data_9NAM # _entry.id 9NAM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.410 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9NAM pdb_00009nam 10.2210/pdb9nam/pdb WWPDB D_1000292907 ? ? EMDB EMD-49199 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2026-03-04 ? 2 'EM metadata' 1 0 2026-03-04 ? 3 'Additional map' 1 0 2026-03-04 1 4 'Half map' 1 0 2026-03-04 1 5 'Half map' 1 0 2026-03-04 2 6 Image 1 0 2026-03-04 ? 7 Mask 1 0 2026-03-04 1 8 'Primary map' 1 0 2026-03-04 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 'Additional map' repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 Mask repository 'Initial release' ? ? 8 8 'Primary map' repository 'Initial release' ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9NAM _pdbx_database_status.recvd_initial_deposition_date 2025-02-12 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'RNA scaffold attached to Mango in the absence of ligand' _pdbx_database_related.db_id EMD-49199 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email adrian.ferre@nih.gov _pdbx_contact_author.name_first "Ferre-D'Amare" _pdbx_contact_author.name_last Adrian _pdbx_contact_author.name_mi R _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4549-1619 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Jones, C.P.' 1 0000-0001-7780-5278 ;Ferre-D'Amare, A.R. ; 2 0000-0003-4549-1619 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Symmetric scaffolds enable de novo modelling of RNA by cryoEM' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jones, C.P.' 1 0000-0001-7780-5278 primary ;Ferre-D'Amare, A.R. ; 2 0000-0003-4549-1619 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'RNA (68-MER)' 41611.629 1 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 water nat water 18.015 11 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GGGCCACUGUUUCACUGUUGCGCUACAUCUCCCUACGAAGGAAGGUUUGGUAUGUGGUAUAUUCGAUGGGAGGCCACACG AAAGUGUGGAGUGACCAGUGGCCCCACCCUGAAGGUAAACUUGUAGCGC ; _entity_poly.pdbx_seq_one_letter_code_can ;GGGCCACUGUUUCACUGUUGCGCUACAUCUCCCUACGAAGGAAGGUUUGGUAUGUGGUAUAUUCGAUGGGAGGCCACACG AAAGUGUGGAGUGACCAGUGGCCCCACCCUGAAGGUAAACUUGUAGCGC ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 G n 1 4 C n 1 5 C n 1 6 A n 1 7 C n 1 8 U n 1 9 G n 1 10 U n 1 11 U n 1 12 U n 1 13 C n 1 14 A n 1 15 C n 1 16 U n 1 17 G n 1 18 U n 1 19 U n 1 20 G n 1 21 C n 1 22 G n 1 23 C n 1 24 U n 1 25 A n 1 26 C n 1 27 A n 1 28 U n 1 29 C n 1 30 U n 1 31 C n 1 32 C n 1 33 C n 1 34 U n 1 35 A n 1 36 C n 1 37 G n 1 38 A n 1 39 A n 1 40 G n 1 41 G n 1 42 A n 1 43 A n 1 44 G n 1 45 G n 1 46 U n 1 47 U n 1 48 U n 1 49 G n 1 50 G n 1 51 U n 1 52 A n 1 53 U n 1 54 G n 1 55 U n 1 56 G n 1 57 G n 1 58 U n 1 59 A n 1 60 U n 1 61 A n 1 62 U n 1 63 U n 1 64 C n 1 65 G n 1 66 A n 1 67 U n 1 68 G n 1 69 G n 1 70 G n 1 71 A n 1 72 G n 1 73 G n 1 74 C n 1 75 C n 1 76 A n 1 77 C n 1 78 A n 1 79 C n 1 80 G n 1 81 A n 1 82 A n 1 83 A n 1 84 G n 1 85 U n 1 86 G n 1 87 U n 1 88 G n 1 89 G n 1 90 A n 1 91 G n 1 92 U n 1 93 G n 1 94 A n 1 95 C n 1 96 C n 1 97 A n 1 98 G n 1 99 U n 1 100 G n 1 101 G n 1 102 C n 1 103 C n 1 104 C n 1 105 C n 1 106 A n 1 107 C n 1 108 C n 1 109 C n 1 110 U n 1 111 G n 1 112 A n 1 113 A n 1 114 G n 1 115 G n 1 116 U n 1 117 A n 1 118 A n 1 119 A n 1 120 C n 1 121 U n 1 122 U n 1 123 G n 1 124 U n 1 125 A n 1 126 G n 1 127 C n 1 128 G n 1 129 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 129 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 ? ? ? A . n A 1 2 G 2 2 ? ? ? A . n A 1 3 G 3 3 ? ? ? A . n A 1 4 C 4 4 ? ? ? A . n A 1 5 C 5 5 ? ? ? A . n