data_5ZEJ # _entry.id 5ZEJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 5ZEJ pdb_00005zej 10.2210/pdb5zej/pdb WWPDB D_1300006933 ? ? # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2018-03-21 _pdbx_database_PDB_obs_spr.pdb_id 5ZEJ _pdbx_database_PDB_obs_spr.replace_pdb_id 4WCR _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 5ZEG unspecified PDB . 5ZEI unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5ZEJ _pdbx_database_status.recvd_initial_deposition_date 2018-02-27 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 _audit_author.identifier_ORCID 'Kanazawa, H.' 1 ? 'Baba, F.' 2 ? 'Koganei, M.' 3 ? 'Kondo, J.' 4 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 45 _citation.language ? _citation.page_first 12529 _citation.page_last 12535 _citation.title 'A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkx882 _citation.pdbx_database_id_PubMed 29036479 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kanazawa, H.' 1 ? primary 'Baba, F.' 2 ? primary 'Koganei, M.' 3 ? primary 'Kondo, J.' 4 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5ZEJ _cell.details ? _cell.formula_units_Z ? _cell.length_a 31.592 _cell.length_a_esd ? _cell.length_b 90.840 _cell.length_b_esd ? _cell.length_c 46.812 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _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 5ZEJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') ; 7063.270 2 ? ? ? ? 2 non-polymer syn PAROMOMYCIN 615.628 1 ? ? ? ? 3 water nat water 18.015 8 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'UGCGUC(1MA)CGUCGACGAAGUCGC' _entity_poly.pdbx_seq_one_letter_code_can UGCGUCACGUCGACGAAGUCGC _entity_poly.pdbx_strand_id A,B _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 U n 1 2 G n 1 3 C n 1 4 G n 1 5 U n 1 6 C n 1 7 1MA n 1 8 C n 1 9 G n 1 10 U n 1 11 C n 1 12 G n 1 13 A n 1 14 C n 1 15 G 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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 22 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5ZEJ _struct_ref.pdbx_db_accession 5ZEJ _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5ZEJ A 1 ? 22 ? 5ZEJ 2 ? 23 ? 2 23 2 1 5ZEJ B 1 ? 22 ? 5ZEJ 25 ? 46 ? 25 46 # 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 1MA 'RNA linking' n "6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O7 P' 361.248 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 PAR non-polymer . PAROMOMYCIN 'PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; MONOMYCIN A; NEOMYCIN E' 'C23 H45 N5 O14' 615.628 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 5ZEJ _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 2.38 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 48.26 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _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 'Sodium cacodylate, Spermine, MPD, Ammonium chloride' _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 CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2013-11-18 # _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 0.98 _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 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.98 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5ZEJ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.5 _reflns.d_resolution_low 32.6 _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 1848 _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 97.2 