data_5TPY # _entry.id 5TPY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 5TPY pdb_00005tpy 10.2210/pdb5tpy/pdb WWPDB D_1000224606 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5TPY _pdbx_database_status.recvd_initial_deposition_date 2016-10-21 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Akiyama, B.M.' 1 'Laurence, H.M.' 2 'Massey, A.R.' 3 'Costantino, D.A.' 4 'Xie, X.' 5 'Yang, Y.' 6 'Shi, P.-Y.' 7 'Nix, J.C.' 8 'Beckham, J.D.' 9 'Kieft, J.S.' 10 # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Science _citation.journal_id_ASTM SCIEAS _citation.journal_id_CSD 0038 _citation.journal_id_ISSN 1095-9203 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 354 _citation.language ? _citation.page_first 1148 _citation.page_last 1152 _citation.title 'Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease.' _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1126/science.aah3963 _citation.pdbx_database_id_PubMed 27934765 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Akiyama, B.M.' 1 ? primary 'Laurence, H.M.' 2 ? primary 'Massey, A.R.' 3 ? primary 'Costantino, D.A.' 4 ? primary 'Xie, X.' 5 ? primary 'Yang, Y.' 6 ? primary 'Shi, P.Y.' 7 ? primary 'Nix, J.C.' 8 ? primary 'Beckham, J.D.' 9 ? primary 'Kieft, J.S.' 10 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 5TPY _cell.details ? _cell.formula_units_Z ? _cell.length_a 111.679 _cell.length_a_esd ? _cell.length_b 111.679 _cell.length_b_esd ? _cell.length_c 90.826 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _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 ? # _symmetry.entry_id 5TPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' _symmetry.pdbx_full_space_group_name_H-M ? # 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 (71-MER)' 23017.770 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn HEXANE-1,6-DIOL 118.174 1 ? ? ? ? 4 water nat water 18.015 10 ? ? ? ? # _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 GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG _entity_poly.pdbx_seq_one_letter_code_can GGGUCAGGCCGGCGAAAGUCGCCACAGUUUGGGGAAAGCUGUGCAGCCUGUAACCCCCCCACGAAAGUGGG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 U n 1 5 C n 1 6 A n 1 7 G n 1 8 G n 1 9 C n 1 10 C n 1 11 G n 1 12 G n 1 13 C n 1 14 G n 1 15 A n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 C n 1 23 C n 1 24 A n 1 25 C n 1 26 A n 1 27 G n 1 28 U n 1 29 U n 1 30 U n 1 31 G n 1 32 G n 1 33 G n 1 34 G n 1 35 A n 1 36 A n 1 37 A n 1 38 G n 1 39 C n 1 40 U n 1 41 G n 1 42 U n 1 43 G n 1 44 C n 1 45 A n 1 46 G n 1 47 C n 1 48 C n 1 49 U n 1 50 G n 1 51 U n 1 52 A n 1 53 A n 1 54 C n 1 55 C n 1 56 C n 1 57 C n 1 58 C n 1 59 C n 1 60 C n 1 61 A n 1 62 C n 1 63 G n 1 64 A n 1 65 A n 1 66 A n 1 67 G n 1 68 U n 1 69 G n 1 70 G n 1 71 G 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 'Zika virus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 64320 _pdbx_entity_src_syn.details MR766-NIID # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5TPY _struct_ref.pdbx_db_accession 5TPY _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 5TPY _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 71 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5TPY _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 71 _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 71 # 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 HEZ non-polymer . HEXANE-1,6-DIOL ? 'C6 H14 O2' 118.174 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 5TPY _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.55 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 65.37 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 1 uL 50 mM sodium cacodylate pH 6.0, 150 mM NaCl, 4 mM CaCl2, 0.6 mM spermine, 36% 1,6-hexanediol. Crystals were flash-frozen in the mother liquor using liquid nitrogen for x-ray diffraction. ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CMOS _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RDI CMOS_8M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-03-02 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0972 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ALS BEAMLINE 4.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0972 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 4.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5TPY _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.805 _reflns.d_resolution_low 55.839 _reflns.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.number_all ? _reflns.number_obs 15501 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.6 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 21.1 _reflns.pdbx_Rmerge_I_obs 0.092 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 31.5 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.81 _reflns_shell.d_res_low 2.91 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.3 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 99.9 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.492 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 21.1 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.82 _reflns_shell.pdbx_R_split ? # _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 5TPY _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 2.805 _refine.ls_d_res_low 55.839 _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 15501 _refine.ls_number_reflns_R_free 1532 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.66 _refine.ls_percent_reflns_R_free 9.88 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1933 _refine.ls_R_factor_R_free 0.2177 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1906 _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.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 1.34 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 4pqv _refine.pdbx_stereochemistry_target_values ? _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 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 22.50 _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 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.36 _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 ? # _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 1527 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 10 _refine_hist.number_atoms_total 1546 _refine_hist.d_res_high 2.805 _refine_hist.d_res_low 55.839 # 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 'X-RAY DIFFRACTION' ? 0.006 ? 1716 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.103 ? 2671 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 12.490 ? 854 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.045 ? 355 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.007 ? 71 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.8046 2.8951 . . 136 1257 99.00 . . . 0.3866 . 0.3305 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8951 2.9986 . . 134 1280 100.00 . . . 0.3252 . 0.3022 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.9986 3.1186 . . 142 1280 100.00 . . . 0.3562 . 0.2767 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.1186 3.2605 . . 140 1255 100.00 . . . 0.2340 . 0.2161 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.2605 3.4324 . . 149 1287 100.00 . . . 0.2191 . 0.2023 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.4324 3.6474 . . 136 1261 100.00 . . . 0.2469 . 0.1895 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.6474 3.9290 . . 145 1267 100.00 . . . 0.1992 . 0.1712 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.9290 4.3242 . . 138 1280 100.00 . . . 0.1572 . 