data_3ND3 # _entry.id 3ND3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3ND3 pdb_00003nd3 10.2210/pdb3nd3/pdb NDB NA0575 ? ? RCSB RCSB059677 ? ? WWPDB D_1000059677 ? ? # 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 1 'Structure model' 1 0 2011-09-21 2 'Structure model' 1 1 2011-11-30 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2024-02-21 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.value' 17 4 'Structure model' '_struct_conn.pdbx_dist_value' 18 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3ND3 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-07 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3ND4 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mooers, B.H.' 1 'Singh, A.' 2 # _citation.id primary _citation.title 'The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.' _citation.journal_abbrev Rna _citation.journal_volume 17 _citation.page_first 1870 _citation.page_last 1883 _citation.year 2011 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21878548 _citation.pdbx_database_id_DOI 10.1261/rna.2880311 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mooers, B.H.' 1 ? primary 'Singh, A.' 2 ? # 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 "5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*UP*UP*UP*UP*UP*UP*U)-3'" 5086.016 1 ? ? ? 'U-helix 16-mer dsRNA' 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 79 ? ? ? ? # _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 AGAGAAGAUUUUUUUU _entity_poly.pdbx_seq_one_letter_code_can AGAGAAGAUUUUUUUU _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 'SODIUM ION' NA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 G n 1 3 A n 1 4 G n 1 5 A n 1 6 A n 1 7 G n 1 8 A n 1 9 U n 1 10 U n 1 11 U n 1 12 U n 1 13 U n 1 14 U n 1 15 U n 1 16 U 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'chemically synthesized' # 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 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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 A 1 1 1 A A A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U A . n A 1 11 U 11 11 11 U U A . n A 1 12 U 12 12 12 U U A . n A 1 13 U 13 13 13 U U A . n A 1 14 U 14 14 14 U U A . n A 1 15 U 15 15 15 U U A . n A 1 16 U 16 16 16 U U 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 17 17 K K A . C 3 NA 1 19 19 NA NA A . D 4 HOH 1 20 20 HOH HOH A . D 4 HOH 2 21 21 HOH HOH A . D 4 HOH 3 22 22 HOH HOH A . D 4 HOH 4 23 23 HOH HOH A . D 4 HOH 5 24 24 HOH HOH A . D 4 HOH 6 25 25 HOH HOH A . D 4 HOH 7 26 26 HOH HOH A . D 4 HOH 8 27 27 HOH HOH A . D 4 HOH 9 28 28 HOH HOH A . D 4 HOH 10 29 29 HOH HOH A . D 4 HOH 11 30 30 HOH HOH A . D 4 HOH 12 31 31 HOH HOH A . D 4 HOH 13 32 32 HOH HOH A . D 4 HOH 14 33 33 HOH HOH A . D 4 HOH 15 34 34 HOH HOH A . D 4 HOH 16 35 35 HOH HOH A . D 4 HOH 17 36 36 HOH HOH A . D 4 HOH 18 37 37 HOH HOH A . D 4 HOH 19 38 38 HOH HOH A . D 4 HOH 20 39 39 HOH HOH A . D 4 HOH 21 40 40 HOH HOH A . D 4 HOH 22 41 41 HOH HOH A . D 4 HOH 23 42 42 HOH HOH A . D 4 HOH 24 43 43 HOH HOH A . D 4 HOH 25 44 44 HOH HOH A . D 4 HOH 26 45 45 HOH HOH A . D 4 HOH 27 46 46 HOH HOH A . D 4 HOH 28 47 47 HOH HOH A . D 4 HOH 29 48 48 HOH HOH A . D 4 HOH 30 49 49 HOH HOH A . D 4 HOH 31 50 50 HOH HOH A . D 4 HOH 32 51 51 HOH HOH A . D 4 HOH 33 52 52 HOH HOH A . D 4 HOH 34 53 53 HOH HOH A . D 4 HOH 35 54 54 HOH HOH