A 1 6 A 6 6 ? ? ? A . n A 1 7 C 7 7 ? ? ? A . n A 1 8 U 8 8 ? ? ? A . n A 1 9 G 9 9 ? ? ? A . n A 1 10 U 10 10 ? ? ? A . n A 1 11 U 11 11 ? ? ? A . n A 1 12 U 12 12 ? ? ? A . n A 1 13 C 13 13 ? ? ? A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n A 1 18 U 18 18 18 U U A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n A 1 24 U 24 24 24 U U A . n A 1 25 A 25 25 25 A A A . n A 1 26 C 26 26 26 C C A . n A 1 27 A 27 27 27 A A A . n A 1 28 U 28 28 28 U U A . n A 1 29 C 29 29 29 C C A . n A 1 30 U 30 30 30 U U A . n A 1 31 C 31 31 31 C C A . n A 1 32 C 32 32 32 C C A . n A 1 33 C 33 33 33 C C A . n A 1 34 U 34 34 34 U U A . n A 1 35 A 35 35 35 A A A . n A 1 36 C 36 36 36 C C A . n A 1 37 G 37 37 37 G G A . n A 1 38 A 38 38 38 A A A . n A 1 39 A 39 39 ? ? ? A . n A 1 40 G 40 40 ? ? ? A . n A 1 41 G 41 41 ? ? ? A . n A 1 42 A 42 42 ? ? ? A . n A 1 43 A 43 43 ? ? ? A . n A 1 44 G 44 44 ? ? ? A . n A 1 45 G 45 45 ? ? ? A . n A 1 46 U 46 46 ? ? ? A . n A 1 47 U 47 47 ? ? ? A . n A 1 48 U 48 48 ? ? ? A . n A 1 49 G 49 49 ? ? ? A . n A 1 50 G 50 50 ? ? ? A . n A 1 51 U 51 51 ? ? ? A . n A 1 52 A 52 52 ? ? ? A . n A 1 53 U 53 53 ? ? ? A . n A 1 54 G 54 54 ? ? ? A . n A 1 55 U 55 55 ? ? ? A . n A 1 56 G 56 56 ? ? ? A . n A 1 57 G 57 57 ? ? ? A . n A 1 58 U 58 58 ? ? ? A . n A 1 59 A 59 59 ? ? ? A . n A 1 60 U 60 60 ? ? ? A . n A 1 61 A 61 61 ? ? ? A . n A 1 62 U 62 62 ? ? ? A . n A 1 63 U 63 63 63 U U A . n A 1 64 C 64 64 64 C C A . n A 1 65 G 65 65 65 G G A . n A 1 66 A 66 66 66 A A A . n A 1 67 U 67 67 67 U U A . n A 1 68 G 68 68 68 G G A . n A 1 69 G 69 69 69 G G A . n A 1 70 G 70 70 70 G G A . n A 1 71 A 71 71 71 A A A . n A 1 72 G 72 72 72 G G A . n A 1 73 G 73 73 73 G G A . n A 1 74 C 74 74 74 C C A . n A 1 75 C 75 75 75 C C A . n A 1 76 A 76 76 76 A A A . n A 1 77 C 77 77 77 C C A . n A 1 78 A 78 78 78 A A A . n A 1 79 C 79 79 79 C C A . n A 1 80 G 80 80 80 G G A . n A 1 81 A 81 81 81 A A A . n A 1 82 A 82 82 82 A A A . n A 1 83 A 83 83 83 A A A . n A 1 84 G 84 84 84 G G A . n A 1 85 U 85 85 85 U U A . n A 1 86 G 86 86 86 G G A . n A 1 87 U 87 87 87 U U A . n A 1 88 G 88 88 88 G G A . n A 1 89 G 89 89 89 G G A . n A 1 90 A 90 90 90 A A A . n A 1 91 G 91 91 91 G G A . n A 1 92 U 92 92 92 U U A . n A 1 93 G 93 93 ? ? ? A . n A 1 94 A 94 94 ? ? ? A . n A 1 95 C 95 95 ? ? ? A . n A 1 96 C 96 96 ? ? ? A . n A 1 97 A 97 97 ? ? ? A . n A 1 98 G 98 98 ? ? ? A . n A 1 99 U 99 99 ? ? ? A . n A 1 100 G 100 100 ? ? ? A . n A 1 101 G 101 101 ? ? ? A . n A 1 102 C 102 102 ? ? ? A . n A 1 103 C 103 103 ? ? ? A . n A 1 104 C 104 104 ? ? ? A . n A 1 105 C 105 105 ? ? ? A . n A 1 106 A 106 106 ? ? ? A . n A 1 107 C 107 107 ? ? ? A . n A 1 108 C 108 108 ? ? ? A . n A 1 109 C 109 109 ? ? ? A . n A 1 110 U 110 110 ? ? ? A . n A 1 111 G 111 111 ? ? ? A . n A 1 112 A 112 112 ? ? ? A . n A 1 113 A 113 113 ? ? ? A . n A 1 114 G 114 114 ? ? ? A . n A 1 115 G 115 115 ? ? ? A . n A 1 116 U 116 116 ? ? ? A . n A 1 117 A 117 117 117 A A A . n A 1 118 A 118 118 118 A A A . n A 1 119 A 119 119 119 A A A . n A 1 120 C 120 120 120 C C A . n A 1 121 U 121 121 121 U U A . n A 1 122 U 122 122 122 U U A . n A 1 123 G 123 123 123 G G A . n A 1 124 U 124 124 124 U U A . n A 1 125 A 125 125 125 A A A . n A 1 126 G 126 126 126 G G A . n A 1 127 C 127 127 127 C C A . n A 1 128 G 128 128 128 G G A . n A 1 129 C 129 129 129 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 K 1 201 1 K K A . C 3 HOH 1 301 2 HOH HOH A . C 3 HOH 2 302 11 HOH HOH A . C 3 HOH 3 303 4 HOH HOH A . C 3 HOH 4 304 1 HOH HOH A . C 3 HOH 5 305 3 HOH HOH A . C 3 HOH 6 306 5 HOH HOH A . C 3 HOH 7 307 10 HOH HOH A . C 3 HOH 8 308 6 HOH HOH A . C 3 HOH 9 309 8 HOH HOH A . C 3 HOH 10 310 9 HOH HOH A . C 3 HOH 11 311 7 HOH HOH A . # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9NAM _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9NAM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9NAM _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9NAM _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.87 _refine.ls_d_res_low ? _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.006 ? 