data_34389 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A quadruplex hybrid structure with lpp loop orientation and 3 syn residues ; _BMRB_accession_number 34389 _BMRB_flat_file_name bmr34389.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" 136 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 8050.835 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GCGTGXXTCAGGGTGGGTGG GACGC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DT 5 DG 6 BGM 7 BGM 8 DT 9 DC 10 DA 11 DG 12 DG 13 DG 14 DT 15 DG 16 DG 17 DG 18 DT 19 DG 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-3s, 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-3s, 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_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 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 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 5.928 0.013 1 2 1 1 DG H2' H 2.728 . 1 3 1 1 DG H2'' H 2.514 0.001 1 4 1 1 DG H3' H 4.789 0.008 1 5 1 1 DG H8 H 7.899 0.004 1 6 2 2 DC H1' H 5.612 0.005 1 7 2 2 DC H2' H 1.946 0.009 1 8 2 2 DC H2'' H 2.289 0.015 1 9 2 2 DC H5 H 5.317 0.009 1 10 2 2 DC H6 H 7.280 0.012 1 11 2 2 DC H41 H 8.317 0.012 1 12 2 2 DC H42 H 6.435 0.011 1 13 3 3 DG H1 H 12.820 0.014 1 14 3 3 DG H1' H 5.900 0.008 1 15 3 3 DG H2' H 2.318 0.006 1 16 3 3 DG H2'' H 2.534 0.007 1 17 3 3 DG H3' H 4.844 0.011 1 18 3 3 DG H8 H 7.705 0.007 1 19 4 4 DT H1' H 5.802 0.009 1 20 4 4 DT H2' H 1.844 0.005 1 21 4 4 DT H2'' H 2.697 0.006 1 22 4 4 DT H3 H 13.414 0.01 1 23 4 4 DT H6 H 6.879 0.005 1 24 4 4 DT H71 H 1.059 0.011 1 25 4 4 DT H72 H 1.059 0.011 1 26 4 4 DT H73 H 1.059 0.011 1 27 5 5 DG H1 H 11.209 0.008 1 28 5 5 DG H1' H 5.899 0.007 1 29 5 5 DG H2' H 3.095 0.005 1 30 5 5 DG H2'' H 2.765 0.005 1 31 5 5 DG H3' H 4.881 . 1 32 5 5 DG H8 H 7.289 0.003 1 33 6 6 BGM H1 H 11.339 0.005 1 34 6 6 BGM H1' H 5.916 0.002 1 35 6 6 BGM H2' H 3.259 0.003 1 36 6 6 BGM H2'' H 2.761 0.005 1 37 6 6 BGM H3' H 4.675 0.004 1 38 7 7 BGM H1 H 10.977 0.006 1 39 7 7 BGM H1' H 5.988 0.003 1 40 7 7 BGM H2' H 3.361 0.006 1 41 7 7 BGM H2'' H 2.211 0.008 1 42 7 7 BGM H3' H 5.130 0.007 1 43 8 8 DT H1' H 5.917 0.003 1 44 8 8 DT H2' H 2.274 0.006 1 45 8 8 DT H2'' H 2.531 0.01 1 46 8 8 DT H6 H 7.585 0.004 1 47 8 8 DT H71 H 1.807 0.007 1 48 8 8 DT H72 H 1.807 0.007 1 49 8 8 DT H73 H 1.807 0.007 1 50 9 9 DC H1' H 5.819 0.011 1 51 9 9 DC H2' H 1.380 0.006 1 52 9 9 DC H2'' H 2.093 0.008 1 53 9 9 DC H3' H 4.693 0.009 1 54 9 9 DC H5 H 5.473 0.005 1 55 9 9 DC H6 H 7.138 0.005 1 56 10 10 DA H1' H 5.412 0.009 1 57 10 10 DA H2 H 7.681 0.003 