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.8 _reflns.pdbx_Rmerge_I_obs 0.143 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 8.2 _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 3.5 _reflns_shell.d_res_low 3.6 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _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 ? _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 0.487 _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 ? _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 ? _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 283.000 _refine.B_iso_mean 137.0700 _refine.B_iso_min 59.070 _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 5ZEJ _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 3.5000 _refine.ls_d_res_low 32.5980 _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 1835 _refine.ls_number_reflns_R_free 166 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.4300 _refine.ls_percent_reflns_R_free 9.0500 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2076 _refine.ls_R_factor_R_free 0.2282 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2054 _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 1.380 _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 3TD1 _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 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 28.6400 _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 0.0000 _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.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 3.5000 _refine_hist.d_res_low 32.5980 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 990 _refine_hist.pdbx_number_residues_total 44 _refine_hist.pdbx_B_iso_mean_ligand 132.15 _refine_hist.pdbx_B_iso_mean_solvent 78.72 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 940 # 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' ? 0.058 ? 1093 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.998 ? 1697 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.185 ? 237 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 ? 44 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 12.294 ? 510 ? f_dihedral_angle_d ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 3.5 _refine_ls_shell.d_res_low 3.6 _refine_ls_shell.number_reflns_all 1835 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 166 _refine_ls_shell.number_reflns_R_work 1669 _refine_ls_shell.percent_reflns_obs 96.0000 _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 0.2282 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.2054 _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 1 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5ZEJ _struct.title 'Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin' _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 5ZEJ _struct_keywords.text 'ribosome, RNA, aminoglycoside, antibiotic-resistance' _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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # 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 covale1 covale both ? A C 6 "O3'" ? ? ? 1_555 A 1MA 7 P ? ? A C 7 A 1MA 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A 1MA 7 "O3'" ? ? ? 1_555 A C 8 P ? ? A 1MA 8 A C 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? B C 6 "O3'" ? ? ? 1_555 B 1MA 7 P ? ? B C 30 B 1MA 31 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale4 covale both ? B 1MA 7 "O3'" ? ? ? 