data_50246 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID 50246 _Entry.Title ; [r(UGGUGGT)]4 G-quadruplex ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2020-04-24 _Entry.Accession_date 2020-04-24 _Entry.Last_release_date 2020-04-27 _Entry.Original_release_date 2020-04-27 _Entry.Origination author _Entry.Format_name . _Entry.NMR_STAR_version 3.2.14.0 _Entry.NMR_STAR_dict_location . _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Source_data_format . _Entry.Source_data_format_version . _Entry.Generated_software_name . _Entry.Generated_software_version . _Entry.Generated_software_ID . _Entry.Generated_software_label . _Entry.Generated_date . _Entry.DOI . _Entry.UUID . _Entry.Related_coordinate_file_name . _Entry.Details . _Entry.BMRB_internal_directory_name . loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.ORCID _Entry_author.Entry_ID 1 Witold Andralojc . . . . 50246 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 50246 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '1H chemical shifts' 50 50246 '31P chemical shifts' 7 50246 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 2 . . 2021-05-17 2020-04-24 update BMRB 'update entry citation' 50246 1 . . 2020-05-20 2020-04-24 original author 'original release' 50246 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID BMRB 50242 '[r(UGGUGG)d(U)]4 G-quadruplex' 50246 BMRB 50244 "[r(UGGUGG)(2'OMeU)]4 G-quadruplex" 50246 BMRB 50245 '[r(UGGUGGC)]4 G-quadruplex' 50246 BMRB 50247 '[r(UGGUGG)d(T)]4 G-quadruplex' 50246 BMRB 50248 '[r(UGGUGG)(LNA-T)]4 G-quadruplex' 50246 BMRB 50249 '[r(UGGUGGPs)]4 G-quadruplex' 50246 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID 50246 _Citation.ID 1 _Citation.Name . _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.PubMed_ID 32967936 _Citation.DOI . _Citation.Full_citation . _Citation.Title ; The origin of the high stability of 3'-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs ; _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev RNA _Citation.Journal_name_full . _Citation.Journal_volume 26 _Citation.Journal_issue 12 _Citation.Journal_ASTM . _Citation.Journal_ISSN . _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 2000 _Citation.Page_last 2016 _Citation.Year 2020 _Citation.Details . loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.ORCID _Citation_author.Entry_ID _Citation_author.Citation_ID 1 Witold Andralojc . . . . 50246 1 2 Karol Pasternak . . . . 50246 1 3 Joanna Sarzynska . . . . 50246 1 4 Karolina Zielinska . . . . 50246 1 5 Ryszard Kierzek . . . . 50246 1 6 Zofia Gdaniec . . . . 50246 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID 50246 _Assembly.ID 1 _Assembly.Name '[r(UGGUGGT)]4 G-quadruplex' _Assembly.BMRB_code . _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Ambiguous_conformational_states no _Assembly.Ambiguous_chem_comp_sites . _Assembly.Molecules_in_chemical_exchange no _Assembly.Paramagnetic no _Assembly.Thiol_state . _Assembly.Molecular_mass . _Assembly.Enzyme_commission_number . _Assembly.Details . _Assembly.DB_query_date . _Assembly.DB_query_revised_last_date . loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 '[r(UGGUGGT)]4 G-quadruplex' 1 $entity_1 . . yes native no no . . . 