data_25746 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; G-quadruplex structure ; _BMRB_accession_number 25746 _BMRB_flat_file_name bmr25746.str _Entry_type original _Submission_date 2015-08-08 _Accession_date 2015-08-08 _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 Heddi Brahim . . 2 Martin-Pintado Nerea . . 3 Serimbetov Zhalgas . . 4 Kari Teuku . . 5 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 114 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-05-31 original BMRB . stop_ _Original_release_date 2016-05-31 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26673723 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Heddi Brahim . . 2 Martin-Pintado Nerea . . 3 Serimbetov Zhalgas . . 4 Kari Teuku . . 5 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 44 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 910 _Page_last 916 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')" $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 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_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') _Molecular_mass 5705.705 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; TTGTGTGGGTGGGTGGGT ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DG 4 DT 5 DG 6 DT 7 DG 8 DG 9 DG 10 DT 11 DG 12 DG 13 DG 14 DT 15 DG 16 DG 17 DG 18 DT 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_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 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 $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') . mM 0.1 1.2 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 0.2-0.4 mM '[U-4% 15N]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 0.6-1.2 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 0.2-0.4 mM '[U-100% 2H]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _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 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'chemical shift calculation' 'data analysis' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' refinement stop_ _Details . save_ save_Spinworks _Saveframe_category software _Name Spinworks _Version . loop_ _Vendor _Address _Electronic_address http://home.cc.umanitoba.ca/~wolowiec/spinworks . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_3 save_ save_2D_1H-1H_HMBC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H HMBC' _Sample_label $sample_1 save_ save_1D_15N-filtered_1H_NMR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 15N-filtered 1H NMR' _Sample_label $sample_2 save_ save_1D_1H_NMR_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H NMR' _Sample_label $sample_4 save_ save_1D_1H_NMR_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H NMR' _Sample_label $sample_1 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' 45 . mM pH 7 . pH pressure 1 . atm temperature 298 . K 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 0.00 internal direct . . . 1.000000000 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_proton_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '1D 15N-filtered 1H NMR' '1D 1H NMR' '2D 1H-1H HMBC' stop_ loop_ _Sample_label $sample_1 $sample_3 $sample_2 $sample_4 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')" _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 DT H1' H 5.784 . . 