0.1554 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.3242 4.9496 . . 141 1273 100.00 . . . 0.1808 . 0.1420 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.9496 6.2347 . . 136 1279 100.00 . . . 0.1809 . 0.1568 . . . . . . . . . . 'X-RAY DIFFRACTION' 6.2347 55.8505 . . 135 1250 97.00 . . . 0.2298 . 0.2133 . . . . . . . . . . # _struct.entry_id 5TPY _struct.title 'Crystal structure of an exonuclease resistant RNA from Zika virus' _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 5TPY _struct_keywords.text 'Zika RNA exonuclease resistance, 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 ? # 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 C 5 OP2 ? ? ? 1_555 B MG . MG ? ? A C 5 A MG 101 1_555 ? ? ? ? ? ? ? 2.382 ? ? metalc2 metalc ? ? A A 6 OP2 ? ? ? 1_555 B MG . MG ? ? A A 6 A MG 101 1_555 ? ? ? ? ? ? ? 2.458 ? ? metalc3 metalc ? ? A C 23 OP2 ? ? ? 1_555 B MG . MG ? ? A C 23 A MG 101 1_555 ? ? ? ? ? ? ? 2.136 ? ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 44 N3 ? ? A G 3 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 44 O2 ? ? A G 3 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 44 N4 ? ? A G 3 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 24 N7 ? ? A U 4 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog5 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 24 N6 ? ? A U 4 A A 24 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog6 hydrog ? ? A U 4 O4 ? ? ? 1_555 A C 25 N4 ? ? A U 4 A C 25 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog7 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 50 N1 ? ? A C 5 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 50 O6 ? ? A C 5 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 50 N2 ? ? A C 5 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 49 N3 ? ? A A 6 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 49 O4 ? ? A A 6 A U 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 48 N3 ? ? A G 7 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 48 O2 ? ? A G 7 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 48 N4 ? ? A G 7 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 47 N3 ? ? A G 8 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 47 O2 ? ? A G 8 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 47 N4 ? ? A G 8 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 9 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 9 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 9 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 19 O2 ? ? A G 12 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog28 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 19 N3 ? ? A G 12 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog29 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 N2 ? ? ? 1_555 A A 17 N7 ? ? A G 14 A A 17 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog33 hydrog ? ? A C 22 O2 ? ? ? 1_555 A C 48 N4 ? ? A C 22 A C 48 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog34 hydrog ? ? A C 23 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 23 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 23 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 23 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 23 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 23 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A A 24 N1 ? ? ? 1_555 A U 42 N3 ? ? A A 24 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A A 24 N6 ? ? ? 1_555 A U 42 O4 ? ? A A 24 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 41 N1 ? ? A C 25 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 41 O6 ? ? A C 25 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 41 N2 ? ? A C 25 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A A 26 N1 ? ? ? 