50246 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID 50246 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name entity_1 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID . _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; UGGUGGX ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer yes _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 7 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method . _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight . _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details 'X is 5-Methyluridine/ribothymidine' _Entity.DB_query_date . _Entity.DB_query_revised_last_date . loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . U . 50246 1 2 . G . 50246 1 3 . G . 50246 1 4 . U . 50246 1 5 . G . 50246 1 6 . G . 50246 1 7 . 38T . 50246 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . U 1 1 50246 1 . G 2 2 50246 1 . G 3 3 50246 1 . U 4 4 50246 1 . G 5 5 50246 1 . G 6 6 50246 1 . 38T 7 7 50246 1 stop_ save_ #################### # Natural source # #################### save_natural_source_1 _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source_1 _Entity_natural_src_list.Entry_ID 50246 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.Entity_chimera_segment_ID _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Organism_acronym _Entity_natural_src.ICTVdb_decimal_code _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Strain _Entity_natural_src.Variant _Entity_natural_src.Organ _Entity_natural_src.Tissue _Entity_natural_src.Tissue_fraction _Entity_natural_src.Cell_line _Entity_natural_src.Cell_type _Entity_natural_src.ATCC_number _Entity_natural_src.Organelle _Entity_natural_src.Secretion _Entity_natural_src.Plasmid _Entity_natural_src.Gene_mnemonic _Entity_natural_src.Details _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $entity_1 . . 'no natural source' . . . . . . . . . . . . . . . . . . . . . . 50246 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source_1 _Entity_experimental_src_list.Entry_ID 50246 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Entity_chimera_segment_ID _Entity_experimental_src.Production_method _Entity_experimental_src.Host_org_scientific_name _Entity_experimental_src.Host_org_name_common _Entity_experimental_src.Host_org_details _Entity_experimental_src.Host_org_NCBI_taxonomy_ID _Entity_experimental_src.Host_org_genus _Entity_experimental_src.Host_org_species _Entity_experimental_src.Host_org_strain _Entity_experimental_src.Host_org_variant _Entity_experimental_src.Host_org_ATCC_number _Entity_experimental_src.Vector_type _Entity_experimental_src.PDBview_host_org_vector_name _Entity_experimental_src.PDBview_plasmid_name _Entity_experimental_src.Vector_name _Entity_experimental_src.Vector_details _Entity_experimental_src.Vendor_name _Entity_experimental_src.Details _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $entity_1 . 'chemical synthesis' . . . . . . . . . . . . . . . . 50246 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_38T _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_38T _Chem_comp.Entry_ID 50246 _Chem_comp.ID 38T _Chem_comp.Provenance PDB _Chem_comp.Name 5-methyluridine _Chem_comp.Type NON-POLYMER _Chem_comp.BMRB_code 38T _Chem_comp.PDB_code 38T _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2014-07-18 _Chem_comp.Modified_date 2014-07-18 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code . _Chem_comp.Three_letter_code 38T _Chem_comp.Number_atoms_all 32 _Chem_comp.Number_atoms_nh 18 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1 _Chem_comp.Mon_nstd_flag . _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID . _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms . _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C10 