1620 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 1.012 ? 2518 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 17.816 ? 807 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.051 ? 340 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.005 ? 68 ? f_plane_restr ? ? # _struct.entry_id 9NAM _struct.title 'RNA scaffold attached to Mango in the absence of ligand' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9NAM _struct_keywords.text 'viral RNA, scaffold, engineering, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9NAM _struct_ref.pdbx_db_accession 9NAM _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9NAM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 129 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 9NAM _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 129 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 129 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? B K . K ? ? ? 1_555 C HOH . O ? ? A K 201 A HOH 311 1_555 ? ? ? ? ? ? ? 3.291 ? ? hydrog1 hydrog ? ? A A 14 N1 ? ? ? 1_555 A U 92 N3 ? ? A A 14 A U 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 14 N6 ? ? ? 1_555 A U 92 O4 ? ? A A 14 A U 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 91 N1 ? ? A C 15 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 91 O6 ? ? A C 15 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 91 N2 ? ? A C 15 A G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 90 N1 ? ? A U 16 A A 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 90 N6 ? ? A U 16 A A 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 17 N1 ? ? ? 1_555 A C 120 N3 ? ? A G 17 A C 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 17 N2 ? ? ? 1_555 A C 120 O2 ? ? A G 17 A C 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 17 O6 ? ? ? 1_555 A C 120 N4 ? ? A G 17 A C 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 18 N3 ? ? ? 1_555 A A 119 N1 ? ? A U 18 A A 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 18 O4 ? ? ? 1_555 A A 119 N6 ? ? A U 18 A A 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 19 N3 ? ? ? 1_555 A A 118 N1 ? ? A U 19 A A 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 19 O4 ? ? ? 1_555 A A 118 N6 ? ? A U 19 A A 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 20 N1 ? ? ? 1_555 A C 129 N3 ? ? A G 20 A C 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 20 N2 ? ? ? 1_555 A C 129 O2 ? ? A G 20 A C 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 20 O6 ? ? ? 1_555 A C 129 N4 ? ? A G 20 A C 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 21 N3 ? ? ? 1_555 A G 128 N1 ? ? A C 21 A G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 21 N4 ? ? ? 1_555 A G 128 O6 ? ? A C 21 A G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 21 O2 ? ? ? 1_555 A G 128 N2 ? ? A C 21 A G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 22 N1 ? ? ? 1_555 A C 127 N3 ? ? A G 22 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 22 N2 ? ? ? 1_555 A C 127 O2 ? ? A G 22 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 22 O6 ? ? ? 