A . D 4 HOH 36 55 55 HOH HOH A . D 4 HOH 37 56 56 HOH HOH A . D 4 HOH 38 57 57 HOH HOH A . D 4 HOH 39 58 58 HOH HOH A . D 4 HOH 40 59 59 HOH HOH A . D 4 HOH 41 60 60 HOH HOH A . D 4 HOH 42 61 61 HOH HOH A . D 4 HOH 43 62 62 HOH HOH A . D 4 HOH 44 63 63 HOH HOH A . D 4 HOH 45 64 64 HOH HOH A . D 4 HOH 46 65 65 HOH HOH A . D 4 HOH 47 66 66 HOH HOH A . D 4 HOH 48 67 67 HOH HOH A . D 4 HOH 49 68 68 HOH HOH A . D 4 HOH 50 70 70 HOH HOH A . D 4 HOH 51 71 71 HOH HOH A . D 4 HOH 52 72 72 HOH HOH A . D 4 HOH 53 73 73 HOH HOH A . D 4 HOH 54 74 74 HOH HOH A . D 4 HOH 55 75 75 HOH HOH A . D 4 HOH 56 76 76 HOH HOH A . D 4 HOH 57 77 77 HOH HOH A . D 4 HOH 58 78 78 HOH HOH A . D 4 HOH 59 79 79 HOH HOH A . D 4 HOH 60 80 80 HOH HOH A . D 4 HOH 61 81 81 HOH HOH A . D 4 HOH 62 82 82 HOH HOH A . D 4 HOH 63 83 83 HOH HOH A . D 4 HOH 64 84 84 HOH HOH A . D 4 HOH 65 85 85 HOH HOH A . D 4 HOH 66 86 86 HOH HOH A . D 4 HOH 67 87 87 HOH HOH A . D 4 HOH 68 88 88 HOH HOH A . D 4 HOH 69 89 89 HOH HOH A . D 4 HOH 70 91 91 HOH HOH A . D 4 HOH 71 94 94 HOH HOH A . D 4 HOH 72 95 95 HOH HOH A . D 4 HOH 73 102 102 HOH HOH A . D 4 HOH 74 105 105 HOH HOH A . D 4 HOH 75 106 106 HOH HOH A . D 4 HOH 76 119 119 HOH HOH A . D 4 HOH 77 219 219 HOH HOH A . D 4 HOH 78 319 319 HOH HOH A . D 4 HOH 79 419 419 HOH HOH A . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALA 3.3.16 2010/01/06 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 2 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 3 PHENIX 1.6.1_357 ? package 'Paul D. Adams' PAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 4 PDB_EXTRACT 3.100 'May. 21, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 Blu-Ice . ? ? ? ? 'data collection' ? ? ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? # _cell.length_a 42.735 _cell.length_b 42.735 _cell.length_c 126.358 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3ND3 _cell.pdbx_unique_axis ? _cell.Z_PDB 18 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'H 3 2' _symmetry.entry_id 3ND3 _symmetry.Int_Tables_number 155 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3ND3 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.65 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '50 mM NaCacodylate pH 6.0, 10 mM MgCl2, and 1 M LiSO4, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date 2008-07-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9184 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list 0.9184 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL9-2 # _reflns.entry_id 3ND3 _reflns.d_resolution_high 1.370 _reflns.d_resolution_low 18.309 _reflns.number_all 9679 _reflns.number_obs 9679 _reflns.pdbx_netI_over_sigmaI 52.000 _reflns.pdbx_Rsym_value 0.026 _reflns.pdbx_redundancy 17.200 _reflns.percent_possible_obs 99.800 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.37 1.44 ? 17829 ? 0.503 1.6 0.503 ? 13.10 ? 1366 99.10 1 1 1.44 1.53 ? 19331 ? 0.261 3.0 0.261 ? 14.60 ? 1325 100.00 2 1 1.53 1.64 ? 17939 ? 0.110 6.8 0.110 ? 14.60 ? 1232 100.00 3 1 1.64 1.77 ? 16894 ? 0.054 11.8 0.054 ? 14.60 ? 1156 100.00 4 1 1.77 1.94 ? 15888 ? 0.046 15.7 0.046 ? 14.70 ? 1082 100.00 5 1 1.94 2.17 ? 16624 ? 0.038 16.8 0.038 ? 17.20 ? 969 100.00 6 1 2.17 2.50 ? 23004 ? 0.035 17.3 0.035 ? 26.40 ? 871 100.00 7 1 2.50 3.06 ? 19373 ? 0.026 18.7 0.026 ? 26.00 ? 745 100.00 8 1 3.06 4.33 ? 13332 ? 0.021 21.3 0.021 ? 