1_555 A U 40 N3 ? ? A A 26 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 26 N6 ? ? ? 1_555 A U 40 O4 ? ? A A 26 A U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 27 N1 ? ? ? 1_555 A C 39 N3 ? ? A G 27 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 27 N2 ? ? ? 1_555 A C 39 O2 ? ? A G 27 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 27 O6 ? ? ? 1_555 A C 39 N4 ? ? A G 27 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A U 28 N3 ? ? ? 1_555 A G 38 O6 ? ? A U 28 A G 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog48 hydrog ? ? A U 28 O2 ? ? ? 1_555 A G 38 N1 ? ? A U 28 A G 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog49 hydrog ? ? A U 29 N3 ? ? ? 1_555 A A 36 N7 ? ? A U 29 A A 36 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog50 hydrog ? ? A U 29 O2 ? ? ? 1_555 A A 36 N6 ? ? A U 29 A A 36 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog51 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 57 N3 ? ? A G 31 A C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 57 O2 ? ? A G 31 A C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 57 N4 ? ? A G 31 A C 57 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 32 N1 ? ? ? 1_555 A C 56 N3 ? ? A G 32 A C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 32 N2 ? ? ? 1_555 A C 56 O2 ? ? A G 32 A C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 32 O6 ? ? ? 1_555 A C 56 N4 ? ? A G 32 A C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 33 N1 ? ? ? 1_555 A C 55 N3 ? ? A G 33 A C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 33 N2 ? ? ? 1_555 A C 55 O2 ? ? A G 33 A C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 33 O6 ? ? ? 1_555 A C 55 N4 ? ? A G 33 A C 55 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 34 N1 ? ? ? 1_555 A C 54 N3 ? ? A G 34 A C 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 34 N2 ? ? ? 1_555 A C 54 O2 ? ? A G 34 A C 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 34 O6 ? ? ? 1_555 A C 54 N4 ? ? A G 34 A C 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A A 37 N1 ? ? ? 1_555 A U 51 N3 ? ? A A 37 A U 51 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog64 hydrog ? ? A A 37 N6 ? ? ? 1_555 A U 51 O2 ? ? A A 37 A U 51 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog65 hydrog ? ? A C 58 N3 ? ? ? 1_555 A G 71 N1 ? ? A C 58 A G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 58 N4 ? ? ? 1_555 A G 71 O6 ? ? A C 58 A G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 58 O2 ? ? ? 1_555 A G 71 N2 ? ? A C 58 A G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 59 N3 ? ? ? 1_555 A G 70 N1 ? ? A C 59 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A C 59 N4 ? ? ? 1_555 A G 70 O6 ? ? A C 59 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A C 59 O2 ? ? ? 1_555 A G 70 N2 ? ? A C 59 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A C 60 N3 ? ? ? 1_555 A G 69 N1 ? ? A C 60 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A C 60 N4 ? ? ? 1_555 A G 69 O6 ? ? A C 60 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A C 60 O2 ? ? ? 1_555 A G 69 N2 ? ? A C 60 A G 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A A 61 N1 ? ? ? 1_555 A U 68 N3 ? ? A A 61 A U 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A A 61 N6 ? ? ? 1_555 A U 68 O4 ? ? A A 61 A U 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A C 62 N3 ? ? ? 1_555 A G 67 N1 ? ? A C 62 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A C 62 N4 ? ? ? 1_555 A G 67 O6 ? ? A C 62 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A C 62 O2 ? ? ? 1_555 A G 67 N2 ? ? A C 62 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A G 63 N2 ? ? ? 1_555 A A 66 N7 ? ? A G 63 A A 66 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 MG 101 ? 3 'binding site for residue MG A 101' AC2 Software A HEZ 102 ? 