2 1 1 DT H2' H 1.938 . . 3 1 1 DT H2'' H 2.291 . . 4 1 1 DT H3' H 4.522 . . 5 1 1 DT H4' H 3.817 . . 6 1 1 DT H5' H 3.480 . . 7 1 1 DT H6 H 7.212 . . 8 1 1 DT H71 H 1.573 . . 9 1 1 DT H72 H 1.573 . . 10 1 1 DT H73 H 1.573 . . 11 2 2 DT H1' H 5.708 . . 12 2 2 DT H2' H 1.758 . . 13 2 2 DT H2'' H 2.274 . . 14 2 2 DT H3' H 4.560 . . 15 2 2 DT H4' H 3.428 . . 16 2 2 DT H5' H 3.152 . . 17 2 2 DT H5'' H 3.660 . . 18 2 2 DT H6 H 7.230 . . 19 2 2 DT H71 H 1.506 . . 20 2 2 DT H72 H 1.506 . . 21 2 2 DT H73 H 1.506 . . 22 3 3 DG H1 H 11.988 . . 23 3 3 DG H1' H 6.423 . . 24 3 3 DG H2' H 2.938 . . 25 3 3 DG H2'' H 3.119 . . 26 3 3 DG H3' H 5.013 . . 27 3 3 DG H4' H 3.957 . . 28 3 3 DG H5' H 3.578 . . 29 3 3 DG H5'' H 3.650 . . 30 3 3 DG H8 H 8.128 . . 31 4 4 DT H1' H 6.433 . . 32 4 4 DT H2' H 2.388 . . 33 4 4 DT H2'' H 2.607 . . 34 4 4 DT H3' H 4.952 . . 35 4 4 DT H4' H 4.066 . . 36 4 4 DT H6 H 7.700 . . 37 4 4 DT H71 H 1.956 . . 38 4 4 DT H72 H 1.956 . . 39 4 4 DT H73 H 1.956 . . 40 5 5 DG H1 H 12.000 . . 41 5 5 DG H1' H 6.409 . . 42 5 5 DG H2' H 2.318 . . 43 5 5 DG H2'' H 2.872 . . 44 5 5 DG H3' H 5.095 . . 45 5 5 DG H4' H 4.197 . . 46 5 5 DG H8 H 7.553 . . 47 7 7 DG H1 H 11.988 . . 48 7 7 DG H1' H 6.183 . . 49 7 7 DG H2' H 2.467 . . 50 7 7 DG H2'' H 2.985 . . 51 7 7 DG H3' H 5.122 . . 52 7 7 DG H8 H 8.139 . . 53 8 8 DG H1 H 11.470 . . 54 8 8 DG H1' H 6.225 . . 55 8 8 DG H2' H 2.648 . . 56 8 8 DG H2'' H 2.984 . . 57 8 8 DG H3' H 5.064 . . 58 8 8 DG H4' H 4.305 . . 59 8 8 DG H8 H 8.025 . . 60 9 9 DG H1 H 11.003 . . 61 9 9 DG H1' H 6.468 . . 62 9 9 DG H2' H 2.453 . . 63 9 9 DG H2'' H 2.710 . . 64 9 9 DG H3' H 5.169 . . 65 9 9 DG H4' H 4.315 . . 66 9 9 DG H8 H 7.815 . . 67 11 11 DG H1 H 11.760 . . 68 11 11 DG H1' H 6.134 . . 69 11 11 DG H2' H 2.557 . . 70 11 11 DG H2'' H 2.999 . . 71 11 11 DG H3' H 5.075 . . 72 11 11 DG H4' H 4.280 . . 73 11 11 DG H8 H 8.022 . . 74 12 12 DG H1 H 11.440 . . 75 12 12 DG H1' H 6.219 . . 76 12 12 DG H2' H 2.650 . . 77 12 12 DG H2'' H 2.920 . . 78 12 12 DG H3' H 5.130 . . 79 12 12 DG H4' H 4.263 . . 80 12 12 DG H8 H 7.924 . . 81 13 13 DG H1 H 11.110 . . 82 13 13 DG H1' H 6.489 . . 83 13 13 DG H2' H 2.581 . . 84 13 13 DG H2'' H 2.705 . . 85 13 13 DG H3' H 5.099 . . 86 13 13 DG H4' H 4.310 . . 87 13 13 DG H8 H 7.837 . . 88 15 15 DG H1 H 11.440 . . 89 15 15 DG H1' H 6.075 . . 90 15 15 DG H2' H 2.397 . . 91 15 15 DG H2'' H 2.807 . . 92 15 15 DG H3' H 5.141 . . 93 15 15 DG H4' H 4.317 . . 94 15 15 DG H8 H 7.939 . . 95 16 16 DG H1 H 11.640 . . 96 16 16 DG H1' H 6.034 . . 97 16 16 DG H2' H 2.739 . . 98 16 16 DG H3' H 5.094 . . 99 16 16 DG H4' H 4.325 . . 100 16 16 DG H8 H 8.020 . . 101 17 17 DG H1' H 6.270 . . 102 17 17 DG H2' H 2.431 . . 103 17 17 DG H2'' H 2.589 . . 104 17 17 DG H3' H 4.893 . . 105 17 17 DG H4' H 4.267 . . 106 17 17 DG H8 H 7.803 . . 107 18 18 DT H1' H 6.003 . . 108 18 18 DT H2' H 2.106 . . 109 18 18 DT H3' H 4.456 . . 110 18 18 DT H4' H 4.050 . . 111 18 18 DT H6 H 7.273 . . 112 18 18 DT H71 H 1.607 . . 113 18 18 DT H72 H 1.607 . . 114 18 18 DT H73 H 1.607 . . stop_ save_