22.60 ? 589 100.00 9 1 4.33 19.06 ? 5965 ? 0.019 26.2 0.019 ? 17.30 ? 344 98.60 10 1 # _refine.entry_id 3ND3 _refine.ls_d_res_high 1.370 _refine.ls_d_res_low 18.309 _refine.pdbx_ls_sigma_F 0.48 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.450 _refine.ls_number_reflns_obs 9641 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.187 _refine.ls_R_factor_R_work 0.182 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.229 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 9.940 _refine.ls_number_reflns_R_free 958 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 34.966 _refine.solvent_model_param_bsol 44.297 _refine.solvent_model_param_ksol 0.448 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.000 _refine.aniso_B[2][2] 0.000 _refine.aniso_B[3][3] 0.000 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.140 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.820 _refine.B_iso_max 61.85 _refine.B_iso_min 19.72 _refine.occupancy_max 1.00 _refine.occupancy_min 0.18 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 336 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 79 _refine_hist.number_atoms_total 417 _refine_hist.d_res_high 1.370 _refine_hist.d_res_low 18.309 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 383 0.019 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 591 1.330 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 79 0.063 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 16 0.020 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 188 12.579 ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 1.370 1.443 7 99.000 1218 . 0.232 0.268 . 128 . 1346 . . 'X-RAY DIFFRACTION' 1.443 1.533 7 100.000 1215 . 0.202 0.274 . 136 . 1351 . . 'X-RAY DIFFRACTION' 1.533 1.651 7 99.000 1216 . 0.168 0.199 . 135 . 1351 . . 'X-RAY DIFFRACTION' 1.651 1.817 7 99.000 1216 . 0.169 0.255 . 135 . 1351 . . 'X-RAY DIFFRACTION' 1.817 2.080 7 100.000 1241 . 0.183 0.251 . 138 . 1379 . . 'X-RAY DIFFRACTION' 2.080 2.619 7 100.000 1260 . 0.183 0.229 . 141 . 1401 . . 'X-RAY DIFFRACTION' 2.619 18.311 7 99.000 1317 . 0.178 0.217 . 145 . 1462 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3ND3 _struct.title 'Uhelix 16-mer dsRNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ND3 _struct_keywords.text 'double-stranded RNA, RNA, U-helix, oligo-U tail, polyU 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 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3ND3 _struct_ref.pdbx_db_accession 3ND3 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code AGAGAAGAUUUUUUUU _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3ND3 _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3ND3 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _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 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1670 ? 1 MORE -28 ? 1 'SSA (A^2)' 5870 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # 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 ? ? A A 5 "O2'" ? ? ? 1_555 C NA . NA ? ? A A 5 A NA 19 1_555 ? ? ? ? ? ? ? 2.545 ? ? metalc2 metalc ? ? A A 6 "O4'" ? ? ? 1_555 C NA . NA ? ? A A 6 A NA 19 1_555 ? ? ? ? ? ? ? 2.569 ? ? metalc3 metalc ? ? A U 13 "O2'" ? ? ? 1_555 B K . K ? ? A U 13 A K 17 1_555 ? ? ? ? ? ? ? 2.958 ? ? metalc4 metalc ? ? C NA . NA ? ? ? 1_555 D HOH . O ? ? A NA 19 A HOH 119 1_555 ? ? ? ? ? ? ? 