H14 N2 O6' _Chem_comp.Formula_weight 258.228 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag no _Chem_comp.Ideal_coordinates_details Corina _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code 4QSW _Chem_comp.Processing_site RCSB _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O SMILES 'OpenEye OEToolkits' 1.7.6 50246 38T CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 50246 38T CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O SMILES_CANONICAL CACTVS 3.385 50246 38T CC1=CN([CH]2O[CH](CO)[CH](O)[CH]2O)C(=O)NC1=O SMILES CACTVS 3.385 50246 38T DWRXFEITVBNRMK-JXOAFFINSA-N InChIKey InChI 1.03 50246 38T InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1 InChI InChI 1.03 50246 38T O=C1NC(=O)N(C=C1C)C2OC(C(O)C2O)CO SMILES ACDLabs 12.01 50246 38T stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID 1-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 50246 38T 5-methyluridine 'SYSTEMATIC NAME' ACDLabs 12.01 50246 38T stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID OAC OAC OAC OAC . O . . N 0 . . . 1 no no . . . . 28.334 . 44.472 . -12.704 . 0.223 -1.043 -1.508 1 . 50246 38T CAM CAM CAM CAM . C . . N 0 . . . 1 no no . . . . 27.317 . 44.579 . -12.007 . 1.135 -0.633 -0.816 2 . 50246 38T NAI NAI NAI NAI . N . . N 0 . . . 1 no no . . . . 26.294 . 43.725 . -12.328 . 2.404 -0.950 -1.134 3 . 50246 38T CAL CAL CAL CAL . C . . N 0 . . . 1 no no . . . . 25.067 . 43.731 . -11.644 . 3.426 -0.503 -0.377 4 . 50246 38T OAB OAB OAB OAB . O . . N 0 . . . 1 no no . . . . 24.275 . 42.890 . -12.040 . 4.574 -0.789 -0.664 5 . 50246 38T CAK CAK CAK CAK . C . . N 0 . . . 1 no no . . . . 24.857 . 44.622 . -10.604 . 3.152 0.302 0.756 6 . 50246 38T CAA CAA CAA CAA . C . . N 0 . . . 1 no no . . . . 23.652 . 44.662 . -9.846 . 4.277 0.814 1.618 7 . 50246 38T CAG CAG CAG CAG . C . . N 0 . . . 1 no no . . . . 25.916 . 45.506 . -10.286 . 1.870 0.605 1.051 8 . 50246 38T NAR NAR NAR NAR . N . . N 0 . . . 1 no no . . . . 27.146 . 45.473 . -10.997 . 0.862 0.135 0.255 9 . 50246 38T C1' C1' C1' C1' . C . . R 0 . . . 1 no no . . . . 28.249 . 46.418 . -10.673 . -0.529 0.469 0.572 10 . 50246 38T O4' O4' O4' O4' . O . . N 0 . . . 1 no no . . . . 28.162 . 46.992 . -9.301 . -1.325 -0.733 0.666 11 . 50246 38T C4' C4' C4' C4' . C . . R 0 . . . 1 no no . . . . 27.887 . 48.434 . -9.448 . -2.691 -0.300 0.482 12 . 50246 38T C5' C5' C5' C5' . C . . N 0 . . . 1 no no . . . . 26.943 . 48.961 . -8.379 . -3.569 -1.477 0.052 13 . 50246 38T O5' O5' O5' O5' . O . . N 0 . . . 1 no no . . . . 25.695 . 48.338 . -8.688 . -3.655 -2.422 1.120 14 . 50246 38T C3' C3' C3' C3' . C . . S 0 . . . 1 no no . . . . 27.289 . 48.576 . -10.881 . -2.621 0.758 -0.642 15 . 50246 38T O3' O3' O3' O3' . O . . N 0 . . . 1 no no . . . . 27.389 . 49.956 . -11.395 . -3.544 1.819 -0.389 16 . 50246 38T C2' C2' C2' C2' . C . . R 0 . . . 1 no no . . . . 28.185 . 47.621 . -11.654 . -1.166 1.275 -0.581 17 . 50246 38T O2' O2' O2' O2' . O . . N 0 . . . 1 no no . . . . 29.509 . 48.223 . -11.896 . -1.144 2.673 -0.286 18 . 50246 38T H1 H1 H1 H1 . H . . N 0 . . . 1 no no . . . . 26.426 . 43.074 . -13.076 . 2.583 -1.502 -1.911 19 . 50246 38T H2 H2 H2 H2 . H . . N 0 . . . 1 no no . . . . 23.725 . 45.449 . -9.081 . 5.229 0.465 1.219 20 . 50246 38T H3 H3 H3 H3 . H . . N 0 . . . 1 no no . . . . 22.806 . 44.878 . -10.514 . 4.262 1.904 1.624 21 . 50246 38T H4 H4 H4 H4 . H . . N 0 . . . 1 no no . . . . 23.494 . 43.689 . -9.357 . 4.152 0.444 2.636 22 . 