1_555 B C 8 P ? ? B 1MA 31 B C 32 1_555 ? ? ? ? ? ? ? 1.602 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B C 20 N3 ? ? A U 6 B C 44 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog11 hydrog ? ? A U 5 O4 ? ? ? 1_555 B C 20 N4 ? ? A U 6 B C 44 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 18 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 18 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 18 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 13 N1 ? ? A U 11 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 13 N6 ? ? A U 11 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 13 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 14 B U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 13 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 14 B U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog41 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 22 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 22 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 B PAR 101 ? 10 'binding site for residue PAR B 101' AC2 Software B C 30 ? 6 'binding site for Di-nucleotide C B 30 and 1MA B 31' AC3 Software B 1MA 31 ? 4 'binding site for Di-nucleotide 1MA B 31 and C B 32' # 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 10 G A 4 ? G A 5 . ? 1_555 ? 2 AC1 10 U A 5 ? U A 6 . ? 1_555 ? 3 AC1 10 C A 6 ? C A 7 . ? 1_555 ? 4 AC1 10 1MA A 7 ? 1MA A 8 . ? 1_555 ? 5 AC1 10 A B 13 ? A B 37 . ? 1_555 ? 6 AC1 10 G B 15 ? G B 39 . ? 1_555 ? 7 AC1 10 A B 16 ? A B 40 . ? 1_555 ? 8 AC1 10 A B 17 ? A B 41 . ? 1_555 ? 9 AC1 10 G B 18 ? G B 42 . ? 1_555 ? 10 AC1 10 U B 19 ? U B 43 . ? 1_555 ? 11 AC2 6 G A 15 ? G A 16 . ? 1_555 ? 12 AC2 6 G A 18 ? G A 19 . ? 1_555 ? 13 AC2 6 U A 19 ? U A 20 . ? 1_555 ? 14 AC2 6 U B 5 ? U B 29 . ? 1_555 ? 15 AC2 6 C B 8 ? C B 32 . ? 1_555 ? 16 AC2 6 G B 18 ? G B 42 . ? 4_556 ? 17 AC3 4 G A 15 ? G A 16 . ? 1_555 ? 18 AC3 4 G A 18 ? G A 19 . ? 1_555 ? 19 AC3 4 C B 6 ? C B 30 . ? 1_555 ? 20 AC3 4 G B 9 ? G B 33 . ? 1_555 ? # _atom_sites.entry_id 5ZEJ _atom_sites.fract_transf_matrix[1][1] 0.031654 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.011008 _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] 0.021362 _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 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 U 1 2 2 U U A . n A 1 2 G 2 3 3 G G A . n A 1 3 C 3 4 4 C C A . n A 1 4 G 4 5 5 G G A . n A 1 5 U 5 6 6 U U A . n A 1 6 C 6 7 7 C C A . n A 1 7 1MA 7 8 8 1MA 1MA A . n A 1 8 C 8 9 9 C C A . n A 1 9 G 9 10 10 G G A . n A 1 10 U 10 11 11 U U A . n A 1 11 C 11 12 12 C C A . n A 1 12 G 12 13 13 G G A . n A 1 13 A 13 14 14 A A A . n A 1 14 C 14 15 15 C C A . n A 1 15 G 15 16 16 G G A . n A 1 16 A 16 17 17 A A A . n A 1 17 A 17 18 18 A A A . n A 1 18 G 18 19 19 G G A . n A 1 19 U 19 20 20 U U A . n A 1 20 C 20 21 21 C C A . n A 1 21 G 21 22 22 G G A . n A 1 22 C 22 23 23 C C A . n B 1 1 U 1 25 25 U U B . n B 1 2 G 2 26 26 G G B . n B 1 3 C 3 27 27 C C B . n B 1 4 G 4 28 28 G G B . n B 1 5 U 5 29 29 U U B . n B 1 6 C 6 30 30 C C B . n B 1 7 1MA 7 31 31 1MA 1MA B . n B 1 8 C 8 32 32 C C B . n B 1 9 G 9 33 33 G G B . n B 1 10 U 10 34 34 U U B . n B 1 11 C 11 35 35 C C B . n B 1 12 G 12 36 36 G G B . n B 1 13 A 13 37 37 A A B . n B 1 14 C 14 38 38 C C B . n B 1 15 G 15 39 39 G G B . n B 1 16 A 16 40 40 A A B . n B 1 17 A 17 41 41 A A B . n B 1 18 G 18 42 42 G G B . n B 1 19 U 19 43 43 U U B . n B 1 20 C 20 44 44 C C B . n B 1 21 G 21 45 45 G G B . n B 1 22 C 22 46 46 C C B . 