data_5NEX # _entry.id 5NEX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.305 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5NEX WWPDB D_1200003994 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5NEX _pdbx_database_status.recvd_initial_deposition_date 2017-03-13 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Huang, L.' 1 ? 'Wang, J.' 2 ? 'Lilley, D.M.J.' 3 ? # _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 'Cell Chem Biol' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2451-9456 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 24 _citation.language ? _citation.page_first 695 _citation.page_last 702.e2 _citation.title 'The Structure of the Guanidine-II Riboswitch.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.chembiol.2017.05.014 _citation.pdbx_database_id_PubMed 28529131 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, L.' 1 ? primary 'Wang, J.' 2 ? primary 'Lilley, D.M.J.' 3 ? # _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 5NEX _cell.details ? _cell.formula_units_Z ? _cell.length_a 55.639 _cell.length_a_esd ? _cell.length_b 55.639 _cell.length_b_esd ? _cell.length_c 135.927 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 18 _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 5NEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3') ; 5880.434 1 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 8 ? ? ? ? 3 non-polymer syn AGMATINE 130.191 1 ? ? ? ? 4 water nat water 18.015 15 ? ? ? ? # _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 'GGUGGGGACGACCCCA(CBV)C' _entity_poly.pdbx_seq_one_letter_code_can GGUGGGGACGACCCCACC _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 U n 1 4 G n 1 5 G n 1 6 G n 1 7 G n 1 8 A n 1 9 C n 1 10 G n 1 11 A n 1 12 C n 1 13 C n 1 14 C n 1 15 C n 1 16 A n 1 17 CBV n 1 18 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 18 _pdbx_entity_src_syn.organism_scientific 'Gloeobacter violaceus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 33072 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5NEX _struct_ref.pdbx_db_accession 5NEX _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 5NEX _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 18 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5NEX _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 18 _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 18 # 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 AG2 non-polymer . AGMATINE '(4-AMINOBUTYL)GUANIDINE' 'C5 H14 N4' 130.191 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CBV 'RNA linking' n ;5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H13 Br N3 O8 P' 402.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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 5NEX _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 3.44 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 64.27 _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 ? _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 ;0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate soaking with 500mM agmatine ; _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 PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 6M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-03-11 # _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 0.9179 _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 'ESRF BEAMLINE ID23-1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9179 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ID23-1 _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5NEX _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.719 _reflns.d_resolution_low 45.42 _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 