50246 38T H5 H5 H5 H5 . H . . N 0 . . . 1 no no . . . . 25.786 . 46.220 . -9.486 . 1.642 1.217 1.911 23 . 50246 38T H6 H6 H6 H6 . H . . N 0 . . . 1 no no . . . . 29.217 . 45.911 . -10.799 . -0.580 1.031 1.505 24 . 50246 38T H7 H7 H7 H7 . H . . N 0 . . . 1 no no . . . . 28.831 . 48.998 . -9.404 . -3.075 0.144 1.400 25 . 50246 38T H8 H8 H8 H8 . H . . N 0 . . . 1 no no . . . . 27.287 . 48.672 . -7.375 . -4.567 -1.115 -0.194 26 . 50246 38T H9 H9 H9 H9 . H . . N 0 . . . 1 no no . . . . 26.859 . 50.056 . -8.436 . -3.131 -1.956 -0.824 27 . 50246 38T H10 H10 H10 H10 . H . . N 0 . . . 1 no no . . . . 25.038 . 48.616 . -8.060 . -4.197 -3.197 0.917 28 . 50246 38T H11 H11 H11 H11 . H . . N 0 . . . 1 no no . . . . 26.248 . 48.222 . -10.891 . -2.823 0.300 -1.610 29 . 50246 38T H12 H12 H12 H12 . H . . N 0 . . . 1 no no . . . . 26.818 . 50.524 . -10.891 . -4.468 1.537 -0.357 30 . 50246 38T H13 H13 H13 H13 . H . . N 0 . . . 1 no no . . . . 27.706 . 47.317 . -12.596 . -0.649 1.073 -1.519 31 . 50246 38T H14 H14 H14 H14 . H . . N 0 . . . 1 no no . . . . 30.052 . 47.611 . -12.379 . -1.585 3.222 -0.949 32 . 50246 38T stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . DOUB OAC CAM no N 1 . 50246 38T 2 . SING NAI CAM no N 2 . 50246 38T 3 . SING NAI CAL no N 3 . 50246 38T 4 . DOUB OAB CAL no N 4 . 50246 38T 5 . SING CAM NAR no N 5 . 50246 38T 6 . SING O2' C2' no N 6 . 50246 38T 7 . SING C2' C3' no N 7 . 50246 38T 8 . SING C2' C1' no N 8 . 50246 38T 9 . SING CAL CAK no N 9 . 50246 38T 10 . SING O3' C3' no N 10 . 50246 38T 11 . SING NAR C1' no N 11 . 50246 38T 12 . SING NAR CAG no N 12 . 50246 38T 13 . SING C3' C4' no N 13 . 50246 38T 14 . SING C1' O4' no N 14 . 50246 38T 15 . DOUB CAK CAG no N 15 . 50246 38T 16 . SING CAK CAA no N 16 . 50246 38T 17 . SING C4' O4' no N 17 . 50246 38T 18 . SING C4' C5' no N 18 . 50246 38T 19 . SING O5' C5' no N 19 . 50246 38T 20 . SING NAI H1 no N 20 . 50246 38T 21 . SING CAA H2 no N 21 . 50246 38T 22 . SING CAA H3 no N 22 . 50246 38T 23 . SING CAA H4 no N 23 . 50246 38T 24 . SING CAG H5 no N 24 . 50246 38T 25 . SING C1' H6 no N 25 . 50246 38T 26 . SING C4' H7 no N 26 . 50246 38T 27 . SING C5' H8 no N 27 . 50246 38T 28 . SING C5' H9 no N 28 . 50246 38T 29 . SING O5' H10 no N 29 . 50246 38T 30 . SING C3' H11 no N 30 . 50246 38T 31 . SING O3' H12 no N 31 . 50246 38T 32 . SING C2' H13 no N 32 . 50246 38T 33 . SING O2' H14 no N 33 . 50246 38T stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID 50246 _Sample.ID 1 _Sample.Name Na _Sample.Type solution _Sample.Sub_type . _Sample.Details . _Sample.Aggregate_sample_number 1 _Sample.Solvent_system '100% D2O' _Sample.Preparation_date . _Sample.Preparation_expiration_date . _Sample.Polycrystallization_protocol . _Sample.Single_crystal_protocol . _Sample.Crystal_grow_apparatus . _Sample.Crystal_grow_atmosphere . _Sample.Crystal_grow_details . _Sample.Crystal_grow_method . _Sample.Crystal_grow_method_cit_ID . _Sample.Crystal_grow_pH . _Sample.Crystal_grow_pH_range . _Sample.Crystal_grow_pressure . _Sample.Crystal_grow_pressure_esd . _Sample.Crystal_grow_seeding . _Sample.Crystal_grow_seeding_cit_ID . _Sample.Crystal_grow_temp . _Sample.Crystal_grow_temp_details . _Sample.Crystal_grow_temp_esd . _Sample.Crystal_grow_time . _Sample.Oriented_sample_prep_protocol . _Sample.Lyophilization_cryo_protectant . _Sample.Storage_protocol . loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Assembly_ID _Sample_component.Assembly_label _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Product_ID _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_min _Sample_component.Concentration_val_max _Sample_component.Concentration_val_units _Sample_component.Concentration_val_err _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Vendor_product_code _Sample_component.Entry_ID _Sample_component.Sample_ID 1 '[r(UGGUGGT)]4 G-quadruplex' 'natural abundance' . . 