2.280 ? ? metalc5 metalc ? ? C NA . NA ? ? ? 1_555 D HOH . O ? ? A NA 19 A HOH 219 1_555 ? ? ? ? ? ? ? 2.326 ? ? metalc6 metalc ? ? C NA . NA ? ? ? 1_555 D HOH . O ? ? A NA 19 A HOH 319 1_555 ? ? ? ? ? ? ? 2.275 ? ? metalc7 metalc ? ? C NA . NA ? ? ? 1_555 D HOH . O ? ? A NA 19 A HOH 419 1_555 ? ? ? ? ? ? ? 2.252 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 1 A U 16 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 15 O2 ? ? A G 2 A U 15 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 15 N3 ? ? A G 2 A U 15 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 3 A U 14 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 A U 13 O2 ? ? A G 4 A U 13 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 13 N3 ? ? A G 4 A U 13 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 12 N3 ? ? A A 5 A U 12 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 12 O4 ? ? A A 5 A U 12 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 11 N3 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 11 O4 ? ? A A 6 A U 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N1 ? ? ? 1_555 A U 10 O2 ? ? A G 7 A U 10 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A G 7 O6 ? ? ? 1_555 A U 10 N3 ? ? A G 7 A U 10 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 9 N3 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 9 O4 ? ? A A 8 A U 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 8 N1 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 8 N6 ? ? A U 9 A A 8 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 10 N3 ? ? ? 1_555 A G 7 O6 ? ? A U 10 A G 7 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog20 hydrog ? ? A U 10 O2 ? ? ? 1_555 A G 7 N1 ? ? A U 10 A G 7 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 6 N1 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 6 N6 ? ? A U 11 A A 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 12 A A 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 12 A A 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 13 N3 ? ? ? 1_555 A G 4 O6 ? ? A U 13 A G 4 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A U 13 O2 ? ? ? 1_555 A G 4 N1 ? ? A U 13 A G 4 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog27 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 3 N1 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 3 N6 ? ? A U 14 A A 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 15 N3 ? ? ? 1_555 A G 2 O6 ? ? A U 15 A G 2 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog30 hydrog ? ? A U 15 O2 ? ? ? 1_555 A G 2 N1 ? ? A U 15 A G 2 4_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog31 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 1 N1 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 1 N6 ? ? A U 16 A A 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 "O2'" ? A A 5 ? A A 5 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 "O4'" ? A A 6 ? A A 6 ? 1_555 81.7 ? 2 "O2'" ? A A 5 ? A A 5 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 119 ? 1_555 158.6 ? 3 "O4'" ? A A 6 ? A A 6 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 119 ? 1_555 78.8 ? 4 "O2'" ? A A 5 ? A A 5 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 219 ? 1_555 86.6 ? 5 "O4'" ? A A 6 ? A A 6 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 219 ? 1_555 88.3 ? 