16643 _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 1.4 _reflns.percent_possible_obs 100 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 18.5 _reflns.pdbx_Rmerge_I_obs 0.129 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.7 _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 0.031 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.996 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.719 _reflns_shell.d_res_low 1.75 _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 452 _reflns_shell.percent_possible_all 99.8 _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 1.5 _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 17.8 _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 0.948 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.752 _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 5NEX _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 1.72 _refine.ls_d_res_low 45.416 _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 16643 _refine.ls_number_reflns_R_free 930 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.50 _refine.ls_percent_reflns_R_free 5.59 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2022 _refine.ls_R_factor_R_free 0.2331 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2005 _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 1.33 _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 SAD _refine.pdbx_starting_model ? _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 25.40 _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 0.24 _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 386 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 418 _refine_hist.d_res_high 1.72 _refine_hist.d_res_low 45.416 # 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' ? 0.008 ? 447 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.383 ? 689 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 11.776 ? 212 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.044 ? 88 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.009 ? 20 ? 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' 1.7193 1.8099 . . 135 2237 99.00 . . . 0.3276 . 0.3159 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.8099 1.9233 . . 129 2267 100.00 . . . 0.2988 . 0.2953 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9233 2.0718 . . 115 2272 100.00 . . . 0.2795 . 0.2532 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.0718 2.2803 . . 133 2209 100.00 . . . 0.2800 . 0.2148 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.2803 2.6103 . . 151 2248 100.00 . . . 0.2657 . 0.2186 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.6103 3.2885 . . 169 2202 99.00 . . . 0.2417 . 0.2150 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.2885 45.4314 . . 98 2278 99.00 . . . 0.1735 . 0.1605 . . . . . . . . . . # _struct.entry_id 5NEX _struct.title 'The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with agmatine' _struct.pdbx_descriptor ;RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3') ; _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 5NEX _struct_keywords.text 'guanidine II riboswitch, stem-loop, tetra loop, dimer, RNA, agmatine' _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 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 3 ? K 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 metalc1 metalc ? ? A G 5 "O2'" ? ? ? 1_555 F NA . NA ? ? A G 5 A NA 105 1_555 ? ? ? ? ? ? ? 2.842 ? metalc2 metalc ? ? A G 5 "O2'" ? ? ? 1_555 I NA . NA ? ? A G 5 A NA 108 1_555 ? ? ? ? ? ? ? 3.100 ? metalc3 metalc ? ? A G 6 OP1 ? ? ? 1_555 C NA . NA ? ? A G 6 A NA 102 1_555 ? ? ? ? ? ? ? 2.809 ? metalc4 metalc ? ? A G 6 "O2'" ? ? ? 