1_555 A C 127 N4 ? ? A G 22 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 23 N3 ? ? ? 1_555 A G 126 N1 ? ? A C 23 A G 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 23 N4 ? ? ? 1_555 A G 126 O6 ? ? A C 23 A G 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 23 O2 ? ? ? 1_555 A G 126 N2 ? ? A C 23 A G 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 24 N3 ? ? ? 1_555 A A 125 N1 ? ? A U 24 A A 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 24 O4 ? ? ? 1_555 A A 125 N6 ? ? A U 24 A A 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 25 N1 ? ? ? 1_555 A U 124 N3 ? ? A A 25 A U 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 25 N6 ? ? ? 1_555 A U 124 O4 ? ? A A 25 A U 124 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 26 N3 ? ? ? 1_555 A G 123 N1 ? ? A C 26 A G 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 26 N4 ? ? ? 1_555 A G 123 O6 ? ? A C 26 A G 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 26 O2 ? ? ? 1_555 A G 123 N2 ? ? A C 26 A G 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A A 27 N1 ? ? ? 1_555 A U 122 N3 ? ? A A 27 A U 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 27 N6 ? ? ? 1_555 A U 122 O4 ? ? A A 27 A U 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 28 N3 ? ? ? 1_555 A U 121 O4 ? ? A U 28 A U 121 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog37 hydrog ? ? A U 28 O2 ? ? ? 1_555 A U 121 N3 ? ? A U 28 A U 121 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog38 hydrog ? ? A C 29 N3 ? ? ? 1_555 A G 72 N1 ? ? A C 29 A G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 29 N4 ? ? ? 1_555 A G 72 O6 ? ? A C 29 A G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 29 O2 ? ? ? 1_555 A G 72 N2 ? ? A C 29 A G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 30 N3 ? ? ? 1_555 A A 71 N1 ? ? A U 30 A A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 30 O4 ? ? ? 1_555 A A 71 N6 ? ? A U 30 A A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 31 N3 ? ? ? 1_555 A G 70 N1 ? ? A C 31 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 31 N4 ? ? ? 1_555 A G 70 O6 ? ? A C 31 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 31 O2 ? ? ? 1_555 A G 70 N2 ? ? A C 31 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 32 N3 ? ? ? 1_555 A G 69 N1 ? ? A C 32 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 32 N4 ? ? ? 1_555 A G 69 O6 ? ? A C 32 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 32 O2 ? ? ? 1_555 A G 69 N2 ? ? A C 32 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 33 N3 ? ? ? 1_555 A G 68 N1 ? ? A C 33 A G 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 33 N4 ? ? ? 1_555 A G 68 O6 ? ? A C 33 A G 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 33 O2 ? ? ? 1_555 A G 68 N2 ? ? A C 33 A G 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A U 34 N3 ? ? ? 1_555 A U 67 O4 ? ? A U 34 A U 67 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog53 hydrog ? ? A U 34 O2 ? ? ? 1_555 A U 67 N3 ? ? A U 34 A U 67 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog54 hydrog ? ? A A 35 N6 ? ? ? 1_555 A A 66 N3 ? ? A A 35 A A 66 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog55 hydrog ? ? A C 36 N3 ? ? ? 1_555 A G 65 N1 ? ? A C 36 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 36 N4 ? ? ? 1_555 A G 65 O6 ? ? A C 36 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 36 O2 ? ? ? 1_555 A G 65 N2 ? ? A C 36 A G 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 37 N1 ? ? ? 1_555 A C 64 N3 ? ? A G 37 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 37 N2 ? ? ? 