3 'binding site for residue HEZ A 102' # 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 C A 5 ? C A 5 . ? 1_555 ? 2 AC1 3 A A 6 ? A A 6 . ? 1_555 ? 3 AC1 3 C A 23 ? C A 23 . ? 1_555 ? 4 AC2 3 A A 36 ? A A 36 . ? 1_555 ? 5 AC2 3 A A 53 ? A A 53 . ? 1_555 ? 6 AC2 3 C A 54 ? C A 54 . ? 1_555 ? # _atom_sites.entry_id 5TPY _atom_sites.fract_transf_matrix[1][1] 0.008954 _atom_sites.fract_transf_matrix[1][2] 0.005170 _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] 0.010339 _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] 0.011010 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P # 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 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C 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 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 A 15 15 15 A A A . n A 1 16 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n A 1 23 C 23 23 23 C C A . n A 1 24 A 24 24 24 A A A . n A 1 25 C 25 25 25 C C A . n A 1 26 A 26 26 26 A A A . n A 1 27 G 27 27 27 G G A . n A 1 28 U 28 28 28 U U A . n A 1 29 U 29 29 29 U U A . n A 1 30 U 30 30 30 U U A . n A 1 31 G 31 31 31 G G A . n A 1 32 G 32 32 32 G G A . n A 1 33 G 33 33 33 G G A . n A 1 34 G 34 34 34 G G A . n A 1 35 A 35 35 35 A A A . n A 1 36 A 36 36 36 A A A . n A 1 37 A 37 37 37 A A A . n A 1 38 G 38 38 38 G G A . n A 1 39 C 39 39 39 C C A . n A 1 40 U 40 40 40 U U A . n A 1 41 G 41 41 41 G G A . n A 1 42 U 42 42 42 U U A . n A 1 43 G 43 43 43 G G A . n A 1 44 C 44 44 44 C C A . n A 1 45 A 45 45 45 A A A . n A 1 46 G 46 46 46 G G A . n A 1 47 C 47 47 47 C C A . n A 1 48 C 48 48 48 C C A . n A 1 49 U 49 49 49 U U A . n A 1 50 G 50 50 50 G G A . n A 1 51 U 51 51 51 U U A . n A 1 52 A 52 52 52 A A A . n A 1 53 A 53 53 53 A A A . n A 1 54 C 54 54 54 C C A . n A 1 55 C 55 55 55 C C A . n A 1 56 C 56 56 56 C C A . n A 1 57 C 57 57 57 C C A . n A 1 58 C 58 58 58 C C A . n A 1 59 C 59 59 59 C C A . n A 1 60 C 60 60 60 C C A . n A 1 61 A 61 61 61 A A A . n A 1 62 C 62 62 62 C C A . n A 1 63 G 63 63 63 G G A . n A 1 64 A 64 64 64 A A A . n A 1 65 A 65 65 65 A A A . n A 1 66 A 66 66 66 A A A . n A 1 67 G 67 67 67 G G A . n A 1 68 U 68 68 68 U U 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 G 71 71 71 G G 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 MG 1 101 76 MG MG A . C 3 HEZ 1 102 100 HEZ HEZ A . D 4 HOH 1 201 99 HOH HOH A . D 4 HOH 2 202 88 HOH HOH A . D 4 HOH 3 203 86 HOH HOH A . D 4 HOH 4 204 90 HOH HOH A . D 4 HOH 5 205 91 HOH HOH A . D 4 HOH 6 206 97 HOH HOH A . D 4 HOH 7 207 94 HOH HOH A . D 4 HOH 8 208 85 HOH HOH A . D 4 HOH 9 209 87 HOH HOH A . D 4 HOH 10 210 89 HOH HOH A . # _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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)' 6770 ? 1 MORE -71 ? 1 'SSA (A^2)' 41680 ? # 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_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 111.6790000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 8_555 x-y,-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 4 'crystal symmetry operation' 11_655 -x+y+1,y,-z -1.0000000000 0.0000000000 0.0000000000 111.6790000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 OP2 ? A A 6 ? A A 6 ? 1_555 75.1 ? 2 OP2 ? A C 5 ? A C 5 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 OP2 ? A C 23 ? A C 23 ? 1_555 81.1 ? 3 OP2 ? A A 6 ? A A 6 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 OP2 ? A C 23 ? A C 23 ? 