1_555 H NA . NA ? ? A G 6 A NA 107 1_555 ? ? ? ? ? ? ? 2.856 ? covale1 covale both ? A A 16 "O3'" ? ? ? 1_555 A CBV 17 P ? ? A A 16 A CBV 17 1_555 ? ? ? ? ? ? ? 1.625 ? metalc5 metalc ? ? A A 16 "O2'" ? ? ? 1_555 G NA . NA ? ? A A 16 A NA 106 1_555 ? ? ? ? ? ? ? 2.934 ? metalc6 metalc ? ? A A 16 "O2'" ? ? ? 1_555 B NA . NA ? ? A A 16 A NA 101 1_555 ? ? ? ? ? ? ? 2.892 ? metalc7 metalc ? ? A CBV 17 O2P ? ? ? 1_555 D NA . NA ? ? A CBV 17 A NA 103 1_555 ? ? ? ? ? ? ? 2.851 ? covale2 covale one ? A CBV 17 "O3'" ? ? ? 1_555 A C 18 P ? ? A CBV 17 A C 18 1_555 ? ? ? ? ? ? ? 1.605 ? metalc8 metalc ? ? A CBV 17 "O2'" ? ? ? 1_555 E NA . NA ? ? A CBV 17 A NA 104 1_555 ? ? ? ? ? ? ? 2.780 ? metalc9 metalc ? ? A G 5 "O2'" ? ? ? 1_555 F NA . NA ? ? A G 5 A NA 105 2_565 ? ? ? ? ? ? ? 2.842 ? metalc10 metalc ? ? A G 6 OP1 ? ? ? 1_555 C NA . NA ? ? A G 6 A NA 102 2_565 ? ? ? ? ? ? ? 2.810 ? metalc11 metalc ? ? A G 6 OP2 ? ? ? 1_555 H NA . NA ? ? A G 6 A NA 107 2_565 ? ? ? ? ? ? ? 2.908 ? metalc12 metalc ? ? A A 16 "O2'" ? ? ? 1_555 G NA . NA ? ? A A 16 A NA 106 2_565 ? ? ? ? ? ? ? 2.935 ? metalc13 metalc ? ? A CBV 17 O1P ? ? ? 1_555 E NA . NA ? ? A CBV 17 A NA 104 3_455 ? ? ? ? ? ? ? 2.944 ? metalc14 metalc ? ? A CBV 17 O2P ? ? ? 1_555 D NA . NA ? ? A CBV 17 A NA 103 2_565 ? ? ? ? ? ? ? 2.852 ? metalc15 metalc ? ? E NA . NA ? ? ? 1_555 K HOH . O ? ? A NA 104 A HOH 215 2_565 ? ? ? ? ? ? ? 3.028 ? metalc16 metalc ? ? I NA . NA ? ? ? 1_555 K HOH . O ? ? A NA 108 A HOH 214 3_455 ? ? ? ? ? ? ? 2.835 ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A CBV 17 N3 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A CBV 17 O2 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A CBV 17 N4 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 16 N1 ? ? A U 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 16 N6 ? ? A U 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? 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 A NA 101 ? 3 'binding site for residue NA A 101' AC2 Software A NA 102 ? 6 'binding site for residue NA A 102' AC3 Software A NA 103 ? 3 'binding site for residue NA A 103' AC4 Software A NA 104 ? 3 'binding site for residue NA A 104' AC5 Software A NA 105 ? 9 'binding site for residue NA A 105' AC6 Software A NA 106 ? 6 'binding site for residue NA A 106' AC7 Software A NA 107 ? 2 'binding site for residue NA A 107' AC8 Software A NA 108 ? 4 'binding site for residue NA A 108' AC9 Software A AG2 109 ? 8 'binding site for residue AG2 A 109' # 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 A A 16 ? A A 16 . ? 2_565 ? 2 AC1 3 A A 16 ? A A 16 . ? 1_555 ? 3 AC1 3 CBV A 17 ? CBV A 17 . ? 1_555 ? 4 AC2 6 G A 6 ? G A 6 . ? 3_455 ? 5 AC2 6 G A 6 ? G A 6 . ? 2_565 ? 6 AC2 6 G A 6 ? G A 6 . ? 1_555 ? 7 AC2 6 NA F . ? NA A 105 . ? 3_455 ? 8 AC2 6 NA F . ? NA A 105 . ? 2_565 ? 9 AC2 6 NA F . ? NA A 105 . ? 1_555 ? 10 AC3 3 CBV A 17 ? CBV A 17 . ? 3_455 ? 11 AC3 3 CBV A 17 ? CBV A 17 . ? 2_565 ? 12 AC3 3 CBV A 17 ? CBV A 17 . ? 1_555 ? 13 AC4 3 CBV A 17 ? CBV A 17 . ? 1_555 ? 14 AC4 3 CBV A 17 ? CBV A 17 . ? 2_565 ? 15 AC4 3 HOH K . ? HOH A 215 . ? 2_565 ? 16 AC5 9 G A 5 ? G A 5 . ? 3_455 ? 17 AC5 9 G A 5 ? G A 5 . ? 1_555 ? 18 AC5 9 G A 5 ? G A 5 . ? 2_565 ? 19 AC5 9 G A 6 ? G A 6 . ? 2_565 ? 20 AC5 9 G A 6 ? G A 6 . ? 1_555 ? 21 AC5 9 G A 6 ? G A 6 . ? 3_455 ? 22 AC5 9 NA C . ? NA A 102 . ? 3_455 ? 23 AC5 9 NA C . ? NA A 102 . ? 2_565 ? 24 AC5 9 NA C . ? NA A 102 . ? 1_555 ? 25 AC6 6 A A 16 ? A A 16 . ? 3_455 ? 26 AC6 6 A A 16 ? A A 16 . ? 2_565 ? 27 AC6 6 A A 16 ? A A 16 . ? 1_555 ? 28 AC6 6 CBV A 17 ? CBV A 17 . ? 2_565 ? 29 AC6 6 CBV A 17 ? CBV A 17 . ? 1_555 ? 30 AC6 6 CBV A 17 ? CBV A 17 . ? 3_455 ? 31 AC7 2 G A 6 ? G A 6 . ? 3_455 ? 32 AC7 2 G A 6 ? G A 6 . ? 1_555 ? 