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 C 2 PAR 1 101 101 PAR PAR B . D 3 HOH 1 101 101 HOH HOH A . D 3 HOH 2 102 103 HOH HOH A . D 3 HOH 3 103 102 HOH HOH A . D 3 HOH 4 104 104 HOH HOH A . E 3 HOH 1 201 201 HOH HOH B . E 3 HOH 2 202 202 HOH HOH B . E 3 HOH 3 203 203 HOH HOH B . E 3 HOH 4 204 204 HOH HOH B . # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 4220 ? 1 MORE -30 ? 1 'SSA (A^2)' 8240 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2018-03-21 2 'Structure model' 1 1 2023-11-22 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Refinement description' 4 2 'Structure model' 'Structure summary' # 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 2 'Structure model' chem_comp 2 2 'Structure model' chem_comp_atom 3 2 'Structure model' chem_comp_bond 4 2 'Structure model' database_2 5 2 '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 2 'Structure model' '_chem_comp.pdbx_synonyms' 2 2 'Structure model' '_database_2.pdbx_DOI' 3 2 '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 ? ? ? 1.8.3_1479 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.22 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? CrystalClear ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? . 5 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? . 6 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? . 7 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 8 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 OP1 B U 25 ? ? 1_555 "O3'" B C 46 ? ? 1_654 1.22 2 1 "O2'" A U 2 ? ? 1_555 "O2'" A C 23 ? ? 1_456 2.11 # 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 1MA P P N N 1 1MA OP1 O N N 2 1MA OP2 O N N 3 1MA OP3 O N N 4 1MA "O5'" O N N 5 1MA "C5'" C N N 6 1MA "C4'" C N R 7 1MA "O4'" O N N 8 1MA "C3'" C N S 9 1MA "O3'" O N N 10 1MA "C2'" C N R 11 1MA "O2'" O N N 12 1MA "C1'" C N R 13 1MA N9 N Y N 14 1MA C8 C Y N 15 1MA N7 N Y N 16 1MA C5 C Y N 17 1MA C6 C N N 18 1MA N6 N N N 19 1MA N1 N N N 20 1MA CM1 C N N 21 1MA C2 C N N 22 1MA N3 N N N 23 1MA C4 C Y N 24 1MA HOP2 H N N 25 1MA HOP3 H N N 26 1MA "H5'" H N N 27 1MA "H5''" H N N 28 1MA "H4'" H N N 29 1MA "H3'" H N N 30 1MA "HO3'" H N N 31 1MA "H2'" H N N 32 1MA "HO2'" H N N 33 1MA "H1'" H N N 34 1MA H8 H N N 35 1MA HN61 H N N 36 1MA HM11 H N N 37 1MA HM12 H N N 38 1MA HM13 H N N 39 1MA H2 H N N 40 A OP3 O N N 41 A P P N N 42 A OP1 O N N 43 A OP2 O N N 44 A "O5'" O N N 45 A "C5'" C N N 46 A "C4'" C N R 47 A "O4'" O N N 48 A "C3'" C N S 49 A "O3'" O N N 50 A "C2'" C N R 51 A "O2'" O N N 52 A "C1'" C N R 53 A N9 N Y N 54 A C8 C Y N 55 A N7 N Y N 56 A C5 C Y N 57 A C6 C Y N 58 A N6 N N N 59 A N1 N Y N 60 A C2 C Y N 61 A N3 N Y N 62 A C4 C Y N 63 A HOP3 H N N 64 A HOP2 H N N 65 A "H5'" H N N 66 A "H5''" H N N 67 A "H4'" H N N 68 A "H3'" H N N 69 A "HO3'" H N N 70 A "H2'" H N N 71 A "HO2'" H N N 72 A "H1'" H N N 73 A H8 H N N 74 A H61 H N N 75 A H62 H N N 76 A H2 H N N 77 C OP3 O N N 78 C P P N N 79 C OP1 O N N 80 C OP2 O N N 81 C "O5'" O N N 82 C "C5'" C N N 83 C "C4'" C N R 84 C "O4'" O N N 85 C "C3'" C N S 86 C "O3'" O N N 87 C "C2'" C N R 88 C "O2'" O N N 89 C "C1'" C N R 90 C N1 N N N 91 C C2 C N N 92 C O2 O N N 93 C N3 N N N 94 C C4 C N N 95 C N4 N N N 96 C C5 C N N 97 C C6 C N N 98 C HOP3 H N N 99 C HOP2 H N N 100 C "H5'" H N N 101 C "H5''" H N N 102 C "H4'" H N N 103 C "H3'" H N N 104 C "HO3'" H N N 105 C "H2'" H N N 106 C "HO2'" H N N 107 C "H1'" H N N 108 C H41 H N N 109 C H42 H N N 110 C H5 H N N 111 C H6 H N N 112 G OP3 O N N 113 G P P N N 114 G OP1 O N N 115 G OP2 O N N 116 G "O5'" O N N 117 G "C5'" C N N 118 G "C4'" C N R 119 G "O4'" O N N 120 G "C3'" C N S 121 G "O3'" O N N 122 G "C2'" C N R 123 G "O2'" O N N 124 G "C1'" C N R 125 G N9 N Y N 126 G C8 C Y N 127 G N7 N Y N 128 G C5 C Y N 129 G C6 C N N 130 G O6 O N N 131 G N1 N N N 132 G C2 C N N 133 G N2 N N N 134 G N3 N N N 135 G C4 C Y N 136 G HOP3 H N N 137 G HOP2 H N N 138 G "H5'" H N N 139 G "H5''" H N N 140 G "H4'" H N N 141 G "H3'" H N N 142 G "HO3'" H N N 143 G "H2'" H N N 144 G "HO2'" H N N 145 G "H1'" H N N 146 G H8 H N N 147 G H1 H N N 148 G H21 H N N 149 G H22 H N N 150 HOH O O N N 151 HOH H1 H N N 152 HOH H2 H N N 153 PAR C11 C N S 154 PAR O11 O N N 155 PAR C21 C N R 156 PAR N21 N N N 157 PAR C31 C N R 158 PAR O31 O N N 159 PAR C41 C N S 160 PAR O41 O N N 161 PAR C51 C N R 162 PAR O51 O N N 163 PAR C61 C N N 164 PAR O61 O N N 165 PAR C12 C N R 166 PAR N12 N N N 167 PAR C22 C N N 168 PAR C32 C N S 169 PAR N32 N N N 170 PAR C42 C N R 171 PAR C52 C N R 172 PAR O52 O N N 173 PAR C62 C N S 174 PAR O62 O N N 175 PAR C13 C N S 176 PAR C23 C N R 177 PAR O23 O N N 178 PAR C33 C N S 179 PAR O33 O N N 180 PAR C43 C N R 181 PAR O43 O N N 182 PAR C53 C N N 183 PAR O53 O N N 184 PAR C14 C N R 185 PAR C24 C N R 186 PAR N24 N N N 187 PAR C34 C N R 188 PAR O34 O N N 189 PAR C44 C N S 190 PAR O44 O N N 191 PAR C54 C N S 192 PAR O54 O N N 193 PAR C64 C N N 194 PAR N64 N N N 195 PAR H11 H N N 196 PAR H21 H N N 197 PAR HN21 H N N 198 PAR HN22 H N N 199 PAR H31 H N N 200 PAR HO31 H N N 201 PAR H41 H N N 202 PAR HO41 H N N 203 PAR H51 H N N 204 PAR H611 H N N 205 PAR H612 H N N 206 PAR HO61 H N N 207 PAR H12 H N N 208 PAR H121 H N N 209 PAR H122 H N N 210 PAR H221 H N N 211 PAR H222 H N N 212 PAR H32 H N N 213 PAR H321 H N N 214 PAR H322 H N N 215 PAR H42 H N N 216 PAR H52 H N N 217 PAR H62 H N N 218 PAR HO62 H N N 219 PAR H13 H N N 220 PAR H23 H N N 221 PAR HO23 H N N 222 PAR H33 H N N 223 PAR H43 H N N 224 PAR H531 H N N 225 PAR H532 H N N 226 PAR HO53 H N N 227 PAR H14 H N N 228 PAR H24 H N N 229 PAR H241 H N N 230 PAR H242 H N N 231 PAR H34 H N N 232 PAR HO34 H N N 233 PAR H44 H N N 234 PAR HO44 H N N 235 PAR H54 H N N 236 PAR H641 H N N 237 PAR H642 H N N 238 PAR HN61 H N N 239 PAR HN62 H N N 240 U OP3 O N N 241 U P P N N 242 U OP1 O N N 243 U OP2 O N N 244 U "O5'" O N N 245 U "C5'" C N N 246 U "C4'" C N R 247 U "O4'" O N N 248 U "C3'" C N S 249 U "O3'" O N N 250 U "C2'" C N R 251 U "O2'" O N N 252 U "C1'" C N R 253 U N1 N N N 254 U C2 C N N 255 U O2 O N N 256 U N3 N N N 257 U C4 C N N 258 U O4 O N N 259 U C5 C N N 260 U C6 C N N 261 U HOP3 H N N 262 U HOP2 H N N 263 U "H5'" H N N 264 U "H5''" H N N 265 U "H4'" H N N 266 U "H3'" H N N 267 U "HO3'" H N N 268 U "H2'" H N N 269 U "HO2'" H N N 270 U "H1'" H N N 271 U H3 H N N 272 U H5 H N N 273 U H6 H N N 274 # 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 1MA P OP1 doub N N 1 1MA P OP2 sing N N 2 1MA P OP3 sing N N 3 1MA P "O5'" sing N N 4 1MA OP2 HOP2 sing N N 5 1MA OP3 HOP3 sing N N 6 1MA "O5'" "C5'" sing N N 7 1MA "C5'" "C4'" sing N N 8 1MA "C5'" "H5'" sing N N 9 1MA "C5'" "H5''" sing N N 10 1MA "C4'" "O4'" sing N N 11 1MA "C4'" "C3'" sing N N 12 1MA "C4'" "H4'" sing N N 13 1MA "O4'" "C1'" sing N N 14 1MA "C3'" "O3'" sing N N 15 1MA "C3'" "C2'" sing N N 16 1MA "C3'" "H3'" sing N N 17 1MA "O3'" "HO3'" sing N N 18 1MA "C2'" "O2'" sing N N 19 1MA "C2'" "C1'" sing N N 20 1MA "C2'" "H2'" sing N N 21 1MA "O2'" "HO2'" sing N N 22 1MA "C1'" N9 sing N N 23 1MA "C1'" "H1'" sing N N 24 1MA N9 C8 sing Y N 25 1MA N9 C4 sing Y N 26 1MA C8 N7 doub Y N 27 1MA C8 H8 sing N N 28 1MA N7 C5 sing Y N 29 1MA C5 C6 sing N N 30 1MA C5 C4 doub Y N 31 1MA C6 N6 doub N N 32 1MA C6 N1 sing N N 33 1MA N6 HN61 sing N N 34 1MA N1 CM1 sing N N 35 1MA N1 C2 sing N N 36 1MA CM1 HM11 sing N N 37 1MA CM1 HM12 sing N N 38 1MA CM1 HM13 sing N N 39 1MA C2 N3 doub N N 40 1MA C2 H2 sing N N 41 1MA N3 C4 sing N N 42 A OP3 P sing N N 43 A OP3 HOP3 sing N N 44 A P OP1 doub N N 45 A P OP2 sing N N 46 A P "O5'" sing N N 47 A OP2 HOP2 sing N N 48 A "O5'" "C5'" sing N N 49 A "C5'" "C4'" sing N N 50 A "C5'" "H5'" sing N N 51 A "C5'" "H5''" sing N N 52 A "C4'" "O4'" sing N N 53 A "C4'" "C3'" sing N N 54 A "C4'" "H4'" sing N N 55 A "O4'" "C1'" sing N N 56 A "C3'" "O3'" sing N N 57 A "C3'" "C2'" sing N N 58 A "C3'" "H3'" sing N N 59 A "O3'" "HO3'" sing N N 60 A "C2'" "O2'" sing N N 61 A "C2'" "C1'" sing N N 62 A "C2'" "H2'" sing N N 63 A "O2'" "HO2'" sing N N 64 A "C1'" N9 sing N N 65 A "C1'" "H1'" sing N N 66 A N9 C8 sing Y N 67 A N9 C4 sing Y N 68 A C8 N7 doub Y N 69 A C8 H8 sing N N 70 A N7 C5 sing Y N 71 A C5 C6 sing Y N 72 A C5 C4 doub Y N 73 A C6 N6 sing N N 74 A C6 N1 doub Y N 75 A N6 H61 sing N N 76 A N6 H62 sing N N 77 A N1 C2 sing Y N 78 A C2 N3 doub Y N 79 A C2 H2 sing N N 80 A N3 C4 sing Y N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 HOH O H1 sing N N 158 HOH O H2 sing N N 159 PAR C11 O11 sing N N 160 PAR C11 C21 sing N N 161 PAR C11 O51 sing N N 162 PAR C11 H11 sing N N 163 PAR O11 C42 sing N N 164 PAR C21 N21 sing N N 165 PAR C21 C31 sing N N 166 PAR C21 H21 sing N N 167 PAR N21 HN21 sing N N 168 PAR N21 HN22 sing N N 169 PAR C31 O31 sing N N 170 PAR C31 C41 sing N N 171 PAR C31 H31 sing N N 172 PAR O31 HO31 sing N N 173 PAR C41 O41 sing N N 174 PAR C41 C51 sing N N 175 PAR C41 H41 sing N N 176 PAR O41 HO41 sing N N 177 PAR C51 O51 sing N N 178 PAR C51 C61 sing N N 179 PAR C51 H51 sing N N 180 PAR C61 O61 sing N N 181 PAR C61 H611 sing N N 182 PAR C61 H612 sing N N 183 PAR O61 HO61 sing N N 184 PAR C12 N12 sing N N 185 PAR C12 C22 sing N N 186 PAR C12 C62 sing N N 187 PAR C12 H12 sing N N 188 PAR N12 H121 sing N N 189 PAR N12 H122 sing N N 190 PAR C22 C32 sing N N 191 PAR C22 H221 sing N N 192 PAR C22 H222 sing N N 193 PAR C32 N32 sing N N 194 PAR C32 C42 sing N N 195 PAR C32 H32 sing N N 196 PAR N32 H321 sing N N 197 PAR N32 H322 sing N N 198 PAR C42 C52 sing N N 199 PAR C42 H42 sing N N 200 PAR C52 O52 sing N N 201 PAR C52 C62 sing N N 202 PAR C52 H52 sing N N 203 PAR O52 C13 sing N N 204 PAR C62 O62 sing N N 205 PAR C62 H62 sing N N 206 PAR O62 HO62 sing N N 207 PAR C13 C23 sing N N 208 PAR C13 O43 sing N N 209 PAR C13 H13 sing N N 210 PAR C23 O23 sing N N 211 PAR C23 C33 sing N N 212 PAR C23 H23 sing N N 213 PAR O23 HO23 sing N N 214 PAR C33 O33 sing N N 215 PAR C33 C43 sing N N 216 PAR C33 H33 sing N N 217 PAR O33 C14 sing N N 218 PAR C43 O43 sing N N 219 PAR C43 C53 sing N N 220 PAR C43 H43 sing N N 221 PAR C53 O53 sing N N 222 PAR C53 H531 sing N N 223 PAR C53 H532 sing N N 224 PAR O53 HO53 sing N N 225 PAR C14 C24 sing N N 226 PAR C14 O54 sing N N 227 PAR C14 H14 sing N N 228 PAR C24 N24 sing N N 229 PAR C24 C34 sing N N 230 PAR C24 H24 sing N N 231 PAR N24 H241 sing N N 232 PAR N24 