1_555 A C 64 O2 ? ? A G 37 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 37 O6 ? ? ? 1_555 A C 64 N4 ? ? A G 37 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A A 38 N1 ? ? ? 1_555 A U 63 N3 ? ? A A 38 A U 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A A 38 N6 ? ? ? 1_555 A U 63 O4 ? ? A A 38 A U 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 74 N3 ? ? ? 1_555 A G 89 N1 ? ? A C 74 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 74 N4 ? ? ? 1_555 A G 89 O6 ? ? A C 74 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 74 O2 ? ? ? 1_555 A G 89 N2 ? ? A C 74 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 75 N3 ? ? ? 1_555 A G 88 N1 ? ? A C 75 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 75 N4 ? ? ? 1_555 A G 88 O6 ? ? A C 75 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 75 O2 ? ? ? 1_555 A G 88 N2 ? ? A C 75 A G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A A 76 N1 ? ? ? 1_555 A U 87 N3 ? ? A A 76 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A A 76 N6 ? ? ? 1_555 A U 87 O4 ? ? A A 76 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A C 77 N3 ? ? ? 1_555 A G 86 N1 ? ? A C 77 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A C 77 N4 ? ? ? 1_555 A G 86 O6 ? ? A C 77 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A C 77 O2 ? ? ? 1_555 A G 86 N2 ? ? A C 77 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A A 78 N1 ? ? ? 1_555 A U 85 N3 ? ? A A 78 A U 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A A 78 N6 ? ? ? 1_555 A U 85 O4 ? ? A A 78 A U 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A C 79 N3 ? ? ? 1_555 A G 84 N1 ? ? A C 79 A G 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A C 79 N4 ? ? ? 1_555 A G 84 O6 ? ? A C 79 A G 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A C 79 O2 ? ? ? 1_555 A G 84 N2 ? ? A C 79 A G 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _pdbx_entry_details.entry_id 9NAM _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N3 A G 91 ? ? C4 A G 91 ? ? C5 A G 91 ? ? 125.40 128.60 -3.20 0.50 N 2 1 N3 A G 91 ? ? C4 A G 91 ? ? N9 A G 91 ? ? 130.45 126.00 4.45 0.60 N # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9NAM _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 9NAM _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.87 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 312599 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.4 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Scaffold RNA attached to Mango in the absence of ligand' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9NAM _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'SPOT SCAN' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_defocus_max 2500 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 9NAM _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 277 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9NAM _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A G 1 ? A G 1 2 1 Y 1 A G 2 ? A G 2 3 1 Y 1 A G 3 ? A G 3 4 1 Y 1 A C 4 ? A C 4 5 1 Y 1 A C 5 ? A C 5 6 1 Y 1 A A 6 ? A A 6 7 1 Y 1 A C 7 ? A C 7 8 1 Y 1 A U 8 ? A U 8 9 1 Y 1 A G 9 ? A G 9 10 1 Y 1 A U 10 ? A U 10 11 1 Y 1 A U 11 ? A U 11 12 1 Y 1 A U 12 ? A U 12 13 1 Y 1 A C 13 ? A C 13 14 1 Y 1 A A 39 ? A A 39 15 1 Y 1 A G 40 ? A G 40 16 1 Y 1 A G 41 ? A G 41 17 1 Y 1 A A 42 ? A A 42 18 1 Y 1 A A 43 ? A A 43 19 1 Y 1 A G 44 ? A G 44 20 1 Y 1 A G 45 ? A G 45 21 1 Y 1 A U 46 ? A U 46 22 1 Y 1 A U 47 ? A U 47 23 1 Y 1 A U 48 ? A U 48 24 1 Y 1 A G 49 ? A G 49 25 