1_555 154.0 ? # 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 2016-12-14 2 'Structure model' 1 1 2017-01-04 3 'Structure model' 1 2 2023-10-04 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Refinement description' # 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' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model # 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' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(dev_2499: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 8 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 8 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 8 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 99.49 _pdbx_validate_rmsd_angle.angle_target_value 105.70 _pdbx_validate_rmsd_angle.angle_deviation -6.21 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # 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 HEZ O1 O N N 111 HEZ C1 C N N 112 HEZ C2 C N N 113 HEZ C3 C N N 114 HEZ C4 C N N 115 HEZ C5 C N N 116 HEZ C6 C N N 117 HEZ O6 O N N 118 HEZ HO1 H N N 119 HEZ H11 H N N 120 HEZ H12 H N N 121 HEZ H21 H N N 122 HEZ H22 H N N 123 HEZ H31 H N N 124 HEZ H32 H N N 125 HEZ H41 H N N 126 HEZ H42 H N N 127 HEZ H51 H N N 128 HEZ H52 H N N 129 HEZ H61 H N N 130 HEZ H62 H N N 131 HEZ HO6 H N N 132 HOH O O N N 133 HOH H1 H N N 134 HOH H2 H N N 135 MG MG MG N N 136 U OP3 O N N 137 U P P N N 138 U OP1 O N N 139 U OP2 O N N 140 U "O5'" O N N 141 U "C5'" C N N 142 U "C4'" C N R 143 U "O4'" O N N 144 U "C3'" C N S 145 U "O3'" O N N 146 U "C2'" C N R 147 U "O2'" O N N 148 U "C1'" C N R 149 U N1 N N N 150 U C2 C N N 151 U O2 O N N 152 U N3 N N N 153 U C4 C N N 154 U O4 O N N 155 U C5 C N N 156 U C6 C N N 157 U HOP3 H N N 158 U HOP2 H N N 159 U "H5'" H N N 160 U "H5''" H N N 161 U "H4'" H N N 162 U "H3'" H N N 163 U "HO3'" H N N 164 U "H2'" H N N 165 U "HO2'" H N N 166 U "H1'" H N N 167 U H3 H N N 168 U H5 H N N 169 U H6 H N N 170 # 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 HEZ O1 C1 sing N N 116 HEZ O1 HO1 sing N N 117 HEZ C1 C2 sing N N 118 HEZ C1 H11 sing N N 119 HEZ C1 H12 sing N N 120 HEZ C2 C3 sing N N 121 HEZ C2 H21 sing N N 122 HEZ C2 H22 sing N N 123 HEZ C3 C4 sing N N 124 HEZ C3 H31 sing N N 125 HEZ C3 H32 sing N N 126 HEZ C4 C5 sing N N 127 HEZ C4 H41 sing N N 128 HEZ C4 H42 sing N N 129 HEZ C5 C6 sing N N 130 HEZ C5 H51 sing N N 131 HEZ C5 H52 sing N N 132 HEZ C6 O6 sing N N 133 HEZ C6 H61 sing N N 134 HEZ C6 H62 sing N N 135 HEZ O6 HO6 sing N N 136 HOH O H1 sing N N 137 HOH O H2 sing N N 138 U OP3 P sing N N 139 U OP3 HOP3 sing N N 140 U P OP1 doub N N 141 U P OP2 sing N N 142 U P "O5'" sing N N 143 U OP2 HOP2 sing N N 144 U "O5'" "C5'" sing N N 145 U "C5'" "C4'" sing N N 146 U "C5'" "H5'" sing N N 147 U "C5'" "H5''" sing N N 148 U "C4'" "O4'" sing N N 149 U "C4'" "C3'" sing N N 150 U "C4'" "H4'" sing N N 151 U "O4'" "C1'" sing N N 152 U "C3'" "O3'" sing N N 153 U "C3'" "C2'" sing N N 154 U "C3'" "H3'" sing N N 155 U "O3'" "HO3'" sing N N 156 U "C2'" "O2'" sing N N 157 U "C2'" "C1'" sing N N 158 U "C2'" "H2'" sing N N 159 U "O2'" "HO2'" sing N N 160 U "C1'" N1 sing N N 161 U "C1'" "H1'" sing N N 162 U N1 C2 sing N N 163 U N1 C6 sing N N 164 U C2 O2 doub N N 165 U C2 N3 sing N N 166 U N3 C4 sing N N 167 U N3 H3 sing N N 168 U C4 O4 doub N N 169 U C4 C5 sing N N 170 U C5 C6 doub N N 171 U C5 H5 sing N N 172 U C6 H6 sing N N 173 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5TPY 'double helix' 5TPY 'a-form double helix' 5TPY tetraloop 5TPY 'bulge loop' 5TPY 'mismatched base pair' 5TPY 'three-way junction' # 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 G 3 1_555 A C 44 1_555 0.102 -0.051 -0.218 1.536 -2.123 -0.001 1 A_G3:C44_A A 3 ? A 44 ? 19 1 1 A C 23 1_555 A G 43 1_555 0.384 0.053 0.453 -8.965 -1.891 7.935 2 A_C23:G43_A A 23 ? A 43 ? 19 1 1 A A 24 1_555 A U 42 1_555 0.095 -0.197 -0.008 3.542 -16.016 1.986 3 A_A24:U42_A A 24 ? A 42 ? 20 1 1 A C 25 1_555 A G 41 1_555 -0.153 -0.018 0.063 8.465 -10.699 5.806 4 A_C25:G41_A A 25 ? A 41 ? 19 1 1 A A 26 1_555 A U 40 1_555 0.215 -0.409 0.297 6.975 -11.492 -1.065 5 A_A26:U40_A A 26 ? A 40 ? 