data_18209 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution-state structure of an intramolecular G-quadruplex w th propeller, diagonal and edgewise loops ; _BMRB_accession_number 18209 _BMRB_flat_file_name bmr18209.str _Entry_type original _Submission_date 2012-01-23 _Accession_date 2012-01-23 _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 Marusic Maja . . 2 Sket Primoz . . 3 Bauer Lubos . . 4 Viglasky Viktor . . 5 Plavec Janez . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 153 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-12 update BMRB 'update entry citation' 2012-05-08 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22532609 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Marusic Maja . . 2 Sket Primoz . . 3 Bauer Lubos . . 4 Viglasky Viktor . . 5 Plavec Janez . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 40 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6946 _Page_last 6956 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DNA_molecule_G3ATG3ACACAG4ACG3 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_molecule_G3ATG3ACACAG4ACG3 $DNA_molecule_G3ATG3ACACAG4ACG3 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_molecule_G3ATG3ACACAG4ACG3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_molecule_G3ATG3ACACAG4ACG3 _Molecular_mass 6972.544 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGATGGGACACAGGGGACG GG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DA 5 5 DT 6 6 DG 7 7 DG 8 8 DG 9 9 DA 10 10 DC 11 11 DA 12 12 DC 13 13 DA 14 14 DG 15 15 DG 16 16 DG 17 17 DG 18 18 DA 19 19 DC 20 20 DG 21 21 DG 22 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_molecule_G3ATG3ACACAG4ACG3 . . . . . . 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 $DNA_molecule_G3ATG3ACACAG4ACG3 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium phosphate' 10 mM 'natural abundance' 'potassium chloride' 40 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' $DNA_molecule_G3ATG3ACACAG4ACG3 1.7 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium phosphate' 10 mM 'natural abundance' 'potassium chloride' 40 mM 'natural abundance' D2O 100 % 'natural abundance' $DNA_molecule_G3ATG3ACACAG4ACG3 2.3 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Uniform NMR System' _Field_strength 800 _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-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_3 _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 temperature 273 . K pH 6.8 . pH pressure 1 . atm 'ionic strength' 50 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 H 1 'methyl protons' ppm 0 external 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name DNA_molecule_G3ATG3ACACAG4ACG3 _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 11.630 0.000 1 2 1 1 DG H1' H 6.194 0.001 1 3 1 1 DG H2' H 2.743 0.002 1 4 1 1 DG H2'' H 3.261 0.001 1 5 1 1 DG H3' H 5.022 0.001 1 6 1 1 DG H4' H 4.465 0.000 1 7 1 1 DG H8 H 7.551 0.000 1 8 2 2 DG H1 H 11.615 0.003 1 9 2 2 DG H1' H 5.989 0.001 1 10 2 2 DG H2' H 2.535 0.002 1 11 2 2 DG H2'' H 2.725 0.002 1 12 2 2 DG H3' H 5.036 0.000 1 13 2 2 DG H4' H 4.435 0.003 1 14 2 2 DG H8 H 7.932 0.001 1 15 3 3 DG H1 H 11.049 0.000 1 16 3 3 DG H1' H 6.231 0.001 1 17 3 3 DG H2' H 2.725 0.002 1 18 3 3 DG H2'' H 2.624 0.001 1 19 3 3 DG H3' H 5.040 0.001 1 20 3 3 DG H8 H 7.626 0.001 1 21 4 4 DA H1' H 6.590 0.001 1 22 4 4 DA H2' H 2.908 0.003 1 23 4 4 DA H2'' H 2.887 0.001 1 24 4 4 DA H3' H 4.850 0.002 1 25 4 4 DA H4' H 4.623 0.000 1 26 4 4 DA H5' H 4.131 0.000 2 27 4 4 DA H8 H 8.563 0.000 1 28 5 5 DT H1' H 6.595 0.002 1 29 5 5 DT H2'' H 2.619 0.001 1 30 5 5 DT H3' H 5.049 0.001 1 31 5 5 DT H4' H 4.469 0.003 1 32 5 5 DT H5' H 4.221 0.000 2 33 5 5 DT H5'' H 4.284 0.000 2 34 5 5 DT H6 H 7.850 0.001 1 35 5 5 DT H71 H 2.002 