1 Y 1 A G 50 ? A G 50 26 1 Y 1 A U 51 ? A U 51 27 1 Y 1 A A 52 ? A A 52 28 1 Y 1 A U 53 ? A U 53 29 1 Y 1 A G 54 ? A G 54 30 1 Y 1 A U 55 ? A U 55 31 1 Y 1 A G 56 ? A G 56 32 1 Y 1 A G 57 ? A G 57 33 1 Y 1 A U 58 ? A U 58 34 1 Y 1 A A 59 ? A A 59 35 1 Y 1 A U 60 ? A U 60 36 1 Y 1 A A 61 ? A A 61 37 1 Y 1 A U 62 ? A U 62 38 1 Y 1 A G 93 ? A G 93 39 1 Y 1 A A 94 ? A A 94 40 1 Y 1 A C 95 ? A C 95 41 1 Y 1 A C 96 ? A C 96 42 1 Y 1 A A 97 ? A A 97 43 1 Y 1 A G 98 ? A G 98 44 1 Y 1 A U 99 ? A U 99 45 1 Y 1 A G 100 ? A G 100 46 1 Y 1 A G 101 ? A G 101 47 1 Y 1 A C 102 ? A C 102 48 1 Y 1 A C 103 ? A C 103 49 1 Y 1 A C 104 ? A C 104 50 1 Y 1 A C 105 ? A C 105 51 1 Y 1 A A 106 ? A A 106 52 1 Y 1 A C 107 ? A C 107 53 1 Y 1 A C 108 ? A C 108 54 1 Y 1 A C 109 ? A C 109 55 1 Y 1 A U 110 ? A U 110 56 1 Y 1 A G 111 ? A G 111 57 1 Y 1 A A 112 ? A A 112 58 1 Y 1 A A 113 ? A A 113 59 1 Y 1 A G 114 ? A G 114 60 1 Y 1 A G 115 ? A G 115 61 1 Y 1 A U 116 ? A U 116 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 K K K N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # _em_admin.current_status REL _em_admin.deposition_date 2025-02-12 _em_admin.deposition_site RCSB _em_admin.entry_id 9NAM _em_admin.last_update 2026-03-04 _em_admin.map_release_date 2026-03-04 _em_admin.title 'RNA scaffold attached to Mango in the absence of ligand' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 32644 _em_entity_assembly_naturalsource.organism unidentified _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 905931 _em_entity_assembly_recombinant.organism 'in vitro transcription vector pT7-TP(deltai)' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 60 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'MODEL REFINEMENT' ? 2 ? ? ? PHENIX 1.19.2_4158 'IMAGE ACQUISITION' ? 3 ? ? 1 ? ? MASKING ? 4 ? ? ? ? ? 'CTF CORRECTION' ? 5 1 ? ? ? ? 'LAYERLINE INDEXING' ? 6 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 7 ? ? ? ? ? 'MODEL FITTING' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9NAM 'double helix' 9NAM 'a-form double helix' 9NAM 'hairpin loop' 9NAM 'bulge loop' 9NAM 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A A 14 1_555 A U 92 1_555 0.125 -0.144 0.389 -4.703 -7.741 -11.189 1 A_A14:U92_A A 14 ? A 92 ? 20 1 1 A C 15 1_555 A G 91 1_555 0.171 -0.083 0.322 -4.878 -6.572 -6.425 2 A_C15:G91_A A 15 ? A 91 ? 19 1 1 A U 16 1_555 A A 90 1_555 -0.060 -0.055 0.349 0.878 -6.653 -11.079 3 A_U16:A90_A A 16 ? A 90 ? 20 1 1 A C 74 1_555 A G 89 1_555 0.170 -0.116 0.066 3.015 -3.036 -0.298 4 A_C74:G89_A A 74 ? A 89 ? 19 1 1 A C 75 1_555 A G 88 1_555 0.179 -0.079 0.027 -0.266 -13.720 -1.877 5 A_C75:G88_A A 75 ? A 88 ? 19 1 1 A A 76 1_555 A U 87 1_555 0.298 0.145 0.087 -12.871 1.461 -6.433 6 A_A76:U87_A A 76 ? A 87 ? 20 1 1 A C 77 1_555 A G 86 1_555 0.171 -0.085 0.061 -5.272 3.362 0.583 7 A_C77:G86_A A 77 ? A 86 ? 19 1 1 A A 78 1_555 A U 85 1_555 0.021 -0.268 0.500 -4.184 -8.595 0.748 8 A_A78:U85_A A 78 ? A 85 ? 20 1 1 A C 79 1_555 A G 84 1_555 0.169 -0.229 0.266 0.026 -3.352 -2.063 9 A_C79:G84_A A 79 ? A 84 ? 19 1 1 A G 17 1_555 A C 120 1_555 -0.219 -0.191 0.042 -11.944 -8.640 -2.825 10 A_G17:C120_A A 17 ? A 120 ? 19 1 1 A U 18 1_555 A A 119 1_555 -0.146 -0.032 0.294 -7.986 -8.789 -6.225 11 A_U18:A119_A A 18 ? A 119 ? 20 1 1 A U 19 1_555 A A 118 1_555 -0.082 -0.031 0.491 -1.960 -6.312 -4.209 12 A_U19:A118_A A 19 ? A 118 ? 20 1 1 A G 20 1_555 A C 129 1_555 -0.243 -0.235 0.539 -0.469 4.027 1.442 13 A_G20:C129_A A 20 ? A 129 ? 19 1 1 A C 21 1_555 A G 128 1_555 0.131 -0.205 0.138 1.604 -6.103 -4.928 14 A_C21:G128_A A 21 ? A 128 ? 