1 $entity_1 . . 1 . . mM . . . . 50246 1 2 'sodium phosphate' 'natural abundance' . . . . . . 10 . . mM . . . . 50246 1 3 'sodium chloride' 'natural abundance' . . . . . . 150 . . mM . . . . 50246 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID 50246 _Sample_condition_list.ID 1 _Sample_condition_list.Name Na_25C_D2O _Sample_condition_list.Details . loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_err _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID 'ionic strength' 150 . mM 50246 1 pH 6.8 . pH 50246 1 pressure 1 . atm 50246 1 temperature 298 . K 50246 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID 50246 _Software.ID 1 _Software.Type . _Software.Name TOPSPIN _Software.Version . _Software.DOI . _Software.Details . loop_ _Task.Task _Task.Software_module _Task.Entry_ID _Task.Software_ID collection . 50246 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID 50246 _Software.ID 2 _Software.Type . _Software.Name SPARKY _Software.Version . _Software.DOI . _Software.Details . loop_ _Task.Task _Task.Software_module _Task.Entry_ID _Task.Software_ID 'chemical shift assignment' . 50246 2 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 _NMR_spectrometer.Entry_ID 50246 _NMR_spectrometer.ID 1 _NMR_spectrometer.Name '700 MHz' _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model 'Avance III' _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 700 save_ ############################# # NMR applied experiments # ############################# save_experiment_list_1 _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list_1 _Experiment_list.Entry_ID 50246 _Experiment_list.ID 1 _Experiment_list.Details . loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.NUS_flag _Experiment.Interleaved_flag _Experiment.NMR_spec_expt_ID _Experiment.NMR_spec_expt_label _Experiment.MS_expt_ID _Experiment.MS_expt_label _Experiment.SAXS_expt_ID _Experiment.SAXS_expt_label _Experiment.FRET_expt_ID _Experiment.FRET_expt_label _Experiment.EMR_expt_ID _Experiment.EMR_expt_label _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_volume _Experiment.Sample_volume_units _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.Sample_spinning_rate _Experiment.Sample_angle _Experiment.NMR_tube_type _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.NMR_spectrometer_probe_ID _Experiment.NMR_spectrometer_probe_label _Experiment.NMR_spectral_processing_ID _Experiment.NMR_spectral_processing_label _Experiment.Mass_spectrometer_ID _Experiment.Mass_spectrometer_label _Experiment.Xray_instrument_ID _Experiment.Xray_instrument_label _Experiment.Fluorescence_instrument_ID _Experiment.Fluorescence_instrument_label _Experiment.EMR_instrument_ID _Experiment.EMR_instrument_label _Experiment.Chromatographic_system_ID _Experiment.Chromatographic_system_label _Experiment.Chromatographic_column_ID _Experiment.Chromatographic_column_label _Experiment.Details _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '2D 1H-1H NOESY' no . . . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 50246 1 2 '2D 1H-13C HSQC' no . . . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 50246 1 3 '2D 1H-31H COSY' no . . . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 50246 1 4 '2D DQF-COSY' no . . . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 50246 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference_1 _Chem_shift_reference.Entry_ID 50246 _Chem_shift_reference.ID 1 _Chem_shift_reference.Name TSP _Chem_shift_reference.Details . loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Concentration_val _Chem_shift_ref.Concentration_units _Chem_shift_ref.Solvent _Chem_shift_ref.Rank _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.External_ref_loc _Chem_shift_ref.External_ref_sample_geometry _Chem_shift_ref.External_ref_axis _Chem_shift_ref.Ref_correction_type _Chem_shift_ref.Correction_val _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 TSP 'methyl protons' . . . . ppm 0.00 internal direct 1 . . . . . 50246 1 P 31 TSP 'methyl protons' . . . . ppm 0.00 internal indirect . . . . . . 50246 1 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 _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts_1 _Assigned_chem_shift_list.Entry_ID 50246 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Name 'non-exchangeable protons and 31P' _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference_1 _Assigned_chem_shift_list.Chem_shift_1H_err . _Assigned_chem_shift_list.Chem_shift_13C_err . _Assigned_chem_shift_list.Chem_shift_15N_err . _Assigned_chem_shift_list.Chem_shift_31P_err . _Assigned_chem_shift_list.Chem_shift_2H_err . _Assigned_chem_shift_list.Chem_shift_19F_err . _Assigned_chem_shift_list.Error_derivation_method . _Assigned_chem_shift_list.Details 'The protons of the 5-methyl group are marked as H7 in the CS file.' _Assigned_chem_shift_list.Text_data_format . _Assigned_chem_shift_list.Text_data . loop_ _Chem_shift_experiment.Experiment_ID _Chem_shift_experiment.Experiment_name _Chem_shift_experiment.Sample_ID _Chem_shift_experiment.Sample_label _Chem_shift_experiment.Sample_state _Chem_shift_experiment.Entry_ID _Chem_shift_experiment.Assigned_chem_shift_list_ID 1 '2D 1H-1H NOESY' . . . 50246 1 2 '2D 1H-13C HSQC' . . . 50246 1 3 '2D 1H-31H COSY' . . . 50246 1 4 '2D DQF-COSY' . . . 50246 1 stop_ loop_ _Chem_shift_software.Software_ID _Chem_shift_software.Software_label _Chem_shift_software.Method_ID _Chem_shift_software.Method_label _Chem_shift_software.Entry_ID _Chem_shift_software.Assigned_chem_shift_list_ID 2 $software_2 . . 50246 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Assembly_atom_ID _Atom_chem_shift.Entity_assembly_ID _Atom_chem_shift.Entity_assembly_asym_ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Seq_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Val_err _Atom_chem_shift.Assign_fig_of_merit _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Ambiguity_set_ID _Atom_chem_shift.Occupancy _Atom_chem_shift.Resonance_ID _Atom_chem_shift.Auth_entity_assembly_ID _Atom_chem_shift.Auth_asym_ID _Atom_chem_shift.Auth_seq_ID _Atom_chem_shift.Auth_comp_ID _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Details _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 . 1 . 1 1 1 U H1' H 1 5.335 0.01 . 1 . . . . . 1 U H1' . 50246 1 2 . 1 . 1 1 1 U H2' H 1 3.843 0.01 . 1 . . . . . 1 U H2' . 50246 1 3 . 1 . 1 1 1 U H3' H 1 4.553 0.01 . 1 . . . . . 1 U H3' . 50246 1 4 . 1 . 1 1 1 U H4' H 1 4.315 0.01 . 1 . . . . . 1 U H4' . 50246 1 5 . 1 . 1 1 1 U H5 H 1 5.717 0.01 . 1 . . . . . 1 U H5 . 50246 1 6 . 1 . 1 1 1 U H5' H 1 4.045 0.01 . 2 . . . . . 