H242 sing N N 233 PAR C34 O34 sing N N 234 PAR C34 C44 sing N N 235 PAR C34 H34 sing N N 236 PAR O34 HO34 sing N N 237 PAR C44 O44 sing N N 238 PAR C44 C54 sing N N 239 PAR C44 H44 sing N N 240 PAR O44 HO44 sing N N 241 PAR C54 O54 sing N N 242 PAR C54 C64 sing N N 243 PAR C54 H54 sing N N 244 PAR C64 N64 sing N N 245 PAR C64 H641 sing N N 246 PAR C64 H642 sing N N 247 PAR N64 HN61 sing N N 248 PAR N64 HN62 sing N N 249 U OP3 P sing N N 250 U OP3 HOP3 sing N N 251 U P OP1 doub N N 252 U P OP2 sing N N 253 U P "O5'" sing N N 254 U OP2 HOP2 sing N N 255 U "O5'" "C5'" sing N N 256 U "C5'" "C4'" sing N N 257 U "C5'" "H5'" sing N N 258 U "C5'" "H5''" sing N N 259 U "C4'" "O4'" sing N N 260 U "C4'" "C3'" sing N N 261 U "C4'" "H4'" sing N N 262 U "O4'" "C1'" sing N N 263 U "C3'" "O3'" sing N N 264 U "C3'" "C2'" sing N N 265 U "C3'" "H3'" sing N N 266 U "O3'" "HO3'" sing N N 267 U "C2'" "O2'" sing N N 268 U "C2'" "C1'" sing N N 269 U "C2'" "H2'" sing N N 270 U "O2'" "HO2'" sing N N 271 U "C1'" N1 sing N N 272 U "C1'" "H1'" sing N N 273 U N1 C2 sing N N 274 U N1 C6 sing N N 275 U C2 O2 doub N N 276 U C2 N3 sing N N 277 U N3 C4 sing N N 278 U N3 H3 sing N N 279 U C4 O4 doub N N 280 U C4 C5 sing N N 281 U C5 C6 doub N N 282 U C5 H5 sing N N 283 U C6 H6 sing N N 284 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5ZEJ 'double helix' 5ZEJ 'a-form double helix' # 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 2 1_555 B C 22 1_555 0.409 -0.197 -0.127 5.987 10.430 -1.363 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 3 1_555 B G 21 1_555 0.743 -0.429 -1.169 8.621 -4.140 -0.294 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 4 1_555 B C 20 1_555 0.517 -0.024 -0.801 -16.743 -4.443 -1.590 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A C 6 1_555 B G 18 1_555 0.564 -0.285 0.133 -6.864 -0.775 1.219 4 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 8 1_555 B G 15 1_555 0.661 0.009 0.231 11.303 -18.443 8.197 5 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A G 9 1_555 B C 14 1_555 -0.134 -0.145 -0.116 -2.685 -13.933 -0.866 6 A_G10:C38_B A 10 ? B 38 ? 19 1 1 A U 10 1_555 B A 13 1_555 0.099 -0.001 -0.556 5.894 -12.127 3.460 7 A_U11:A37_B A 11 ? B 37 ? 20 1 1 A C 11 1_555 B G 12 1_555 0.756 -0.240 0.624 -3.286 1.724 -0.436 8 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 12 1_555 B C 11 1_555 -0.243 0.548 -0.502 1.639 -10.398 -0.395 9 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A A 13 1_555 B U 10 1_555 0.425 0.089 0.500 9.151 15.267 -2.314 10 A_A14:U34_B A 14 ? B 34 ? 20 1 1 A C 14 1_555 B G 9 1_555 -0.087 -0.096 -0.318 -2.405 -12.677 4.038 11 A_C15:G33_B A 15 ? B 33 ? 19 1 1 A G 15 1_555 B C 8 1_555 -0.007 -0.103 -0.492 -15.210 -13.874 3.007 12 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 18 1_555 B C 6 1_555 -0.189 0.186 0.256 4.233 -10.578 8.927 13 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 19 1_555 B U 5 1_555 1.254 -1.040 -0.383 10.860 -24.626 4.077 14 A_U20:U29_B A 20 ? B 29 ? ? ? 1 A C 20 1_555 B G 4 1_555 0.147 -0.093 -0.346 14.183 -15.850 3.076 15 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 21 1_555 B C 3 1_555 0.136 0.193 -0.065 1.065 -9.285 -5.488 16 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.402 0.230 0.013 10.148 -8.607 -5.929 17 A_C23:G26_B A 23 ? B 26 ? 