6 O ? D HOH . ? A HOH 119 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 219 ? 1_555 83.9 ? 7 "O2'" ? A A 5 ? A A 5 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 319 ? 1_555 112.9 ? 8 "O4'" ? A A 6 ? A A 6 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 319 ? 1_555 164.7 ? 9 O ? D HOH . ? A HOH 119 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 319 ? 1_555 86.0 ? 10 O ? D HOH . ? A HOH 219 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 319 ? 1_555 88.3 ? 11 "O2'" ? A A 5 ? A A 5 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 419 ? 1_555 96.4 ? 12 "O4'" ? A A 6 ? A A 6 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 419 ? 1_555 81.7 ? 13 O ? D HOH . ? A HOH 119 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 419 ? 1_555 89.6 ? 14 O ? D HOH . ? A HOH 219 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 419 ? 1_555 169.0 ? 15 O ? D HOH . ? A HOH 319 ? 1_555 NA ? C NA . ? A NA 19 ? 1_555 O ? D HOH . ? A HOH 419 ? 1_555 100.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A K 17 ? 3 'BINDING SITE FOR RESIDUE K A 17' AC2 Software A NA 19 ? 6 'BINDING SITE FOR RESIDUE NA A 19' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 U A 13 ? U A 13 . ? 3_565 ? 2 AC1 3 U A 13 ? U A 13 . ? 1_555 ? 3 AC1 3 U A 13 ? U A 13 . ? 2_665 ? 4 AC2 6 A A 5 ? A A 5 . ? 1_555 ? 5 AC2 6 A A 6 ? A A 6 . ? 1_555 ? 6 AC2 6 HOH D . ? HOH A 119 . ? 1_555 ? 7 AC2 6 HOH D . ? HOH A 219 . ? 1_555 ? 8 AC2 6 HOH D . ? HOH A 319 . ? 1_555 ? 9 AC2 6 HOH D . ? HOH A 419 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C5 _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 5 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 C6 _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 5 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N1 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 5 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 114.58 _pdbx_validate_rmsd_angle.angle_target_value 117.70 _pdbx_validate_rmsd_angle.angle_deviation -3.12 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A K 17 ? B K . 2 1 A HOH 27 ? D HOH . 3 1 A HOH 28 ? D HOH . 4 1 A HOH 66 ? D HOH . # _phasing.method MR # 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 G OP3 O N N 38 G P P N N 39 G OP1 O N N 40 G OP2 O N N 41 G "O5'" O N N 42 G "C5'" C N N 43 G "C4'" C N R 44 G "O4'" O N N 45 G "C3'" C N S 46 G "O3'" O N N 47 G "C2'" C N R 48 G "O2'" O N N 49 G "C1'" C N R 50 G N9 N Y N 51 G C8 C Y N 52 G N7 N Y N 53 G C5 C Y N 54 G C6 C N N 55 G O6 O N N 56 G N1 N N N 57 G C2 C N N 58 G N2 N N N 59 G N3 N N N 60 G C4 C Y N 61 G HOP3 H N N 62 G HOP2 H N N 63 G "H5'" H N N 64 G "H5''" H N N 65 G "H4'" H N N 66 G "H3'" H N N 67 G "HO3'" H N N 68 G "H2'" H N N 69 G "HO2'" H N N 70 G "H1'" H N N 71 G H8 H N N 72 G H1 H N N 73 G H21 H N N 74 G H22 H N N 75 HOH O O N N 76 HOH H1 H N N 77 HOH H2 H N N 78 K K K N N 79 NA NA NA N N 80 U OP3 O N N 81 U P P N N 82 U OP1 O N N 83 U OP2 O N N 84 U "O5'" O N N 85 U "C5'" C N N 86 U "C4'" C N R 87 U "O4'" O N N 88 U "C3'" C N S 89 U "O3'" O N N 90 U "C2'" C N R 91 U "O2'" O N N 92 U "C1'" C N R 93 U N1 N N N 94 U C2 C N N 95 U O2 O N N 96 U N3 N N N 97 U C4 C N N 98 U O4 O N N 99 U C5 C N N 100 U C6 C N N 101 U HOP3 H N N 102 U HOP2 H N N 103 U "H5'" H N N 104 U "H5''" H N N 105 U "H4'" H N N 106 U "H3'" H N N 107 U "HO3'" H N N 108 U "H2'" H N N 109 U "HO2'" H N N 110 U "H1'" H N N 111 U H3 H N N 112 U H5 H N N 113 U H6 H N N 114 # 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 G OP3 P sing N N 40 G OP3 HOP3 sing N N 41 G P OP1 doub N N 42 G P OP2 sing N N 43 G P "O5'" sing N N 44 G OP2 HOP2 sing N N 45 G "O5'" "C5'" sing N N 46 G "C5'" "C4'" sing N N 47 G "C5'" "H5'" sing N N 48 G "C5'" "H5''" sing N N 49 G "C4'" "O4'" sing N N 50 G "C4'" "C3'" sing N N 51 G "C4'" "H4'" sing N N 52 G "O4'" "C1'" sing N N 53 G "C3'" "O3'" sing N N 54 G "C3'" "C2'" sing N N 55 G "C3'" "H3'" sing N N 56 G "O3'" "HO3'" sing N N 57 G "C2'" "O2'" sing N N 58 G "C2'" "C1'" sing N N 59 G "C2'" "H2'" sing N N 60 G "O2'" "HO2'" sing N N 61 G "C1'" N9 sing N N 62 G "C1'" "H1'" sing N N 63 G N9 C8 sing Y N 64 G N9 C4 sing Y N 65 G C8 N7 doub Y N 66 G C8 H8 sing N N 67 G N7 C5 sing Y N 68 G C5 C6 sing N N 69 G C5 C4 doub Y N 70 G C6 O6 doub N N 71 G C6 N1 sing N N 72 G N1 C2 sing N N 73 G N1 H1 sing N N 74 G C2 N2 sing N N 75 G C2 N3 doub N N 76 G N2 H21 sing N N 77 G N2 H22 sing N N 78 G N3 C4 sing N N 79 HOH O H1 sing N N 80 HOH O H2 sing N N 81 U OP3 P sing N N 82 U OP3 HOP3 sing N N 83 U P OP1 doub N N 84 U P OP2 sing N N 85 U P "O5'" sing N N 86 U OP2 HOP2 sing N N 87 U "O5'" "C5'" sing N N 88 U "C5'" "C4'" sing N N 89 U "C5'" "H5'" sing N N 90 U "C5'" "H5''" sing N N 91 U "C4'" "O4'" sing N N 92 U "C4'" "C3'" sing N N 93 U "C4'" "H4'" sing N N 94 U "O4'" "C1'" sing N N 95 U "C3'" "O3'" sing N N 96 U "C3'" "C2'" sing N N 97 U "C3'" "H3'" sing N N 98 U "O3'" "HO3'" sing N N 99 U "C2'" "O2'" sing N N 100 U "C2'" "C1'" sing N N 101 U "C2'" "H2'" sing N N 102 U "O2'" "HO2'" sing N N 103 U "C1'" N1 sing N N 104 U "C1'" "H1'" sing N N 105 U N1 C2 sing N N 106 U N1 C6 sing N N 107 U C2 O2 doub N N 108 U C2 N3 sing N N 109 U N3 C4 sing N N 110 U N3 H3 sing N N 111 U C4 O4 doub N N 112 U C4 C5 sing N N 113 U C5 C6 doub N N 114 U C5 H5 sing N N 115 U C6 H6 sing N N 116 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3ND3 'a-form double helix' 3ND3 '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 1 1_555 A U 16 4_555 0.015 -0.082 -0.104 -6.868 -8.027 1.041 1 A_A1:U16_A A 1 ? A 16 ? 20 1 1 A G 2 1_555 A U 15 4_555 -2.384 -0.608 0.064 0.827 -13.188 -2.005 2 A_G2:U15_A A 2 ? A 15 ? 28 1 1 A A 3 1_555 A U 14 4_555 -0.048 -0.128 0.019 -0.475 -12.498 2.783 3 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A U 13 4_555 -2.494 -0.561 0.038 -0.256 -10.345 -2.026 4 A_G4:U13_A A 4 ? A 13 ? 28 1 1 A A 5 1_555 A U 12 4_555 0.006 -0.015 -0.001 2.790 -11.197 6.647 5 A_A5:U12_A A 5 ? A 12 ? 20 1 1 A A 6 1_555 A U 11 4_555 0.119 -0.048 0.055 1.766 -13.876 5.641 6 A_A6:U11_A A 6 ? A 11 ? 20 1 1 A G 7 1_555 A U 10 4_555 -2.415 -0.560 0.108 -0.482 -10.612 -0.503 7 A_G7:U10_A A 7 ? A 10 ? 28 1 1 A A 8 1_555 A U 9 4_555 -0.079 -0.044 0.227 0.261 -15.149 4.056 8 A_A8:U9_A A 8 ? A 9 ? 20 1 1 A U 9 1_555 A A 8 4_555 0.079 -0.044 0.227 -0.261 -15.149 4.056 9 A_U9:A8_A A 9 ? A 8 ? 20 1 1 A U 10 1_555 A G 7 4_555 2.415 -0.560 0.108 0.482 -10.612 -0.503 10 A_U10:G7_A A 10 ? A 7 ? 28 1 1 A U 11 1_555 A A 6 4_555 -0.119 -0.048 0.055 -1.766 -13.876 5.641 11 A_U11:A6_A A 11 ? A 6 ? 20 1 1 A U 12 1_555 A A 5 4_555 -0.006 -0.015 -0.001 -2.790 -11.197 6.647 12 A_U12:A5_A A 12 ? A 5 ? 20 1 1 A U 13 1_555 A G 4 4_555 2.494 -0.561 0.038 0.256 -10.345 -2.026 13 A_U13:G4_A A 13 ? A 4 ? 