1 U H5' . 50246 1 7 . 1 . 1 1 1 U H5'' H 1 4.216 0.01 . 2 . . . . . 1 U H5'' . 50246 1 8 . 1 . 1 1 1 U H6 H 1 7.958 0.01 . 1 . . . . . 1 U H6 . 50246 1 9 . 1 . 1 1 1 U P P 31 -0.947 0.05 . 1 . . . . . 1 U P . 50246 1 10 . 1 . 1 2 2 G H1' H 1 5.898 0.01 . 1 . . . . . 2 G H1' . 50246 1 11 . 1 . 1 2 2 G H2' H 1 5.066 0.01 . 1 . . . . . 2 G H2' . 50246 1 12 . 1 . 1 2 2 G H3' H 1 4.934 0.01 . 1 . . . . . 2 G H3' . 50246 1 13 . 1 . 1 2 2 G H4' H 1 4.610 0.01 . 1 . . . . . 2 G H4' . 50246 1 14 . 1 . 1 2 2 G H5' H 1 4.165 0.01 . 2 . . . . . 2 G H5' . 50246 1 15 . 1 . 1 2 2 G H5'' H 1 4.374 0.01 . 2 . . . . . 2 G H5'' . 50246 1 16 . 1 . 1 2 2 G H8 H 1 8.304 0.01 . 1 . . . . . 2 G H8 . 50246 1 17 . 1 . 1 2 2 G P P 31 -5.007 0.05 . 1 . . . . . 2 G P . 50246 1 18 . 1 . 1 3 3 G H1' H 1 6.247 0.01 . 1 . . . . . 3 G H1' . 50246 1 19 . 1 . 1 3 3 G H2' H 1 4.862 0.01 . 1 . . . . . 3 G H2' . 50246 1 20 . 1 . 1 3 3 G H3' H 1 4.368 0.01 . 1 . . . . . 3 G H3' . 50246 1 21 . 1 . 1 3 3 G H4' H 1 4.728 0.01 . 1 . . . . . 3 G H4' . 50246 1 22 . 1 . 1 3 3 G H5' H 1 4.372 0.01 . 2 . . . . . 3 G H5' . 50246 1 23 . 1 . 1 3 3 G H5'' H 1 4.592 0.01 . 2 . . . . . 3 G H5'' . 50246 1 24 . 1 . 1 3 3 G H8 H 1 8.156 0.01 . 1 . . . . . 3 G H8 . 50246 1 25 . 1 . 1 3 3 G P P 31 -2.050 0.05 . 1 . . . . . 3 G P . 50246 1 26 . 1 . 1 4 4 U H1' H 1 5.428 0.01 . 1 . . . . . 4 U H1' . 50246 1 27 . 1 . 1 4 4 U H2' H 1 4.254 0.01 . 1 . . . . . 4 U H2' . 50246 1 28 . 1 . 1 4 4 U H3' H 1 4.399 0.01 . 1 . . . . . 4 U H3' . 50246 1 29 . 1 . 1 4 4 U H4' H 1 4.527 0.01 . 1 . . . . . 4 U H4' . 50246 1 30 . 1 . 1 4 4 U H5 H 1 4.623 0.01 . 1 . . . . . 4 U H5 . 50246 1 31 . 1 . 1 4 4 U H6 H 1 7.330 0.01 . 1 . . . . . 4 U H6 . 50246 1 32 . 1 . 1 4 4 U P P 31 -2.969 0.05 . 1 . . . . . 4 U P . 50246 1 33 . 1 . 1 5 5 G H1' H 1 5.858 0.01 . 1 . . . . . 5 G H1' . 50246 1 34 . 1 . 1 5 5 G H2' H 1 4.324 0.01 . 1 . . . . . 5 G H2' . 50246 1 35 . 1 . 1 5 5 G H3' H 1 4.976 0.01 . 1 . . . . . 5 G H3' . 50246 1 36 . 1 . 1 5 5 G H4' H 1 4.514 0.01 . 1 . . . . . 5 G H4' . 50246 1 37 . 1 . 1 5 5 G H5' H 1 4.199 0.01 . 2 . . . . . 5 G H5' . 50246 1 38 . 1 . 1 5 5 G H5'' H 1 4.709 0.01 . 2 . . . . . 5 G H5'' . 50246 1 39 . 1 . 1 5 5 G H8 H 1 8.427 0.01 . 1 . . . . . 5 G H8 . 50246 1 40 . 1 . 1 5 5 G P P 31 -5.074 0.05 . 1 . . . . . 5 G P . 50246 1 41 . 1 . 1 6 6 G H1' H 1 6.172 0.01 . 1 . . . . . 6 G H1' . 50246 1 42 . 1 . 1 6 6 G H2' H 1 4.369 0.01 . 1 . . . . . 6 G H2' . 50246 1 43 . 1 . 1 6 6 G H3' H 1 4.747 0.01 . 1 . . . . . 6 G H3' . 50246 1 44 . 1 . 1 6 6 G H4' H 1 4.481 0.01 . 1 . . . . . 6 G H4' . 50246 1 45 . 1 . 1 6 6 G H5' H 1 4.151 0.01 . 2 . . . . . 6 G H5' . 50246 1 46 . 1 . 1 6 6 G H5'' H 1 4.664 0.01 . 2 . . . . . 6 G H5'' . 50246 1 47 . 1 . 1 6 6 G H8 H 1 7.724 0.01 . 1 . . . . . 6 G H8 . 50246 1 48 . 1 . 1 6 6 G P P 31 -4.116 0.05 . 1 . . . . . 6 G P . 50246 1 49 . 1 . 1 7 7 38T H1' H 1 5.728 0.01 . 1 . . . . . 7 T H1' . 50246 1 50 . 1 . 1 7 7 38T H2' H 1 4.043 0.01 . 1 . . . . . 7 T H2' . 50246 1 51 . 1 . 1 7 7 38T H3' H 1 4.225 0.01 . 1 . . . . . 7 T H3' . 50246 1 52 . 1 . 1 7 7 38T H4' H 1 4.177 0.01 . 1 . . . . . 7 T H4' . 50246 1 53 . 1 . 1 7 7 38T H5' H 1 4.058 0.01 . 2 . . . . . 7 T H5' . 50246 1 54 . 1 . 1 7 7 38T H5'' H 1 4.240 0.01 . 2 . . . . . 7 T H5'' . 50246 1 55 . 1 . 1 7 7 38T H6 H 1 7.466 0.01 . 1 . . . . . 7 T H6 . 50246 1 56 . 1 . 1 7 7 38T H7 H 1 1.578 0.01 . 1 . . . . . 7 T H7 . 50246 1 57 . 1 . 1 7 7 38T P P 31 -3.799 0.05 . 1 . . . . . 7 T P . 50246 1 stop_ save_