19 1 1 A G 22 1_555 A C 127 1_555 -0.029 -0.058 -0.543 -15.750 -6.510 -6.003 15 A_G22:C127_A A 22 ? A 127 ? 19 1 1 A C 23 1_555 A G 126 1_555 0.309 -0.100 -0.065 0.194 -4.768 5.473 16 A_C23:G126_A A 23 ? A 126 ? 19 1 1 A U 24 1_555 A A 125 1_555 0.070 0.017 -0.087 -0.224 -6.077 -7.899 17 A_U24:A125_A A 24 ? A 125 ? 20 1 1 A A 25 1_555 A U 124 1_555 0.173 -0.272 1.316 11.216 -6.434 -3.915 18 A_A25:U124_A A 25 ? A 124 ? 20 1 1 A C 26 1_555 A G 123 1_555 0.249 -0.183 0.633 4.662 -9.380 0.054 19 A_C26:G123_A A 26 ? A 123 ? 19 1 1 A A 27 1_555 A U 122 1_555 0.042 -0.177 0.401 3.185 -12.193 -1.601 20 A_A27:U122_A A 27 ? A 122 ? 20 1 1 A U 28 1_555 A U 121 1_555 3.214 -1.827 0.090 3.876 -16.204 2.998 21 A_U28:U121_A A 28 ? A 121 ? 16 1 1 A C 29 1_555 A G 72 1_555 0.190 -0.109 -0.049 -8.385 -0.537 0.297 22 A_C29:G72_A A 29 ? A 72 ? 19 1 1 A U 30 1_555 A A 71 1_555 0.012 -0.083 0.260 -1.460 0.972 4.301 23 A_U30:A71_A A 30 ? A 71 ? 20 1 1 A C 31 1_555 A G 70 1_555 0.252 -0.138 0.158 5.198 3.649 4.017 24 A_C31:G70_A A 31 ? A 70 ? 19 1 1 A C 32 1_555 A G 69 1_555 0.162 -0.126 -0.088 -4.391 0.672 0.597 25 A_C32:G69_A A 32 ? A 69 ? 19 1 1 A C 33 1_555 A G 68 1_555 0.195 -0.178 0.381 5.466 6.193 -1.234 26 A_C33:G68_A A 33 ? A 68 ? 19 1 1 A U 34 1_555 A U 67 1_555 2.203 -2.304 0.618 29.972 1.123 7.131 27 A_U34:U67_A A 34 ? A 67 ? 16 1 1 A A 35 1_555 A A 66 1_555 -5.953 -3.929 -0.799 5.986 10.001 -18.969 28 A_A35:A66_A A 35 ? A 66 ? ? 10 1 A C 36 1_555 A G 65 1_555 0.249 -0.257 -0.935 10.220 -6.271 3.601 29 A_C36:G65_A A 36 ? A 65 ? 19 1 1 A G 37 1_555 A C 64 1_555 -0.105 -0.397 -1.454 -16.156 -5.533 -0.119 30 A_G37:C64_A A 37 ? A 64 ? 19 1 1 A A 38 1_555 A U 63 1_555 0.182 -0.917 -2.225 -8.544 12.610 -5.360 31 A_A38:U63_A A 38 ? A 63 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A A 14 1_555 A U 92 1_555 A C 15 1_555 A G 91 1_555 0.642 -0.907 3.457 2.281 2.580 42.601 -1.516 -0.640 3.427 3.545 -3.133 42.734 1 AA_A14C15:G91U92_AA A 14 ? A 92 ? A 15 ? A 91 ? 1 A C 15 1_555 A G 91 1_555 A U 16 1_555 A A 90 1_555 -0.310 -0.973 3.235 -1.036 2.486 30.234 -2.348 0.388 3.155 4.754 1.981 30.351 2 AA_C15U16:A90G91_AA A 15 ? A 91 ? A 16 ? A 90 ? 1 A U 16 1_555 A A 90 1_555 A C 74 1_555 A G 89 1_555 0.241 -1.345 3.508 0.217 7.276 36.106 -3.153 -0.351 3.188 11.595 -0.346 36.808 3 AA_U16C74:G89A90_AA A 16 ? A 90 ? A 74 ? A 89 ? 1 A C 74 1_555 A G 89 1_555 A C 75 1_555 A G 88 1_555 -0.804 -2.523 2.927 0.243 13.408 32.392 -5.708 1.365 1.769 22.852 -0.413 34.990 4 AA_C74C75:G88G89_AA A 74 ? A 89 ? A 75 ? A 88 ? 1 A C 75 1_555 A G 88 1_555 A A 76 1_555 A U 87 1_555 -0.700 -1.993 3.052 1.042 9.353 34.537 -4.396 1.268 2.426 15.402 -1.716 35.758 5 AA_C75A76:U87G88_AA A 75 ? A 88 ? A 76 ? A 87 ? 1 A A 76 1_555 A U 87 1_555 A C 77 1_555 A G 86 1_555 -0.246 -1.238 3.242 -3.819 6.764 26.777 -4.110 -0.357 2.856 14.230 8.034 27.862 6 AA_A76C77:G86U87_AA A 76 ? A 87 ? A 77 ? A 86 ? 1 A C 77 1_555 A G 86 1_555 A A 78 1_555 A U 85 1_555 -0.028 -1.281 2.868 -5.943 18.737 33.925 -3.693 -0.521 1.911 29.265 9.283 39.064 7 AA_C77A78:U85G86_AA A 77 ? A 86 ? A 78 ? A 85 ? 1 A A 78 1_555 A U 85 1_555 A C 79 1_555 A G 84 1_555 -1.029 -1.628 3.329 -5.568 -0.051 32.596 -2.853 0.825 3.456 -0.090 9.830 33.056 8 AA_A78C79:G84U85_AA A 78 ? A 85 ? A 79 ? A 84 ? 1 A G 17 1_555 A C 120 1_555 A U 18 1_555 A A 119 1_555 -0.899 -1.295 3.386 -3.786 2.298 34.653 -2.518 0.904 3.372 3.838 6.324 34.927 9 AA_G17U18:A119C120_AA A 17 ? A 120 ? A 18 ? A 119 ? 1 A U 18 1_555 A A 119 1_555 A U 19 1_555 A A 118 1_555 0.192 -0.969 3.232 -1.511 6.105 32.335 -2.709 -0.587 2.992 10.835 2.682 32.925 10 AA_U18U19:A118A119_AA A 18 ? A 119 ? A 19 ? A 118 ? 1 A G 20 1_555 A C 129 1_555 A C 21 1_555 A G 128 1_555 -0.163 -1.786 3.193 2.601 8.994 38.339 -3.620 0.523 2.706 13.451 -3.890 39.424 11 AA_G20C21:G128C129_AA A 20 ? A 129 ? A 21 ? A 128 ? 1 A C 21 1_555 A G 128 1_555 A G 22 1_555 A C 127 1_555 -0.166 -2.445 3.849 6.799 15.480 26.552 -7.373 1.560 2.048 30.133 -13.235 31.397 12 AA_C21G22:C127G128_AA A 21 ? A 128 ? A 22 ? A 127 ? 1 A G 22 1_555 A C 127 1_555 A C 23 1_555 A G 126 1_555 0.657 -1.148 3.022 -1.738 3.248 29.453 -2.855 -1.611 2.840 6.357 3.401 29.678 13 AA_G22C23:G126C127_AA A 22 ? A 127 ? A 23 ? A 126 ? 1 A C 23 1_555 A G 126 1_555 A U 24 1_555 A A 125 1_555 -1.323 -2.264 3.367 0.817 9.214 27.913 -6.277 2.770 2.470 18.469 -1.638 29.377 14 AA_C23U24:A125G126_AA A 23 ? A 126 ? A 24 ? A 125 ? 1 A U 24 1_555 A A 125 1_555 A A 25 1_555 A U 124 1_555 -0.067 -1.949 2.864 -9.178 3.151 26.981 -4.543 -1.623 2.511 6.492 18.912 28.643 15 AA_U24A25:U124A125_AA A 24 ? A 125 ? A 25 ? A 124 ? 1 A A 25 1_555 A U 124 1_555 A C 26 1_555 A G 123 1_555 0.145 -1.679 3.621 5.143 0.702 37.636 -2.679 0.503 3.578 1.082 -7.926 37.979 16 AA_A25C26:G123U124_AA A 25 ? A 124 ? A 26 ? A 123 ? 1 A C 26 1_555 A G 123 1_555 A A 27 1_555 A U 122 1_555 0.316 -2.363 3.306 -0.238 5.906 22.041 -7.912 -0.877 2.588 15.100 0.608 22.810 17 AA_C26A27:U122G123_AA A 26 ? A 123 ? A 27 ? A 122 ? 1 A A 27 1_555 A U 122 1_555 A U 28 1_555 A U 121 1_555 0.218 -1.653 3.665 1.278 -1.551 44.590 -2.016 -0.154 3.722 -2.043 -1.684 44.633 18 AA_A27U28:U121U122_AA A 27 ? A 122 ? A 28 ? A 121 ? 1 A U 28 1_555 A U 121 1_555 A C 29 1_555 A G 72 1_555 -3.674 -4.210 3.669 -1.046 5.202 -3.714 -1.406 -40.301 4.892 -53.956 -10.852 -6.476 19 AA_U28C29:G72U121_AA A 28 ? A 121 ? A 29 ? A 72 ? 1 A C 29 1_555 A G 72 1_555 A U 30 1_555 A A 71 1_555 0.015 -2.012 3.319 -5.646 4.014 26.008 -5.325 -1.438 2.913 8.724 12.270 26.900 20 AA_C29U30:A71G72_AA A 29 ? A 72 ? A 30 ? A 71 ? 1 A U 30 1_555 A A 71 1_555 A C 31 1_555 A G 70 1_555 -0.113 -1.767 3.121 -1.121 4.507 29.076 -4.359 0.002 2.823 8.905 2.216 29.437 21 AA_U30C31:G70A71_AA A 30 ? A 71 ? A 31 ? A 70 ? 1 A C 31 1_555 A G 70 1_555 A C 32 1_555 A G 69 1_555 -0.131 -2.057 3.208 3.701 14.726 35.303 -4.721 0.599 2.186 23.012 -5.783 38.334 22 AA_C31C32:G69G70_AA A 31 ? A 70 ? A 32 ? A 69 ? 1 A C 32 1_555 A G 69 1_555 A C 33 1_555 A G 68 1_555 -0.671 -1.861 2.862 -4.872 2.355 29.179 -4.067 0.417 2.780 4.624 9.567 29.666 23 AA_C32C33:G68G69_AA A 32 ? A 69 ? A 33 ? A 68 ? 1 A C 33 1_555 A G 68 1_555 A U 34 1_555 A U 67 1_555 -0.035 -1.390 2.379 -4.893 6.540 40.223 -2.480 -0.322 2.127 9.393 7.027 41.011 24 AA_C33U34:U67G68_AA A 33 ? A 68 ? A 34 ? A 67 ? 1 A U 34 1_555 A U 67 1_555 A A 35 1_555 A A 66 1_555 -1.391 -3.084 3.926 -7.804 9.741 -3.282 -3.438 -19.936 2.487 -58.788 -47.097 -12.905 25 AA_U34A35:A66U67_AA A 34 ? A 67 ? A 35 ? A 66 ? 1 A A 35 1_555 A A 66 1_555 A C 36 1_555 A G 65 1_555 0.898 -1.263 3.218 0.729 2.941 61.521 -1.368 -0.844 3.170 2.874 -0.712 61.588 26 AA_A35C36:G65A66_AA A 35 ? A 66 ? A 36 ? A 65 ? 1 A C 36 1_555 A G 65 1_555 A G 37 1_555 A C 64 1_555 -0.992 -1.184 4.139 4.883 23.196 30.666 -5.063 2.190 2.496 37.613 -7.918 38.584 27 AA_C36G37:C64G65_AA A 36 ? A 65 ? A 37 ? A 64 ? 1 A G 37 1_555 A C 64 1_555 A A 38 1_555 A U 63 1_555 -1.331 -0.527 3.746 -1.799 9.752 30.839 -2.900 2.027 3.492 17.771 3.278 32.357 28 AA_G37A38:U63C64_AA A 37 ? A 64 ? A 38 ? A 63 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 9NAM _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C K N O P # loop_ #