19 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 G 2 1_555 B C 22 1_555 A C 3 1_555 B G 21 1_555 -0.337 -2.024 3.404 5.550 3.187 33.745 -3.931 1.445 3.112 5.429 -9.455 34.329 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 3 1_555 B G 21 1_555 A G 4 1_555 B C 20 1_555 -0.540 -1.574 4.349 0.542 12.029 28.993 -5.720 1.126 3.430 22.824 -1.028 31.344 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 4 1_555 B C 20 1_555 A C 6 1_555 B G 18 1_555 1.073 -4.104 6.118 -0.713 2.179 64.820 -3.995 -1.055 5.981 2.032 0.665 64.856 3 AA_G5C7:G42C44_BB A 5 ? B 44 ? A 7 ? B 42 ? 1 A C 6 1_555 B G 18 1_555 A C 8 1_555 B G 15 1_555 1.954 -3.954 5.749 -5.075 18.211 73.590 -4.113 -1.841 4.686 14.964 4.170 75.645 4 AA_C7C9:G39G42_BB A 7 ? B 42 ? A 9 ? B 39 ? 1 A C 8 1_555 B G 15 1_555 A G 9 1_555 B C 14 1_555 -0.274 -1.604 3.130 0.376 14.902 31.207 -4.673 0.512 2.160 25.929 -0.654 34.505 5 AA_C9G10:C38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A G 9 1_555 B C 14 1_555 A U 10 1_555 B A 13 1_555 -0.093 -1.737 3.044 1.794 3.734 30.466 -3.935 0.492 2.806 7.065 -3.395 30.740 6 AA_G10U11:A37C38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A U 10 1_555 B A 13 1_555 A C 11 1_555 B G 12 1_555 -0.063 -1.268 3.542 -6.313 8.428 36.487 -3.076 -0.746 3.150 13.127 9.834 37.927 7 AA_U11C12:G36A37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 11 1_555 B G 12 1_555 A G 12 1_555 B C 11 1_555 -0.139 -1.632 2.739 9.566 10.205 29.613 -4.234 1.497 1.950 18.708 -17.537 32.684 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 12 1_555 B C 11 1_555 A A 13 1_555 B U 10 1_555 -0.589 -1.395 2.902 -10.882 7.668 31.617 -3.421 -0.493 2.564 13.358 18.956 34.239 9 AA_G13A14:U34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A A 13 1_555 B U 10 1_555 A C 14 1_555 B G 9 1_555 0.056 -1.962 3.569 5.897 13.881 30.157 -5.589 0.838 2.428 24.823 -10.546 33.640 10 AA_A14C15:G33U34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A C 14 1_555 B G 9 1_555 A G 15 1_555 B C 8 1_555 0.464 -1.318 3.617 -0.417 15.820 32.629 -4.397 -0.807 2.707 26.317 0.694 36.171 11 AA_C15G16:C32G33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 15 1_555 B C 8 1_555 A G 18 1_555 B C 6 1_555 -1.912 -2.763 6.144 -0.969 7.839 71.884 -2.822 1.562 5.880 6.658 0.823 72.258 12 AA_G16G19:C30C32_BB A 16 ? B 32 ? A 19 ? B 30 ? 1 A G 18 1_555 B C 6 1_555 A U 19 1_555 B U 5 1_555 -0.388 -1.169 3.024 6.536 3.971 39.193 -2.125 1.245 2.799 5.852 -9.632 39.903 13 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 19 1_555 B U 5 1_555 A C 20 1_555 B G 4 1_555 0.414 -1.159 3.145 1.492 6.851 31.586 -3.205 -0.498 2.854 12.396 -2.699 32.336 14 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 20 1_555 B G 4 1_555 A G 21 1_555 B C 3 1_555 -1.516 -2.186 3.455 -3.769 15.279 30.645 -5.932 2.015 2.304 26.806 6.612 34.363 15 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 21 1_555 B C 3 1_555 A C 22 1_555 B G 2 1_555 0.162 -1.369 3.363 2.354 -2.046 30.038 -2.194 0.188 3.449 -3.935 -4.526 30.196 16 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 23790054 1 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 26860025 2 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 17K08248 3 'Kurata Grant' Japan '2013- 20' 4 'Ichiro Kanehara Foundation' Japan 15KI192 5 'Japan Science Society' Japan 28-325 6 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 17K08248 7 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 PAROMOMYCIN PAR 3 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 3TD1 _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #