT H2' H 2.444 0.002 2 113 18 18 DT H2'' H 2.786 0.007 2 114 18 18 DT H6 H 7.937 0.001 1 115 18 18 DT H71 H 2.030 . 1 116 18 18 DT H72 H 2.030 . 1 117 18 18 DT H73 H 2.030 . 1 118 18 18 DT C6 C 139.963 . 1 119 19 19 BGM H1 H 11.525 0.002 1 120 19 19 BGM H1' H 6.154 0.001 1 121 19 19 BGM H2' H 3.015 0.003 2 122 19 19 BGM H2'' H 3.071 0.007 2 123 20 20 DG H1 H 11.973 0.002 1 124 20 20 DG H1' H 5.888 0.002 1 125 20 20 DG H2' H 2.863 0.002 2 126 20 20 DG H2'' H 2.627 0.004 2 127 20 20 DG H3' H 5.130 . 1 128 20 20 DG H8 H 8.240 0.002 1 129 20 20 DG C8 C 139.652 . 1 130 21 21 DG H1 H 10.994 0.008 1 131 21 21 DG H1' H 5.949 0.004 1 132 21 21 DG H2' H 2.770 0.002 2 133 21 21 DG H2'' H 2.675 0.011 2 134 21 21 DG H3' H 5.115 0.005 1 135 21 21 DG H8 H 7.884 0.002 1 136 21 21 DG C8 C 138.236 . 1 137 22 22 DA H1' H 6.320 0.002 1 138 22 22 DA H2 H 7.633 0.002 1 139 22 22 DA H2' H 2.688 0.005 2 140 22 22 DA H2'' H 2.904 0.01 2 141 22 22 DA H3' H 5.118 0.002 1 142 22 22 DA H8 H 8.303 0.002 1 143 22 22 DA C2 C 154.905 . 1 144 22 22 DA C8 C 141.146 . 1 145 23 23 DC H1' H 5.624 0.003 1 146 23 23 DC H2' H 2.316 0.005 2 147 23 23 DC H2'' H 1.964 0.002 2 148 23 23 DC H5 H 5.259 0.003 1 149 23 23 DC H6 H 7.263 0.003 1 150 23 23 DC H41 H 6.411 0.009 1 151 23 23 DC H42 H 8.024 0.002 1 152 23 23 DC C6 C 142.519 . 1 153 24 24 DG H1 H 12.975 0.002 1 154 24 24 DG H1' H 5.931 0.006 1 155 24 24 DG H2' H 2.615 0.007 2 156 24 24 DG H2'' H 2.720 0.004 2 157 24 24 DG H8 H 7.882 0.001 1 158 24 24 DG C8 C 138.750 . 1 159 25 25 DC H1' H 6.188 0.001 1 160 25 25 DC H2' H 2.175 0.008 1 161 25 25 DC H2'' H 2.175 0.008 1 162 25 25 DC H5 H 5.542 0.002 1 163 25 25 DC H6 H 7.473 0.002 1 164 25 25 DC C6 C 143.283 . 1 stop_ save_