20 1 1 A G 27 1_555 A C 39 1_555 -0.088 0.000 0.131 -3.192 -22.911 5.453 6 A_G27:C39_A A 27 ? A 39 ? 19 1 1 A U 28 1_555 A G 38 1_555 2.513 -0.615 0.471 -10.424 -14.464 -3.576 7 A_U28:G38_A A 28 ? A 38 ? 28 1 1 A U 29 1_555 A A 36 1_555 4.276 -2.316 -0.030 -4.151 1.219 -93.583 8 A_U29:A36_A A 29 ? A 36 ? 24 4 1 A C 54 1_555 A G 34 1_555 0.022 -0.155 -0.577 15.794 -16.039 2.442 9 A_C54:G34_A A 54 ? A 34 ? 19 1 1 A C 55 1_555 A G 33 1_555 0.039 -0.308 -0.567 7.899 -4.271 -7.066 10 A_C55:G33_A A 55 ? A 33 ? 19 1 1 A C 56 1_555 A G 32 1_555 -0.055 -0.180 -0.250 6.823 -7.011 -1.934 11 A_C56:G32_A A 56 ? A 32 ? 19 1 1 A C 57 1_555 A G 31 1_555 0.416 -0.223 -0.179 8.204 -10.536 -0.924 12 A_C57:G31_A A 57 ? A 31 ? 19 1 1 A C 58 1_555 A G 71 1_555 0.068 0.142 -0.561 8.948 -9.110 6.367 13 A_C58:G71_A A 58 ? A 71 ? 19 1 1 A C 59 1_555 A G 70 1_555 0.262 -0.123 -0.772 6.970 -20.089 7.508 14 A_C59:G70_A A 59 ? A 70 ? 19 1 1 A C 60 1_555 A G 69 1_555 0.156 -0.213 0.064 -0.892 -8.141 -0.229 15 A_C60:G69_A A 60 ? A 69 ? 19 1 1 A A 61 1_555 A U 68 1_555 0.097 -0.104 -0.085 0.259 -8.950 -3.113 16 A_A61:U68_A A 61 ? A 68 ? 20 1 1 A C 62 1_555 A G 67 1_555 -0.104 -0.130 -0.297 7.188 -7.888 -1.570 17 A_C62:G67_A A 62 ? A 67 ? 19 1 1 A G 63 1_555 A A 66 1_555 6.909 -5.119 0.931 15.726 2.130 -18.552 18 A_G63:A66_A A 63 ? A 66 ? ? ? 1 A A 17 1_555 A G 14 1_555 -6.992 -4.697 1.151 -17.141 -2.674 -21.007 19 A_A17:G14_A A 17 ? A 14 ? ? ? 1 A G 18 1_555 A C 13 1_555 0.609 0.239 0.000 0.269 -4.331 3.452 20 A_G18:C13_A A 18 ? A 13 ? 19 1 1 A U 19 1_555 A G 12 1_555 2.554 -0.525 0.101 0.042 -13.781 5.558 21 A_U19:G12_A A 19 ? A 12 ? 28 1 1 A C 20 1_555 A G 11 1_555 0.438 0.023 0.122 2.190 -15.661 5.649 22 A_C20:G11_A A 20 ? A 11 ? 19 1 1 A G 21 1_555 A C 10 1_555 -0.065 0.040 0.055 24.182 4.613 1.942 23 A_G21:C10_A A 21 ? A 10 ? 19 1 1 A G 46 1_555 A C 9 1_555 -0.223 -0.159 0.017 13.527 -10.062 2.598 24 A_G46:C9_A A 46 ? A 9 ? 19 1 1 A C 47 1_555 A G 8 1_555 0.007 0.013 0.300 6.434 -15.493 -2.037 25 A_C47:G8_A A 47 ? A 8 ? 19 1 1 A C 48 1_555 A G 7 1_555 0.580 -0.066 0.034 4.920 -16.349 1.102 26 A_C48:G7_A A 48 ? A 7 ? 19 1 1 A U 49 1_555 A A 6 1_555 0.112 -0.028 0.053 0.651 -17.372 2.996 27 A_U49:A6_A A 49 ? A 6 ? 20 1 1 A G 50 1_555 A C 5 1_555 -0.049 -0.006 0.552 2.184 -9.625 0.484 28 A_G50:C5_A A 50 ? A 5 ? 19 1 1 A U 51 1_555 A A 37 1_555 -0.105 -1.117 0.042 -4.033 -14.670 -166.440 29 A_U51:A37_A A 51 ? A 37 ? 21 2 # 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 G 3 1_555 A C 44 1_555 A C 23 1_555 A G 43 1_555 -1.564 -1.006 3.329 -9.762 2.038 49.313 -1.340 1.101 3.517 2.415 11.563 50.250 1 AA_G3C23:G43C44_AA A 3 ? A 44 ? A 23 ? A 43 ? 1 A C 23 1_555 A G 43 1_555 A A 24 1_555 A U 42 1_555 -1.149 -1.571 2.807 5.521 8.130 26.625 -4.626 3.308 1.977 16.938 -11.503 28.350 2 AA_C23A24:U42G43_AA A 23 ? A 43 ? A 24 ? A 42 ? 1 A A 24 1_555 A U 42 1_555 A C 25 1_555 A G 41 1_555 0.707 -1.064 3.182 -0.660 12.820 27.296 -4.413 -1.482 2.431 25.457 1.310 30.112 3 AA_A24C25:G41U42_AA A 24 ? A 42 ? A 25 ? A 41 ? 1 A C 25 1_555 A G 41 1_555 A A 26 1_555 A U 40 1_555 -0.237 -1.260 3.197 -0.823 10.714 34.472 -3.439 0.274 2.703 17.558 1.348 36.059 4 AA_C25A26:U40G41_AA A 25 ? A 41 ? A 26 ? A 40 ? 1 A A 26 1_555 A U 40 1_555 A G 27 1_555 A C 39 1_555 0.471 -1.514 3.443 3.554 8.116 30.507 -4.264 -0.206 2.986 15.031 -6.582 31.738 5 AA_A26G27:C39U40_AA A 26 ? A 40 ? A 27 ? A 39 ? 1 A G 27 1_555 A C 39 1_555 A U 28 1_555 A G 38 1_555 0.297 -1.304 3.377 -0.237 2.779 46.301 -1.896 -0.398 3.296 3.531 0.301 46.381 6 AA_G27U28:G38C39_AA A 27 ? A 39 ? A 28 ? A 38 ? 1 A U 28 1_555 A G 38 1_555 A U 29 1_555 A A 36 1_555 -3.621 -2.223 2.855 10.896 4.218 63.120 -2.234 3.773 2.134 3.994 -10.316 64.082 7 AA_U28U29:A36G38_AA A 28 ? A 38 ? A 29 ? A 36 ? 