33 AC8 4 G A 4 ? G A 4 . ? 3_455 ? 34 AC8 4 G A 5 ? G A 5 . ? 3_455 ? 35 AC8 4 G A 5 ? G A 5 . ? 1_555 ? 36 AC8 4 HOH K . ? HOH A 214 . ? 3_455 ? 37 AC9 8 G A 7 ? G A 7 . ? 1_555 ? 38 AC9 8 A A 8 ? A A 8 . ? 10_455 ? 39 AC9 8 A A 8 ? A A 8 . ? 1_555 ? 40 AC9 8 C A 9 ? C A 9 . ? 10_455 ? 41 AC9 8 C A 9 ? C A 9 . ? 1_555 ? 42 AC9 8 G A 10 ? G A 10 . ? 1_555 ? 43 AC9 8 HOH K . ? HOH A 201 . ? 1_555 ? 44 AC9 8 HOH K . ? HOH A 211 . ? 1_555 ? # _atom_sites.entry_id 5NEX _atom_sites.fract_transf_matrix[1][1] 0.017973 _atom_sites.fract_transf_matrix[1][2] 0.010377 _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] 0.020753 _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] 0.007357 _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 BR C H N NA 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 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 C 15 15 15 C C A . n A 1 16 A 16 16 16 A A A . n A 1 17 CBV 17 17 17 CBV CBV A . n A 1 18 C 18 18 18 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NA 1 101 1 NA NA A . C 2 NA 1 102 2 NA NA A . D 2 NA 1 103 3 NA NA A . E 2 NA 1 104 4 NA NA A . F 2 NA 1 105 5 NA NA A . G 2 NA 1 106 6 NA NA A . H 2 NA 1 107 7 NA NA A . I 2 NA 1 108 8 NA NA A . J 3 AG2 1 109 1 AG2 AG2 A . K 4 HOH 1 201 9 HOH HOH A . K 4 HOH 2 202 8 HOH HOH A . K 4 HOH 3 203 3 HOH HOH A . K 4 HOH 4 204 12 HOH HOH A . K 4 HOH 5 205 1 HOH HOH A . K 4 HOH 6 206 4 HOH HOH A . K 4 HOH 7 207 10 HOH HOH A . K 4 HOH 8 208 14 HOH HOH A . K 4 HOH 9 209 7 HOH HOH A . K 4 HOH 10 210 6 HOH HOH A . K 4 HOH 11 211 11 HOH HOH A . K 4 HOH 12 212 2 HOH HOH A . K 4 HOH 13 213 5 HOH HOH A . K 4 HOH 14 214 13 HOH HOH A . K 4 HOH 15 215 15 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F,G,H,I,J,K 1 2 A,B,C,D,E,F,G,H,I,J,K # 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' 10_455 y-1/3,x+1/3,-z+1/3 -0.5000000000 0.8660254038 0.0000000000 -27.8195000000 0.8660254038 0.5000000000 0.0000000000 16.0615958137 0.0000000000 0.0000000000 -1.0000000000 45.3090000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A NA 102 ? C NA . 2 1 A NA 103 ? D NA . 3 1 A NA 105 ? F NA . 4 1 A NA 106 ? G NA . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 "O2'" ? A G 5 ? A G 5 ? 1_555 NA ? F NA . ? A NA 105 ? 1_555 "O2'" ? A G 5 ? A G 5 ? 1_555 0.0 ? 2 "O2'" ? A G 5 ? A G 5 ? 1_555 NA ? I NA . ? A NA 108 ? 1_555 O ? K HOH . ? A HOH 214 ? 3_455 144.9 ? 3 OP1 ? A G 6 ? A G 6 ? 1_555 NA ? C NA . ? A NA 102 ? 1_555 OP1 ? A G 6 ? A G 6 ? 1_555 0.0 ? 4 "O2'" ? A G 6 ? A G 6 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 OP2 ? A G 6 ? A G 6 ? 1_555 52.9 ? 5 "O2'" ? A A 16 ? A A 16 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O2'" ? A A 16 ? A A 16 ? 1_555 0.0 ? 6 O2P ? A CBV 17 ? A CBV 17 ? 1_555 NA ? D NA . ? A NA 103 ? 1_555 O2P ? A CBV 17 ? A CBV 17 ? 1_555 0.0 ? 7 "O2'" ? A CBV 17 ? A CBV 17 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 O1P ? A CBV 17 ? A CBV 17 ? 1_555 51.6 ? 8 "O2'" ? A CBV 17 ? A CBV 17 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 O ? K HOH . ? A HOH 215 ? 2_565 98.9 ? 9 O1P ? A CBV 17 ? A CBV 17 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 O ? K HOH . ? A HOH 215 ? 