1 58 10 10 DA H2' H 2.660 0.005 1 59 10 10 DA H2'' H 2.552 0.006 1 60 10 10 DA H3' H 4.939 0.003 1 61 10 10 DA H8 H 8.102 0.003 1 62 11 11 DG H1 H 11.382 0.001 1 63 11 11 DG H1' H 6.115 0.003 1 64 11 11 DG H2' H 2.709 0.005 1 65 11 11 DG H2'' H 3.048 0.01 1 66 11 11 DG H3' H 5.005 0.003 1 67 11 11 DG H8 H 7.951 0.002 1 68 12 12 DG H1 H 11.277 0.011 1 69 12 12 DG H1' H 6.262 0.005 1 70 12 12 DG H2' H 2.540 0.015 1 71 12 12 DG H2'' H 2.969 0.003 1 72 12 12 DG H3' H 4.875 0.003 1 73 12 12 DG H8 H 7.622 0.003 1 74 13 13 DG H1 H 11.207 0.006 1 75 13 13 DG H1' H 6.463 0.004 1 76 13 13 DG H2' H 2.730 0.017 1 77 13 13 DG H2'' H 2.679 0.007 1 78 13 13 DG H3' H 5.167 . 1 79 13 13 DG H8 H 7.794 0.005 1 80 14 14 DT H3' H 5.186 0.005 1 81 15 15 DG H1 H 11.644 0.008 1 82 15 15 DG H1' H 6.211 0.006 1 83 15 15 DG H2' H 2.566 0.009 1 84 15 15 DG H2'' H 3.081 0.005 1 85 15 15 DG H3' H 5.209 0.004 1 86 15 15 DG H8 H 8.122 0.005 1 87 16 16 DG H1 H 11.378 0.006 1 88 16 16 DG H1' H 6.165 0.006 1 89 16 16 DG H2' H 2.706 0.003 1 90 16 16 DG H2'' H 2.911 0.003 1 91 16 16 DG H3' H 5.137 0.008 1 92 16 16 DG H8 H 7.936 0.002 1 93 17 17 DG H1 H 11.242 0.011 1 94 17 17 DG H1' H 6.513 0.002 1 95 17 17 DG H2' H 2.723 0.001 1 96 17 17 DG H2'' H 2.652 0.016 1 97 17 17 DG H3' H 5.165 0.008 1 98 17 17 DG H8 H 7.861 0.004 1 99 19 19 DG H1 H 11.317 0.002 1 100 19 19 DG H1' H 6.177 0.004 1 101 19 19 DG H2' H 2.447 0.006 1 102 19 19 DG H2'' H 3.013 0.009 1 103 19 19 DG H3' H 5.229 0.003 1 104 19 19 DG H8 H 8.121 0.0 1 105 20 20 DG H1' H 6.033 0.004 1 106 20 20 DG H3' H 5.169 0.01 1 107 20 20 DG H8 H 8.046 0.002 1 108 21 21 DG H1 H 11.159 0.005 1 109 21 21 DG H1' H 5.867 0.007 1 110 21 21 DG H2' H 2.758 0.0 1 111 21 21 DG H3' H 5.114 0.006 1 112 21 21 DG H8 H 7.929 0.006 1 113 22 22 DA H1' H 6.357 0.008 1 114 22 22 DA H2 H 7.703 0.007 1 115 22 22 DA H2' H 2.730 0.008 1 116 22 22 DA H2'' H 2.935 0.006 1 117 22 22 DA H3' H 5.148 0.007 1 118 22 22 DA H8 H 8.372 0.003 1 119 23 23 DC H1' H 5.626 0.011 1 120 23 23 DC H2' H 1.951 0.011 1 121 23 23 DC H2'' H 2.304 0.002 1 122 23 23 DC H3' H 4.881 . 1 123 23 23 DC H5 H 5.299 0.008 1 124 23 23 DC H6 H 7.277 0.013 1 125 23 23 DC H41 H 8.052 0.008 1 126 23 23 DC H42 H 6.418 0.005 1 127 24 24 DG H1 H 12.972 0.015 1 128 24 24 DG H1' H 5.927 0.007 1 129 24 24 DG H2' H 2.627 0.011 1 130 24 24 DG H2'' H 2.720 0.019 1 131 24 24 DG H3' H 4.981 0.008 1 132 24 24 DG H8 H 7.885 0.003 1 133 25 25 DC H1' H 6.179 0.003 1 134 25 25 DC H3' H 4.489 0.006 1 135 25 25 DC H5 H 5.549 0.004 1 136 25 25 DC H6 H 7.472 0.004 1 stop_ save_