1 A U 29 1_555 A A 36 1_555 A C 54 1_555 A G 34 1_555 0.155 -1.935 6.527 -12.583 16.982 94.002 -1.887 -0.537 6.156 11.498 8.520 95.801 8 AA_U29C54:G34A36_AA A 29 ? A 36 ? A 54 ? A 34 ? 1 A C 54 1_555 A G 34 1_555 A C 55 1_555 A G 33 1_555 -0.857 -2.361 3.530 -3.581 14.738 31.199 -6.105 0.921 2.298 25.595 6.218 34.608 9 AA_C54C55:G33G34_AA A 54 ? A 34 ? A 55 ? A 33 ? 1 A C 55 1_555 A G 33 1_555 A C 56 1_555 A G 32 1_555 -0.486 -2.183 3.299 -1.909 14.838 26.715 -6.641 0.601 1.882 29.369 3.779 30.552 10 AA_C55C56:G32G33_AA A 55 ? A 33 ? A 56 ? A 32 ? 1 A C 56 1_555 A G 32 1_555 A C 57 1_555 A G 31 1_555 0.638 -1.510 3.200 1.999 6.957 35.342 -3.368 -0.765 2.891 11.312 -3.251 36.053 11 AA_C56C57:G31G32_AA A 56 ? A 32 ? A 57 ? A 31 ? 1 A C 57 1_555 A G 31 1_555 A C 58 1_555 A G 71 1_555 -1.130 -2.256 3.232 -0.111 9.336 19.949 -8.922 2.924 1.991 25.239 0.299 22.006 12 AA_C57C58:G71G31_AA A 57 ? A 31 ? A 58 ? A 71 ? 1 A C 58 1_555 A G 71 1_555 A C 59 1_555 A G 70 1_555 -0.176 -1.344 3.451 1.194 10.956 31.977 -4.070 0.495 2.842 19.188 -2.091 33.776 13 AA_C58C59:G70G71_AA A 58 ? A 71 ? A 59 ? A 70 ? 1 A C 59 1_555 A G 70 1_555 A C 60 1_555 A G 69 1_555 -0.689 -1.536 3.584 -7.688 12.067 31.616 -4.514 -0.075 2.909 20.863 13.292 34.627 14 AA_C59C60:G69G70_AA A 59 ? A 70 ? A 60 ? A 69 ? 1 A C 60 1_555 A G 69 1_555 A A 61 1_555 A U 68 1_555 -0.249 -1.737 3.045 0.917 9.542 29.358 -4.841 0.619 2.368 18.224 -1.751 30.851 15 AA_C60A61:U68G69_AA A 60 ? A 69 ? A 61 ? A 68 ? 1 A A 61 1_555 A U 68 1_555 A C 62 1_555 A G 67 1_555 0.421 -1.681 3.099 3.473 7.992 30.643 -4.366 -0.202 2.619 14.751 -6.410 31.829 16 AA_A61C62:G67U68_AA A 61 ? A 68 ? A 62 ? A 67 ? 1 A C 62 1_555 A G 67 1_555 A G 63 1_555 A A 66 1_555 -2.315 -1.327 3.128 -4.605 12.446 54.675 -2.079 2.212 2.956 13.332 4.932 56.141 17 AA_C62G63:A66G67_AA A 62 ? A 67 ? A 63 ? A 66 ? 1 A A 17 1_555 A G 14 1_555 A G 18 1_555 A C 13 1_555 2.667 -1.058 2.741 4.973 8.598 52.528 -1.639 -2.701 2.773 9.617 -5.562 53.393 18 AA_A17G18:C13G14_AA A 17 ? A 14 ? A 18 ? A 13 ? 1 A G 18 1_555 A C 13 1_555 A U 19 1_555 A G 12 1_555 -0.014 -1.443 3.270 1.261 8.374 37.685 -3.170 0.170 2.894 12.766 -1.922 38.591 19 AA_G18U19:G12C13_AA A 18 ? A 13 ? A 19 ? A 12 ? 1 A U 19 1_555 A G 12 1_555 A C 20 1_555 A G 11 1_555 0.327 -1.740 2.941 3.831 6.009 27.191 -4.786 0.092 2.527 12.510 -7.977 28.092 20 AA_U19C20:G11G12_AA A 19 ? A 12 ? A 20 ? A 11 ? 1 A C 20 1_555 A G 11 1_555 A G 21 1_555 A C 10 1_555 -0.666 -1.605 2.667 -2.178 15.035 15.633 -8.005 1.221 0.886 43.979 6.370 21.766 21 AA_C20G21:C10G11_AA A 20 ? A 11 ? A 21 ? A 10 ? 1 A G 21 1_555 A C 10 1_555 A G 46 1_555 A C 9 1_555 -2.065 -0.191 3.335 -8.614 4.606 42.756 -0.729 1.884 3.627 6.221 11.634 43.807 22 AA_G21G46:C9C10_AA A 21 ? A 10 ? A 46 ? A 9 ? 1 A G 46 1_555 A C 9 1_555 A C 47 1_555 A G 8 1_555 0.215 -1.169 3.420 -6.468 0.505 33.891 -2.053 -1.404 3.306 0.856 10.970 34.488 23 AA_G46C47:G8C9_AA A 46 ? A 9 ? A 47 ? A 8 ? 1 A C 47 1_555 A G 8 1_555 A C 48 1_555 A G 7 1_555 -0.475 -1.714 3.293 -1.305 3.098 33.288 -3.482 0.613 3.141 5.390 2.270 33.452 24 AA_C47C48:G7G8_AA A 47 ? A 8 ? A 48 ? A 7 ? 1 A C 48 1_555 A G 7 1_555 A U 49 1_555 A A 6 1_555 0.138 -1.253 3.207 0.644 8.761 33.698 -3.345 -0.139 2.806 14.803 -1.088 34.792 25 AA_C48U49:A6G7_AA A 48 ? A 7 ? A 49 ? A 6 ? 1 A U 49 1_555 A A 6 1_555 A G 50 1_555 A C 5 1_555 -0.082 -1.379 3.219 -3.544 3.240 31.368 -3.098 -0.478 3.055 5.949 6.507 31.724 26 AA_U49G50:C5A6_AA A 49 ? A 6 ? A 50 ? A 5 ? 1 A G 50 1_555 A C 5 1_555 A U 51 1_555 A A 37 1_555 -1.354 0.501 3.040 5.508 -3.255 102.640 0.364 0.940 2.974 -2.083 -3.526 102.783 27 AA_G50U51:A37C5_AA A 50 ? A 5 ? A 51 ? A 37 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 HEXANE-1,6-DIOL HEZ 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 4PQV _pdbx_initial_refinement_model.details ? #