0.000 1 36 5 5 DT H72 H 2.002 0.000 1 37 5 5 DT H73 H 2.002 0.000 1 38 6 6 DG H1 H 11.587 0.001 1 39 6 6 DG H1' H 5.977 0.002 1 40 6 6 DG H2' H 3.054 0.002 1 41 6 6 DG H2'' H 2.956 0.003 1 42 6 6 DG H3' H 4.878 0.002 1 43 6 6 DG H4' H 4.368 0.000 1 44 6 6 DG H8 H 7.245 0.000 1 45 7 7 DG H1 H 11.587 0.004 1 46 7 7 DG H1' H 5.752 0.002 1 47 7 7 DG H2' H 2.611 0.003 1 48 7 7 DG H2'' H 2.139 0.000 1 49 7 7 DG H3' H 5.059 0.002 1 50 7 7 DG H4' H 4.347 0.000 1 51 7 7 DG H8 H 7.815 0.001 1 52 8 8 DG H1 H 11.091 0.001 1 53 8 8 DG H1' H 5.931 0.000 1 54 8 8 DG H2' H 2.143 0.001 1 55 8 8 DG H2'' H 2.424 0.001 1 56 8 8 DG H3' H 4.935 0.001 1 57 8 8 DG H4' H 4.429 0.000 1 58 8 8 DG H8 H 7.535 0.000 1 59 9 9 DA H1' H 6.045 0.002 1 60 9 9 DA H2' H 2.698 0.002 1 61 9 9 DA H2'' H 2.584 0.002 1 62 9 9 DA H3' H 4.946 0.002 1 63 9 9 DA H4' H 4.409 0.001 1 64 9 9 DA H5' H 4.161 0.000 2 65 9 9 DA H5'' H 4.201 0.000 2 66 9 9 DA H8 H 8.073 0.001 1 67 10 10 DC H1' H 5.753 0.002 1 68 10 10 DC H2' H 1.741 0.002 1 69 10 10 DC H2'' H 2.141 0.003 1 70 10 10 DC H3' H 4.599 0.001 1 71 10 10 DC H4' H 3.975 0.000 1 72 10 10 DC H5 H 5.852 0.000 1 73 10 10 DC H6 H 7.592 0.003 1 74 11 11 DA H1' H 5.735 0.001 1 75 11 11 DA H2' H 2.304 0.087 1 76 11 11 DA H2'' H 2.150 0.084 1 77 11 11 DA H3' H 4.454 0.001 1 78 11 11 DA H4' H 3.939 0.003 1 79 11 11 DA H5' H 3.723 0.001 2 80 11 11 DA H5'' H 3.765 0.000 2 81 11 11 DA H8 H 7.925 0.002 1 82 12 12 DC H1' H 5.545 0.001 1 83 12 12 DC H2' H 1.717 0.001 1 84 12 12 DC H2'' H 2.076 0.002 1 85 12 12 DC H3' H 4.412 0.001 1 86 12 12 DC H4' H 3.563 0.000 1 87 12 12 DC H5 H 5.260 0.000 1 88 12 12 DC H6 H 7.171 0.003 1 89 13 13 DA H1' H 5.842 0.001 1 90 13 13 DA H2' H 2.384 0.002 1 91 13 13 DA H2'' H 2.678 0.002 1 92 13 13 DA H8 H 7.919 0.001 1 93 14 14 DG H1 H 11.065 0.002 1 94 14 14 DG H1' H 6.042 0.001 1 95 14 14 DG H2' H 3.503 0.001 1 96 14 14 DG H2'' H 3.060 0.002 1 97 14 14 DG H3' H 4.860 0.000 1 98 14 14 DG H4' H 4.476 0.003 1 99 14 14 DG H8 H 7.245 0.000 1 100 15 15 DG H1 H 11.357 0.001 1 101 15 15 DG H1' H 5.763 0.001 1 102 15 15 DG H2' H 2.139 0.000 1 103 15 15 DG H2'' H 2.521 0.002 1 104 15 15 DG H3' H 4.976 0.002 1 105 15 15 DG H4' H 4.236 0.002 1 106 15 15 DG H8 H 7.357 0.001 1 107 16 16 DG H1 H 11.609 0.004 1 108 16 16 DG H1' H 5.939 0.002 1 109 16 16 DG H2' H 2.557 0.001 1 110 16 16 DG H2'' H 2.423 0.000 1 111 16 16 DG H3' H 5.039 0.001 1 112 16 16 DG H4' H 4.441 0.001 1 113 16 16 DG H8 H 7.622 0.001 1 114 17 17 DG H1' H 6.133 0.001 1 115 17 17 DG H2' H 2.751 0.003 1 116 17 17 DG H2'' H 2.651 0.004 1 117 17 17 DG H3' H 4.904 0.001 1 118 17 17 DG H4' H 4.440 0.001 1 119 17 17 DG H8 H 8.085 0.001 1 120 18 18 DA H1' H 6.032 0.003 1 121 18 18 DA H2' H 2.110 0.001 1 122 18 18 DA H2'' H 2.346 0.004 1 123 18 18 DA H3' H 4.717 0.003 1 124 18 18 DA H4' H 3.872 0.002 1 125 18 18 DA H8 H 7.794 0.002 1 126 19 19 DC H1' H 5.751 0.001 1 127 19 19 DC H2' H 1.763 0.003 1 128 19 19 DC H2'' H 2.353 0.001 1 129 19 19 DC H3' H 4.601 0.003 1 130 19 19 DC H4' H 4.000 0.000 1 131 19 19 DC H5 H 5.749 0.000 1 132 19 19 DC H6 H 7.534 0.002 1 133 20 20 DG H1 H 11.806 0.000 1 134 20 20 DG H1' H 6.009 0.002 1 135 20 20 DG H2' H 3.593 0.004 1 136 20 20 DG H2'' H 2.969 0.003 1 137 20 20 DG H3' H 4.822 0.002 1 138 20 20 DG H4' H 4.390 0.000 1 139 20 20 DG H8 H 7.414 0.001 1 140 21 21 DG H1 H 11.920 0.000 1 141 21 21 DG H1' H 5.789 0.001 1 142 21 21 DG H2' H 2.484 0.001 1 143 21 21 DG H2'' H 2.693 0.004 1 144 21 21 DG H3' H 5.036 0.002 1 145 21 21 DG H4' H 4.352 0.001 1 146 21 21 DG H8 H 7.876 0.000 1 147 22 22 DG H1 H 11.231 0.000 1 148 22 22 DG H1' H 6.261 0.001 1 149 22 22 DG H2' H 2.494 0.003 1 150 22 22 DG H2'' H 2.371 0.002 1 151 22 22 DG H3' H 4.653 0.001 1 152 22 22 DG H4' H 4.297 0.002 1 153 22 22 DG H8 H 7.741 0.001 1 stop_ save_