28 1 1 A U 14 1_555 A A 3 4_555 0.048 -0.128 0.019 0.475 -12.498 2.783 14 A_U14:A3_A A 14 ? A 3 ? 20 1 1 A U 15 1_555 A G 2 4_555 2.384 -0.608 0.064 -0.827 -13.188 -2.005 15 A_U15:G2_A A 15 ? A 2 ? 28 1 1 A U 16 1_555 A A 1 4_555 -0.015 -0.082 -0.104 6.868 -8.027 1.041 16 A_U16:A1_A A 16 ? A 1 ? 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 1 1_555 A U 16 4_555 A G 2 1_555 A U 15 4_555 -0.090 -1.416 2.897 -3.624 5.816 24.623 -4.593 -0.662 2.489 13.310 8.294 25.545 1 AA_A1G2:U15U16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A U 15 4_555 A A 3 1_555 A U 14 4_555 0.244 -1.267 3.343 -1.335 3.893 41.835 -2.171 -0.480 3.209 5.437 1.864 42.028 2 AA_G2A3:U14U15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 3 1_555 A U 14 4_555 A G 4 1_555 A U 13 4_555 0.062 -2.228 2.988 -4.043 11.663 21.496 -7.835 -1.060 1.552 28.447 9.861 24.751 3 AA_A3G4:U13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A U 13 4_555 A A 5 1_555 A U 12 4_555 0.067 -1.317 3.256 -1.976 7.468 39.988 -2.688 -0.306 2.967 10.798 2.857 40.698 4 AA_G4A5:U12U13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A A 5 1_555 A U 12 4_555 A A 6 1_555 A U 11 4_555 -0.097 -1.269 3.269 1.529 9.595 31.744 -3.747 0.413 2.771 17.049 -2.716 33.161 5 AA_A5A6:U11U12_AA A 5 ? A 12 ? A 6 ? A 11 ? 1 A A 6 1_555 A U 11 4_555 A G 7 1_555 A U 10 4_555 0.203 -2.201 3.007 -2.625 12.199 20.731 -8.128 -1.102 1.464 30.583 6.580 24.161 6 AA_A6G7:U10U11_AA A 6 ? A 11 ? A 7 ? A 10 ? 1 A G 7 1_555 A U 10 4_555 A A 8 1_555 A U 9 4_555 -0.060 -1.401 3.237 -1.902 3.501 39.886 -2.433 -0.124 3.107 5.117 2.779 40.076 7 AA_G7A8:U9U10_AA A 7 ? A 10 ? A 8 ? A 9 ? 1 A A 8 1_555 A U 9 4_555 A U 9 1_555 A A 8 4_555 0.000 -1.367 3.152 0.000 3.744 33.111 -2.970 0.000 2.984 6.544 0.000 33.317 8 AA_A8U9:A8U9_AA A 8 ? A 9 ? A 9 ? A 8 ? 1 A U 9 1_555 A A 8 4_555 A U 10 1_555 A G 7 4_555 0.060 -1.401 3.237 1.902 3.501 39.886 -2.433 0.124 3.107 5.117 -2.779 40.076 9 AA_U9U10:G7A8_AA A 9 ? A 8 ? A 10 ? A 7 ? 1 A U 10 1_555 A G 7 4_555 A U 11 1_555 A A 6 4_555 -0.203 -2.201 3.007 2.625 12.199 20.731 -8.128 1.102 1.464 30.583 -6.580 24.161 10 AA_U10U11:A6G7_AA A 10 ? A 7 ? A 11 ? A 6 ? 1 A U 11 1_555 A A 6 4_555 A U 12 1_555 A A 5 4_555 0.097 -1.269 3.269 -1.529 9.595 31.744 -3.747 -0.413 2.771 17.049 2.716 33.161 11 AA_U11U12:A5A6_AA A 11 ? A 6 ? A 12 ? A 5 ? 1 A U 12 1_555 A A 5 4_555 A U 13 1_555 A G 4 4_555 -0.067 -1.317 3.256 1.976 7.468 39.988 -2.688 0.306 2.967 10.798 -2.857 40.698 12 AA_U12U13:G4A5_AA A 12 ? A 5 ? A 13 ? A 4 ? 1 A U 13 1_555 A G 4 4_555 A U 14 1_555 A A 3 4_555 -0.062 -2.228 2.988 4.043 11.663 21.496 -7.835 1.060 1.552 28.447 -9.861 24.751 13 AA_U13U14:A3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A U 14 1_555 A A 3 4_555 A U 15 1_555 A G 2 4_555 -0.244 -1.267 3.343 1.335 3.893 41.835 -2.171 0.480 3.209 5.437 -1.864 42.028 14 AA_U14U15:G2A3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A U 15 1_555 A G 2 4_555 A U 16 1_555 A A 1 4_555 0.090 -1.416 2.897 3.624 5.816 24.623 -4.593 0.662 2.489 13.310 -8.295 25.545 15 AA_U15U16:A1G2_AA A 15 ? A 2 ? A 16 ? A 1 ? # _atom_sites.entry_id 3ND3 _atom_sites.fract_transf_matrix[1][1] 0.023400 _atom_sites.fract_transf_matrix[1][2] 0.013510 _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] 0.027020 _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] 0.007914 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H K N NA O P # loop_