data_34118 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID 34118 _Entry.Title ; An i-motif containing the neutral cytidine protonated analogue pseudoisocytidine ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2017-03-24 _Entry.Accession_date 2017-03-24 _Entry.Last_release_date 2017-06-07 _Entry.Original_release_date 2017-06-07 _Entry.Origination author _Entry.NMR_STAR_version 3.1.2.6 _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype SOLUTION _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 B. Mir B. . . . 34118 2 X. Soles X. . . . 34118 3 C. Gonzalez C. . . . 34118 4 N. Escaja N. . . . 34118 stop_ loop_ _Struct_keywords.Keywords _Struct_keywords.Text _Struct_keywords.Entry_ID DNA . 34118 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 34118 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '1H chemical shifts' 75 34118 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 1 . . 2017-06-22 . original BMRB . 34118 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID PDB 5NIP 'BMRB Entry Tracking System' 34118 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID 34118 _Citation.ID 1 _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI 10.1038/s41598-017-02723-y _Citation.PubMed_ID 28584239 _Citation.Full_citation . _Citation.Title ; The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures. ; _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Sci. Rep.' _Citation.Journal_name_full . _Citation.Journal_volume 7 _Citation.Journal_issue . _Citation.Journal_ASTM . _Citation.Journal_ISSN 2045-2322 _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 2772 _Citation.Page_last 2772 _Citation.Year 2017 _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 B. Mir B. . . . 34118 1 2 X. Soles X. . . . 34118 1 3 C. Gonzalez C. . . . 34118 1 4 N. Escaja N. . . . 34118 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID 34118 _Assembly.ID 1 _Assembly.Name "DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3')" _Assembly.BMRB_code . _Assembly.Number_of_components . _Assembly.Organic_ligands . _Assembly.Metal_ions . _Assembly.Non_standard_bonds . _Assembly.Ambiguous_conformational_states . _Assembly.Ambiguous_chem_comp_sites . _Assembly.Molecules_in_chemical_exchange . _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 'entity_1, 1' 1 $entity_1 A A yes . . . . . . 34118 1 2 'entity_1, 2' 1 $entity_1 B B yes . . . . . . 34118 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID 34118 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name entity_1 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID A,B _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; TCCGTTTCXGT ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states . _Entity.Ambiguous_chem_comp_sites . _Entity.Nstd_monomer yes _Entity.Nstd_chirality . _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 11 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method syn _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight 3275.146 _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details . _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 . DT . 34118 1 2 . DC . 34118 1 3 . DC . 34118 1 4 . DG . 