2_565 140.7 ? # 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 2017-05-31 2 'Structure model' 1 1 2017-07-05 3 'Structure model' 1 2 2017-08-30 4 'Structure model' 1 3 2019-03-20 # _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 ? # 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' 'Author supporting evidence' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 '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' citation 2 3 'Structure model' pdbx_audit_support 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_assembly_gen 5 4 'Structure model' pdbx_struct_assembly_prop 6 4 'Structure model' pdbx_struct_oper_list 7 4 'Structure model' struct_keywords # 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' '_citation.country' 2 2 'Structure model' '_citation.journal_volume' 3 2 'Structure model' '_citation.page_first' 4 2 'Structure model' '_citation.page_last' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_pdbx_struct_assembly.details' 7 4 'Structure model' '_pdbx_struct_assembly.method_details' 8 4 'Structure model' '_pdbx_struct_assembly.oligomeric_count' 9 4 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 10 4 'Structure model' '_struct_keywords.text' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -18.2507 21.0114 15.3231 0.3151 0.3064 0.2670 -0.0240 0.0130 -0.0451 1.1994 4.0630 5.2628 -0.1740 0.8109 -3.9228 0.0767 -0.0330 0.0351 0.3086 0.0747 0.0064 -0.3426 0.2446 -0.0692 'X-RAY DIFFRACTION' 2 ? refined -16.1787 18.3016 9.1254 0.2330 0.2951 0.2368 -0.0197 0.0117 -0.0031 6.9485 4.4847 6.8891 -2.6352 2.9695 -4.3141 -0.1322 0.1949 0.1844 0.1366 -0.1150 -0.2827 -0.4373 0.6972 0.1979 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 1 through 10 ) ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 11 through 18 ) ; # 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_2219: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "O3'" A A 16 ? ? O3P A CBV 17 ? ? 0.41 2 1 "HO3'" A CBV 17 ? ? P A C 18 ? ? 0.79 3 1 OP2 A G 10 ? ? O A HOH 201 ? ? 2.12 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5NEX 'a-form double helix' 5NEX 'hairpin loop' 5NEX 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 18 1_555 -0.251 -0.151 -0.075 -5.261 -1.600 -1.570 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A CBV 17 1_555 -0.268 -0.199 0.065 -1.152 -10.462 -1.127 2 A_G2:CBV17_A A 2 ? A 17 ? 19 1 1 A U 3 1_555 A A 16 1_555 -0.075 -0.084 -0.036 1.367 -11.336 5.343 3 A_U3:A16_A A 3 ? A 16 ? 20 1 1 A G 4 1_555 A C 15 1_555 -0.375 -0.138 -0.224 -5.058 -9.633 0.625 4 A_G4:C15_A A 4 ? A 15 ? 19 1 1 A G 5 1_555 A C 14 1_555 -0.416 -0.223 -0.304 -10.521 -9.204 -2.943 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A G 6 1_555 A C 13 1_555 -0.162 -0.124 -0.077 -7.317 -4.904 -0.878 6 A_G6:C13_A A 6 ? A 13 ? 19 1 1 A G 7 1_555 A C 12 1_555 0.001 -0.133 -0.132 -0.784 -2.394 -2.728 7 A_G7:C12_A A 7 ? A 12 ? 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 1 1_555 A C 18 1_555 A G 2 1_555 A CBV 17 1_555 -0.089 -1.973 3.228 0.032 1.335 29.172 -4.196 0.183 3.136 2.648 -0.063 29.202 1 AA_G1G2:CBV17C18_AA A 1 ? A 18 ? A 2 ? A 17 ? 1 A G 2 1_555 A CBV 17 1_555 A U 3 1_555 A A 16 1_555 0.882 -1.853 3.225 1.765 3.988 32.079 -4.000 -1.283 3.022 7.174 -3.176 32.367 2 AA_G2U3:A16CBV17_AA A 2 ? A 17 ? A 3 ? A 16 ? 1 A U 3 1_555 A A 16 1_555 A G 4 1_555 A C 15 1_555 -0.549 -1.700 3.442 0.646 11.214 30.746 -4.891 1.082 2.663 20.319 -1.170 32.688 3 AA_U3G4:C15A16_AA A 3 ? A 16 ? A 4 ? A 15 ? 1 A G 4 1_555 A C 15 1_555 A G 5 1_555 A C 14 1_555 0.182 -2.138 3.475 1.298 7.704 27.419 -6.063 -0.080 2.788 15.850 -2.669 28.490 4 AA_G4G5:C14C15_AA A 4 ? A 15 ? A 5 ? A 14 ? 1 A G 5 1_555 A C 14 1_555 A G 6 1_555 A C 13 1_555 0.579 -1.923 3.234 0.847 4.022 32.151 -4.123 -0.895 2.991 7.226 -1.522 32.406 5 AA_G5G6:C13C14_AA A 5 ? A 14 ? A 6 ? A 13 ? 1 A G 6 1_555 A C 13 1_555 A G 7 1_555 A C 12 1_555 -0.027 -2.130 3.219 2.031 0.690 29.968 -4.247 0.459 3.161 1.333 -3.921 30.043 6 AA_G6G7:C12C13_AA A 6 ? A 13 ? A 7 ? A 12 ? # _pdbx_audit_support.funding_organization 'Cancer Research UK' _pdbx_audit_support.country 'United Kingdom' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 AGMATINE AG2 4 water HOH # _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 ? #