34118 1 5 . DT . 34118 1 6 . DT . 34118 1 7 . DT . 34118 1 8 . DC . 34118 1 9 . 8YN . 34118 1 10 . DG . 34118 1 11 . DT . 34118 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 . DT 1 1 34118 1 . DC 2 2 34118 1 . DC 3 3 34118 1 . DG 4 4 34118 1 . DT 5 5 34118 1 . DT 6 6 34118 1 . DT 7 7 34118 1 . DC 8 8 34118 1 . 8YN 9 9 34118 1 . DG 10 10 34118 1 . DT 11 11 34118 1 stop_ save_ #################### # Natural source # #################### save_natural_source _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source _Entity_natural_src_list.Entry_ID 34118 _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 . 32630 'no natural source' . 'synthetic construct' . . . . . . . . . . . . . . . . . . . . 34118 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source _Entity_experimental_src_list.Entry_ID 34118 _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' . . . . . . . . . . . . . . . . 34118 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_8YN _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_8YN _Chem_comp.Entry_ID 34118 _Chem_comp.ID 8YN _Chem_comp.Provenance PDB _Chem_comp.Name pseudopisocytidine _Chem_comp.Type NON-POLYMER _Chem_comp.BMRB_code 8YN _Chem_comp.PDB_code 8YN _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2017-03-27 _Chem_comp.Modified_date 2017-03-27 _Chem_comp.Release_status HOLD _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code . _Chem_comp.Three_letter_code 8YN _Chem_comp.Number_atoms_all 33 _Chem_comp.Number_atoms_nh 19 _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code InChI=1S/C9H14N3O6P/c10-9-11-2-4(8(14)12-9)6-1-5(13)7(18-6)3-17-19(15)16/h2,5-7,13,15-16H,1,3H2,(H3,10,11,12,14)/t5-,6+,7+/m0/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 'C9 H14 N3 O6 P' _Chem_comp.Formula_weight 291.198 _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 5NIP _Chem_comp.Processing_site EBI _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 BAMUBRWKFUNRCR-RRKCRQDMSA-N InChIKey InChI 1.03 34118 8YN C1C(C(OC1C2=CN=C(NC2=O)N)COP(O)O)O SMILES 'OpenEye OEToolkits' 2.0.6 34118 8YN C1[C@@H]([C@H](O[C@H]1C2=CN=C(NC2=O)N)COP(O)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.6 34118 8YN InChI=1S/C9H14N3O6P/c10-9-11-2-4(8(14)12-9)6-1-5(13)7(18-6)3-17-19(15)16/h2,5-7,13,15-16H,1,3H2,(H3,10,11,12,14)/t5-,6+,7+/m0/s1 InChI InChI 1.03 34118 8YN NC1=NC=C([C@H]2C[C@H](O)[C@@H](COP(O)O)O2)C(=O)N1 SMILES_CANONICAL CACTVS 3.385 34118 8YN NC1=NC=C([CH]2C[CH](O)[CH](COP(O)O)O2)C(=O)N1 SMILES CACTVS 3.385 34118 8YN 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 '[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-pyrimidin-5-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.6 34118 8YN 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 P P P P1 . P . . N 0 . . . 1 no no . . . . 31.418 . 22.521 . 28.382 . 4.204 1.094 -0.119 1 . 34118 8YN C1 C1 C1 C1 . C . . N 0 . . . 1 no no . . . . 26.982 . 25.877 . 25.889 . -2.215 -0.369 0.392 2 . 34118 8YN C2 C2 C2 C2 . C . . N 0 . . . 1 no no . . . . 26.189 . 25.590 . 24.745 . -2.234 0.566 -0.658 3 . 34118 8YN C4 C4 C4 C3 . C . . N 0 . . . 1 no no . . . . 24.260 . 25.356 . 26.071 . -4.319 1.305 0.120 4 . 34118 8YN C6 C6 C6 C4 . C . . N 0 . . . 1 no no . . . . 26.329 . 25.876 . 27.153 . -3.269 -0.410 1.257 5 . 34118 8YN O1P O1P O1P O1 . O . . N 0 . . . 1 no no . . . . 32.304 . 22.927 . 27.264 . 3.426 2.402 -0.644 6 . 34118 8YN O2P O2P O2P O2 . O . . N 0 . . . 1 no no . . . . 32.011 . 22.115 . 29.668 . 4.803 1.602 1.286 7 . 34118 8YN O5' O5' O5' O3 . O . . N 0 . . . 1 no no . . . . 30.349 . 23.695 . 28.659 . 2.989 0.150 0.356 8 . 34118 8YN C5' C5' C5' C5 . C . . N 0 . . . 1 no no . . . . 30.607 . 25.063 . 28.395 . 2.339 -0.779 -0.513 9 . 34118 8YN C4' C4' C4' C6 . C . . R 0 . . . 1 no no . . . . 30.404 . 25.447 . 26.921 . 1.235 -1.509 0.255 10 . 34118 8YN O4' O4' O4' O4 . O . . N 0 . . . 1 no no . . . . 29.136 . 25.013 . 26.424 . 0.192 -0.586 0.609 11 . 34118 8YN C1' C1' C1' C7 . C . . R 0 . . . 1 no no . . . . 28.478 . 26.102 . 25.796 . -1.053 -1.315 0.555 12 . 34118 8YN O2 O2 O2 O5 . O . . N 0 . . . 1 no no . . . . 26.719 . 25.581 . 23.633 . -1.308 0.630 -1.450 13 . 34118 8YN N3 N3 N3 N1 . N . . N 0 . . . 1 no no . . . . 24.855 . 25.308 . 24.866 . -3.296 1.391 -0.773 14 . 34118 8YN N4 N4 N4 N2 . N . . N 0 . . . 1 no no . . . . 22.966 . 25.176 . 26.113 . -5.392 2.145 -0.003 15 . 34118 8YN N5 N5 N5 N3 . N . . N 0 . . . 1 no no . . . . 24.953 . 25.643 . 27.217 . -4.294 0.425 1.102 16 . 34118 8YN C2' C2' C2' C8 . C . . N 0 . . . 1 no no . . . . 28.975 . 27.282 . 26.628 . -0.895 -2.208 -0.702 17 . 34118 8YN C3' C3' C3' C9 . C . . S 0 . . . 1 no no . . . . 30.457 . 26.970 . 26.756 . 0.606 -2.595 -0.639 18 . 34118 8YN O3' O3' O3' O6 . O . . N 0 . . . 1 no no . . . . 31.178 . 27.325 . 25.590 . 0.764 -3.888 -0.049 19 . 34118 8YN H6 H6 H6 H1 . H . . N 0 . . . 1 no no . . . . 26.893 . 26.054 . 28.057 . -3.273 -1.122 2.069 20 . 34118 8YN H1 H1 H1 H2 . H . . N 0 . . . 1 no no . . . . 32.937 . 22.239 . 27.095 . 4.008 3.098 -0.978 21 . 34118 8YN H2 H2 H2 H3 . H . . N 0 . . . 1 no no . . . . 31.320 . 21.886 . 30.278 . 5.561 2.196 1.198 22 . 34118 8YN 2H5' 2H5' 2H5' H4 . H . . N 0 . . . 0 no no . . . . 31.649 . 25.282 . 28.672 . 1.901 -0.243 -1.356 23 . 34118 8YN 1H5' 1H5' 1H5' H5 . H . . N 0 . . . 0 no no . . . . 29.928 . 25.671 . 29.011 . 3.066 -1.503 -0.881 24 . 34118 8YN H4' H4' H4' H6 . H . . N 0 . . . 1 no no . . . . 31.215 . 25.000 . 26.327 . 1.649 -1.964 1.155 25 . 34118 8YN H1' H1' H1' H7 . H . . N 0 . . . 1 no no . . . . 28.785 . 26.218 . 24.746 . -1.179 -1.925 1.449 26 . 34118 8YN H3 H3 H3 H8 . H . . N 0 . . . 1 no no . . . . 24.321 . 25.066 . 24.056 . -3.329 2.044 -1.490 27 . 34118 8YN 1H4 1H4 1H4 H9 . H . . N 0 . . . 0 no no . . . . 22.479 . 25.248 . 26.984 . -6.126 2.090 0.629 28 . 34118 8YN 2H4 2H4 2H4 H10 . H . . N 0 . . . 0 no no . . . . 22.463 . 24.967 . 25.275 . -5.419 2.795 -0.723 29 . 34118 8YN 1H2' 1H2' 1H2' H11 . H . . N 0 . . . 0 no no . . . . 28.810 . 28.237 . 26.107 . -1.527 -3.093 -0.632 30 . 34118 8YN 2H2' 2H2' 2H2' H12 . H . . N 0 . . . 0 no no . . . . 28.486 . 27.312 . 27.613 . -1.115 -1.645 -1.609 31 . 34118 8YN H3' H3' H3' H13 . H . . N 0 . . . 1 no no . . . . 30.874 . 27.439 . 27.660 . 1.048 -2.573 -1.635 32 . 34118 8YN H4 H4 H4 H14 . H . . N 0 . . . 1 no no . . . . 32.097 . 27.115 . 25.709 . 0.334 -4.600 -0.542 33 . 34118 8YN 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 O2 C2 no N 1 . 34118 8YN 2 . SING C2 N3 no N 2 . 34118 8YN 3 . SING C2 C1 no N 3 . 34118 8YN 4 . SING N3 C4 no N 4 . 34118 8YN 5 . SING O3' C3' no N 5 . 34118 8YN 6 . SING C1' C1 no N 6 . 34118 8YN 7 . SING C1' O4' no N 7 . 34118 8YN 8 . SING C1' C2' no N 8 . 34118 8YN 9 . DOUB C1 C6 no N 9 . 34118 8YN 10 . SING C4 N4 no N 10 . 34118 8YN 11 . DOUB C4 N5 no N 11 . 34118 8YN 12 . SING O4' C4' no N 12 . 34118 8YN 13 . SING C2' C3' no N 13 . 34118 8YN 14 . SING C3' C4' no N 14 . 34118 8YN 15 . SING C4' C5' no N 15 . 34118 8YN 16 . SING C6 N5 no N 16 . 34118 8YN 17 . SING O1P P no N 17 . 34118 8YN 18 . SING P O5' no N 18 . 34118 8YN 19 . SING P O2P no N 19 . 34118 8YN 20 . SING C5' O5' no N 20 . 34118 8YN 21 . SING C6 H6 no N 21 . 34118 8YN 22 . SING O1P H1 no N 22 . 34118 8YN 23 . SING O2P H2 no N 23 . 34118 8YN 24 . SING C5' 2H5' no N 24 . 34118 8YN 25 . SING C5' 1H5' no N 25 . 34118 8YN 26 . SING C4' H4' no N 26 . 34118 8YN 27 . SING C1' H1' no N 27 . 34118 8YN 28 . SING N3 H3 no N 28 . 34118 8YN 29 . SING N4 1H4 no N 29 . 34118 8YN 30 . SING N4 2H4 no N 30 . 34118 8YN 31 . SING C2' 1H2' no N 31 . 34118 8YN 32 . SING C2' 2H2' no N 32 . 34118 8YN 33 . SING C3' H3' no N 33 . 34118 8YN 34 . SING O3' H4 no N 34 . 34118 8YN stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID 34118 _Sample.ID 1 _Sample.Type solution _Sample.Sub_type . _Sample.Details "0.8 mM DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3'), 90% H2O/10% D2O" _Sample.Aggregate_sample_number . _Sample.Solvent_system '90% H2O/10% 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 "DNA (5'-D(*TP*(DCP)P*CP*GP*TP*TP*TP*CP*(PSC)P*GP*T)-3')" 'natural abundance' 1 $assembly 1 $entity_1 . . 0.8 . . mM . . . . 34118 1 2 NaCl 'natural abundance' . . . . . . 100 . . mM . . . . 34118 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 34118 _Sample_condition_list.ID 1 _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' 100 . mM 34118 1 pH 7 . pH 34118 1 pressure 1 . atm 34118 1 temperature 278 . K 34118 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID 34118 _Software.ID 1 _Software.Name AMBER _Software.Version . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN' . . 34118 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID refinement 34118 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID 34118 _Software.ID 2 _Software.Name DYANA _Software.Version . _Software.Details . loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'structure solution' 34118 2 stop_ save_ save_software_3 _Software.Sf_category software _Software.Sf_framecode software_3 _Software.Entry_ID 34118 _Software.ID 3 _Software.Name SPARKY _Software.Version . _Software.Details . loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'structure solution' 34118 3 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 34118 _NMR_spectrometer.ID 1 _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model Avance _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 600 save_ save_NMR_spectrometer_list _NMR_spectrometer_list.Sf_category NMR_spectrometer_list _NMR_spectrometer_list.Sf_framecode NMR_spectrometer_list _NMR_spectrometer_list.Entry_ID 34118 _NMR_spectrometer_list.ID 1 loop_ _NMR_spectrometer_view.ID _NMR_spectrometer_view.Name _NMR_spectrometer_view.Manufacturer _NMR_spectrometer_view.Model _NMR_spectrometer_view.Serial_number _NMR_spectrometer_view.Field_strength _NMR_spectrometer_view.Details _NMR_spectrometer_view.Citation_ID _NMR_spectrometer_view.Citation_label _NMR_spectrometer_view.Entry_ID _NMR_spectrometer_view.NMR_spectrometer_list_ID 1 NMR_spectrometer_1 Bruker Avance . 600 . . . 34118 1 stop_ save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID 34118 _Experiment_list.ID 1 _Experiment_list.Details . loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_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.Entry_ID _Experiment.Experiment_list_ID 1 '2D 1H-1H NOESY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 34118 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 34118 _Chem_shift_reference.ID 1 _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 DSS 'methyl protons' . . . . ppm 0.0 internal direct 1.0 . . . . . 34118 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 34118 _Assigned_chem_shift_list.ID 1 _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 . _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' . . . 34118 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Assembly_atom_ID _Atom_chem_shift.Entity_assembly_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.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 DT H6 H 1 7.62 0.00 . 1 . . . A 1 DT H6 . 34118 1 2 . 1 1 1 1 DT H71 H 1 1.79 0.00 . 1 . . . A 1 DT H71 . 34118 1 3 . 1 1 1 1 DT H72 H 1 1.79 0.00 . 1 . . . A 1 DT H72 . 34118 1 4 . 1 1 1 1 DT H73 H 1 1.79 0.00 . 1 . . . A 1 DT H73 . 34118 1 5 . 1 1 2 2 DC H1' H 1 6.32 0.00 . 1 . . . A 2 DC H1' . 34118 1 6 . 1 1 2 2 DC H2' H 1 2.06 0.00 . . . . . A 2 DC H2' . 34118 1 7 . 1 1 2 2 DC H2'' H 1 2.45 0.00 . . . . . A 2 DC H2'' . 34118 1 8 . 1 1 2 2 DC H3' H 1 4.71 0.00 . 1 . . . A 2 DC H3' . 34118 1 9 . 1 1 2 2 DC H5 H 1 5.83 0.00 . 1 . . . A 2 DC H5 . 34118 1 10 . 1 1 2 2 DC H6 H 1 7.84 0.00 . 1 . . . A 2 DC H6 . 34118 1 11 . 1 1 2 2 DC H41 H 1 8.09 0.01 . . . . . A 2 DC H41 . 34118 1 12 . 1 1 2 2 DC H42 H 1 9.61 0.00 . . . . . A 2 DC H42 . 34118 1 13 . 1 1 3 3 DC H1' H 1 5.91 0.00 . 1 . . . A 3 DC H1' . 34118 1 14 . 1 1 3 3 DC H2' H 1 1.43 0.00 . . . . . A 3 DC H2' . 34118 1 15 . 1 1 3 3 DC H2'' H 1 1.96 0.01 . . . . . A 3 DC H2'' . 34118 1 16 . 1 1 3 3 DC H3' H 1 4.53 0.00 . 1 . . . A 3 DC H3' . 34118 1 17 . 1 1 3 3 DC H5 H 1 5.54 0.02 . 1 . . . A 3 DC H5 . 34118 1 18 . 1 1 3 3 DC H6 H 1 7.83 0.01 . 1 . . . A 3 DC H6 . 34118 1 19 . 1 1 3 3 DC H41 H 1 7.01 0.01 . . . . . A 3 DC H41 . 34118 1 20 . 1 1 3 3 DC H42 H 1 8.83 0.02 . . . . . A 3 DC H42 . 34118 1 21 . 1 1 4 4 DG H1 H 1 10.39 0.00 . 1 . . . A 4 DG H1 . 34118 1 22 . 1 1 4 4 DG H1' H 1 5.77 0.01 . 1 . . . A 4 DG H1' . 34118 1 23 . 1 1 4 4 DG H2' H 1 2.72 0.00 . . . . . A 4 DG H2' . 34118 1 24 . 1 1 4 4 DG H2'' H 1 2.38 0.00 . . . . . A 4 DG H2'' . 34118 1 25 . 1 1 4 4 DG H8 H 1 8.03 0.01 . 1 . . . A 4 DG H8 . 34118 1 26 . 1 1 4 4 DG H21 H 1 6.00 0.00 . . . . . A 4 DG H21 . 34118 1 27 . 1 1 4 4 DG H22 H 1 8.35 0.00 . . . . . A 4 DG H22 . 34118 1 28 . 1 1 5 5 DT H1' H 1 5.84 0.00 . 1 . . . A 5 DT H1' . 34118 1 29 . 1 1 5 5 DT H2' H 1 2.00 0.00 . . . . . A 5 DT H2' . 34118 1 30 . 1 1 5 5 DT H2'' H 1 2.00 0.00 . . . . . A 5 DT H2'' . 34118 1 31 . 1 1 5 5 DT H3' H 1 4.34 0.00 . 1 . . . A 5 DT H3' . 34118 1 32 . 1 1 5 5 DT H6 H 1 7.50 0.00 . 1 . . . A 5 DT H6 . 34118 1 33 . 1 1 5 5 DT H71 H 1 1.59 0.00 . 1 . . . A 5 DT H71 . 34118 1 34 . 1 1 5 5 DT H72 H 1 1.59 0.00 . 1 . . . A 5 DT H72 . 34118 1 35 . 1 1 5 5 DT H73 H 1 1.59 0.00 . 1 . . . A 5 DT H73 . 34118 1 36 . 1 1 6 6 DT H1' H 1 5.95 0.00 . 1 . . . A 6 DT H1' . 34118 1 37 . 1 1 6 6 DT H2' H 1 2.05 0.00 . . . . . A 6 DT H2' . 34118 1 38 . 1 1 6 6 DT H2'' H 1 2.34 0.00 . . . . . A 6 DT H2'' . 34118 1 39 . 1 1 6 6 DT H3' H 1 4.57 0.00 . 1 . . . A 6 DT H3' . 34118 1 40 . 1 1 6 6 DT H6 H 1 7.38 0.00 . 1 . . . A 6 DT H6 . 34118 1 41 . 1 1 6 6 DT H71 H 1 1.61 0.00 . 1 . . . A 6 DT H71 . 34118 1 42 . 1 1 6 6 DT H72 H 1 1.61 0.00 . 1 . . . A 6 DT H72 . 34118 1 43 . 1 1 6 6 DT H73 H 1 1.61 0.00 . 1 . . . A 6 DT H73 . 34118 1 44 . 1 1 7 7 DT H6 H 1 7.62 0.00 . 1 . . . A 7 DT H6 . 34118 1 45 . 1 1 7 7 DT H71 H 1 1.79 0.00 . 1 . . . A 7 DT H71 . 34118 1 46 . 1 1 7 7 DT H72 H 1 1.79 0.00 . 1 . . . A 7 DT H72 . 34118 1 47 . 1 1 7 7 DT H73 H 1 1.79 0.00 . 1 . . . A 7 DT H73 . 34118 1 48 . 1 1 8 8 DC H1' H 1 6.34 0.01 . 1 . . . A 8 DC H1' . 34118 1 49 . 1 1 8 8 DC H2' H 1 1.68 0.01 . . . . . A 8 DC H2' . 34118 1 50 . 1 1 8 8 DC H2'' H 1 2.37 0.01 . . . . . A 8 DC H2'' . 34118 1 51 . 1 1 8 8 DC H5 H 1 5.78 0.00 . 1 . . . A 8 DC H5 . 34118 1 52 . 1 1 8 8 DC H6 H 1 7.66 0.01 . 1 . . . A 8 DC H6 . 34118 1 53 . 1 1 8 8 DC H41 H 1 7.54 0.00 . . . . . A 8 DC H41 . 34118 1 54 . 1 1 8 8 DC H42 H 1 8.93 0.00 . . . . . A 8 DC H42 . 34118 1 55 . 1 1 9 9 8YN H1' H 1 5.90 0.04 . 1 . . . A 9 8YN H1' . 34118 1 56 . 1 1 9 9 8YN H2' H 1 1.41 0.01 . . . . . A 9 8YN H2' . 34118 1 57 . 1 1 9 9 8YN H2'' H 1 1.95 0.00 . . . . . A 9 8YN H2'' . 34118 1 58 . 1 1 9 9 8YN H6 H 1 7.03 0.04 . 1 . . . A 9 8YN H6 . 34118 1 59 . 1 1 9 9 8YN H41 H 1 6.10 0.00 . . . . . A 9 8YN H41 . 34118 1 60 . 1 1 9 9 8YN H42 H 1 8.67 0.06 . . . . . A 9 8YN H42 . 34118 1 61 . 1 1 10 10 DG H1 H 1 9.70 0.00 . 1 . . . A 10 DG H1 . 34118 1 62 . 1 1 10 10 DG H1' H 1 5.70 0.00 . 1 . . . A 10 DG H1' . 34118 1 63 . 1 1 10 10 DG H2' H 1 2.74 0.00 . . . . . A 10 DG H2' . 34118 1 64 . 1 1 10 10 DG H2'' H 1 2.38 0.00 . . . . . A 10 DG H2'' . 34118 1 65 . 1 1 10 10 DG H8 H 1 8.10 0.00 . 1 . . . A 10 DG H8 . 34118 1 66 . 1 1 10 10 DG H21 H 1 6.49 0.00 . . . . . A 10 DG H21 . 34118 1 67 . 1 1 10 10 DG H22 H 1 8.34 0.00 . . . . . A 10 DG H22 . 34118 1 68 . 1 1 11 11 DT H1' H 1 5.84 0.00 . 1 . . . A 11 DT H1' . 34118 1 69 . 1 1 11 11 DT H2' H 1 2.00 0.00 . . . . . A 11 DT H2' . 34118 1 70 . 1 1 11 11 DT H2'' H 1 2.00 0.00 . . . . . A 11 DT H2'' . 34118 1 71 . 1 1 11 11 DT H3' H 1 4.34 0.00 . 1 . . . A 11 DT H3' . 34118 1 72 . 1 1 11 11 DT H6 H 1 7.50 0.00 . 1 . . . A 11 DT H6 . 34118 1 73 . 1 1 11 11 DT H71 H 1 1.59 0.00 . 1 . . . A 11 DT H71 . 34118 1 74 . 1 1 11 11 DT H72 H 1 1.59 0.00 . 1 . . . A 11 DT H72 . 34118 1 75 . 1 1 11 11 DT H73 H 1 1.59 0.00 . 1 . . . A 11 DT H73 . 34118 1 stop_ save_