data_5NEP # _entry.id 5NEP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.312 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5NEP WWPDB D_1200003976 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5NEP _pdbx_database_status.recvd_initial_deposition_date 2017-03-11 _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 5NEP _cell.details ? _cell.formula_units_Z ? _cell.length_a 55.500 _cell.length_a_esd ? _cell.length_b 55.500 _cell.length_b_esd ? _cell.length_c 132.379 _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 5NEP _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 1-METHYLGUANIDINE 73.097 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 4 ? ? ? ? 5 water nat water 18.015 33 ? ? ? ? # _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 5NEP _struct_ref.pdbx_db_accession 5NEP _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 5NEP _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 5NEP _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 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 MGX non-polymer . 1-METHYLGUANIDINE ? 'C2 H7 N3' 73.097 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 5NEP _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 3.34 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.13 _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 10mM Methylguanidine ; _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 PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-03-04 # _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 0.9201 _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 'DIAMOND BEAMLINE I24' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9201 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5NEP _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 27.75 _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 19703 _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 1.2 _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 18.83 _reflns.pdbx_Rmerge_I_obs 0.062 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.4 _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 0.015 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.63 _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 529 _reflns_shell.percent_possible_all 99.1 _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 1.50 _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 19.1 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.726 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.916 _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 5NEP _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 1.600 _refine.ls_d_res_low 27.750 _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 19703 _refine.ls_number_reflns_R_free 993 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.93 _refine.ls_percent_reflns_R_free 5.04 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2072 _refine.ls_R_factor_R_free 0.2178 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2066 _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 'MOLECULAR REPLACEMENT' _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 32.12 _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 0.27 _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 24 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 443 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 27.750 # 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' ? 1.466 ? 695 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 9.495 ? 204 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.049 ? 88 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.012 ? 19 ? 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' 1.5996 1.6839 . . 164 2514 93.00 . . . 0.4158 . 0.3970 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.6839 1.7894 . . 134 2644 97.00 . . . 0.3424 . 0.3226 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7894 1.9275 . . 127 2697 99.00 . . . 0.2953 . 0.2825 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9275 2.1214 . . 122 2730 99.00 . . . 0.2979 . 0.2413 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1214 2.4282 . . 128 2717 100.00 . . . 0.2514 . 0.2166 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.4282 3.0587 . . 144 2745 100.00 . . . 0.2038 . 0.2117 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0587 27.7543 . . 174 2663 99.00 . . . 0.1831 . 0.1672 . . . . . . . . . . # _struct.entry_id 5NEP _struct.title 'The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with methylguanidine' _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 5NEP _struct_keywords.text 'guanidine II riboswitch, stem-loop, tetra loop, dimer, methylguanidine, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 5 ? # 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 "O3'" ? ? ? 1_555 G NA . NA ? ? A G 5 A NA 106 1_555 ? ? ? ? ? ? ? 3.185 ? metalc2 metalc ? ? A G 5 "O2'" ? ? ? 1_555 G NA . NA ? ? A G 5 A NA 106 1_555 ? ? ? ? ? ? ? 2.864 ? covale1 covale both ? A A 16 "O3'" ? ? ? 1_555 A CBV 17 P ? ? A A 16 A CBV 17 1_555 ? ? ? ? ? ? ? 1.619 ? metalc3 metalc ? ? A A 16 "O2'" ? ? ? 1_555 F NA . NA ? ? A A 16 A NA 105 1_555 ? ? ? ? ? ? ? 2.859 ? covale2 covale one ? A CBV 17 "O3'" ? ? ? 1_555 A C 18 P ? ? A CBV 17 A C 18 1_555 ? ? ? ? ? ? ? 1.628 ? metalc4 metalc ? ? A CBV 17 "O2'" ? ? ? 1_555 I NA . NA ? ? A CBV 17 A NA 108 1_555 ? ? ? ? ? ? ? 2.767 ? metalc5 metalc ? ? A C 18 OP1 ? ? ? 1_555 H NA . NA ? ? A C 18 A NA 107 1_555 ? ? ? ? ? ? ? 2.860 ? metalc6 metalc ? ? A G 5 "O3'" ? ? ? 1_555 G NA . NA ? ? A G 5 A NA 106 2_565 ? ? ? ? ? ? ? 3.186 ? metalc7 metalc ? ? A G 5 "O2'" ? ? ? 1_555 G NA . NA ? ? A G 5 A NA 106 2_565 ? ? ? ? ? ? ? 2.865 ? metalc8 metalc ? ? A A 16 "O2'" ? ? ? 1_555 F NA . NA ? ? A A 16 A NA 105 2_565 ? ? ? ? ? ? ? 2.860 ? metalc9 metalc ? ? A CBV 17 O1P ? ? ? 1_555 I NA . NA ? ? A CBV 17 A NA 108 3_455 ? ? ? ? ? ? ? 2.735 ? metalc10 metalc ? ? A CBV 17 O2P ? ? ? 1_555 H NA . NA ? ? A CBV 17 A NA 107 3_455 ? ? ? ? ? ? ? 2.768 ? 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 MGX 101 ? 4 'binding site for residue MGX A 101' AC2 Software A SO4 102 ? 4 'binding site for residue SO4 A 102' AC3 Software A SO4 103 ? 4 'binding site for residue SO4 A 103' AC4 Software A SO4 104 ? 4 'binding site for residue SO4 A 104' AC5 Software A NA 105 ? 6 '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 ? 5 'binding site for residue NA A 107' AC8 Software A NA 108 ? 5 'binding site for residue NA A 108' # 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 4 G A 7 ? G A 7 . ? 1_555 ? 2 AC1 4 A A 8 ? A A 8 . ? 1_555 ? 3 AC1 4 C A 9 ? C A 9 . ? 1_555 ? 4 AC1 4 G A 10 ? G A 10 . ? 1_555 ? 5 AC2 4 G A 2 ? G A 2 . ? 1_555 ? 6 AC2 4 U A 3 ? U A 3 . ? 1_555 ? 7 AC2 4 HOH J . ? HOH A 201 . ? 2_565 ? 8 AC2 4 HOH J . ? HOH A 211 . ? 1_555 ? 9 AC3 4 A A 16 ? A A 16 . ? 1_555 ? 10 AC3 4 CBV A 17 ? CBV A 17 . ? 1_555 ? 11 AC3 4 HOH J . ? HOH A 208 . ? 1_555 ? 12 AC3 4 HOH J . ? HOH A 217 . ? 1_555 ? 13 AC4 4 NA H . ? NA A 107 . ? 3_455 ? 14 AC4 4 HOH J . ? HOH A 202 . ? 2_565 ? 15 AC4 4 HOH J . ? HOH A 202 . ? 3_455 ? 16 AC4 4 HOH J . ? HOH A 202 . ? 1_555 ? 17 AC5 6 A A 16 ? A A 16 . ? 3_455 ? 18 AC5 6 A A 16 ? A A 16 . ? 2_565 ? 19 AC5 6 A A 16 ? A A 16 . ? 1_555 ? 20 AC5 6 CBV A 17 ? CBV A 17 . ? 2_565 ? 21 AC5 6 CBV A 17 ? CBV A 17 . ? 1_555 ? 22 AC5 6 CBV A 17 ? CBV A 17 . ? 3_455 ? 23 AC6 6 G A 5 ? G A 5 . ? 3_455 ? 24 AC6 6 G A 5 ? G A 5 . ? 2_565 ? 25 AC6 6 G A 5 ? G A 5 . ? 1_555 ? 26 AC6 6 G A 6 ? G A 6 . ? 2_565 ? 27 AC6 6 G A 6 ? G A 6 . ? 1_555 ? 28 AC6 6 G A 6 ? G A 6 . ? 3_455 ? 29 AC7 5 CBV A 17 ? CBV A 17 . ? 2_565 ? 30 AC7 5 CBV A 17 ? CBV A 17 . ? 1_555 ? 31 AC7 5 C A 18 ? C A 18 . ? 1_555 ? 32 AC7 5 SO4 E . ? SO4 A 104 . ? 2_565 ? 33 AC7 5 NA I . ? NA A 108 . ? 1_555 ? 34 AC8 5 A A 16 ? A A 16 . ? 2_565 ? 35 AC8 5 CBV A 17 ? CBV A 17 . ? 2_565 ? 36 AC8 5 CBV A 17 ? CBV A 17 . ? 1_555 ? 37 AC8 5 C A 18 ? C A 18 . ? 1_555 ? 38 AC8 5 NA H . ? NA A 107 . ? 1_555 ? # _atom_sites.entry_id 5NEP _atom_sites.fract_transf_matrix[1][1] 0.018018 _atom_sites.fract_transf_matrix[1][2] 0.010403 _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] 0.020805 _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] 0.007554 _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 S # 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 MGX 1 101 1 MGX MGX A . C 3 SO4 1 102 2 SO4 SO4 A . D 3 SO4 1 103 3 SO4 SO4 A . E 3 SO4 1 104 4 SO4 SO4 A . F 4 NA 1 105 1 NA NA A . G 4 NA 1 106 2 NA NA A . H 4 NA 1 107 3 NA NA A . I 4 NA 1 108 4 NA NA A . J 5 HOH 1 201 7 HOH HOH A . J 5 HOH 2 202 1 HOH HOH A . J 5 HOH 3 203 28 HOH HOH A . J 5 HOH 4 204 6 HOH HOH A . J 5 HOH 5 205 5 HOH HOH A . J 5 HOH 6 206 8 HOH HOH A . J 5 HOH 7 207 3 HOH HOH A . J 5 HOH 8 208 23 HOH HOH A . J 5 HOH 9 209 10 HOH HOH A . J 5 HOH 10 210 11 HOH HOH A . J 5 HOH 11 211 13 HOH HOH A . J 5 HOH 12 212 2 HOH HOH A . J 5 HOH 13 213 22 HOH HOH A . J 5 HOH 14 214 20 HOH HOH A . J 5 HOH 15 215 33 HOH HOH A . J 5 HOH 16 216 25 HOH HOH A . J 5 HOH 17 217 12 HOH HOH A . J 5 HOH 18 218 24 HOH HOH A . J 5 HOH 19 219 17 HOH HOH A . J 5 HOH 20 220 4 HOH HOH A . J 5 HOH 21 221 9 HOH HOH A . J 5 HOH 22 222 21 HOH HOH A . J 5 HOH 23 223 16 HOH HOH A . J 5 HOH 24 224 15 HOH HOH A . J 5 HOH 25 225 18 HOH HOH A . J 5 HOH 26 226 31 HOH HOH A . J 5 HOH 27 227 27 HOH HOH A . J 5 HOH 28 228 14 HOH HOH A . J 5 HOH 29 229 29 HOH HOH A . J 5 HOH 30 230 26 HOH HOH A . J 5 HOH 31 231 32 HOH HOH A . J 5 HOH 32 232 19 HOH HOH A . J 5 HOH 33 233 30 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 1 2 A,B,C,D,E,F,G,H,I,J # 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 -27.7500000000 0.8660254038 0.5000000000 0.0000000000 16.0214699700 0.0000000000 0.0000000000 -1.0000000000 44.1263333333 # 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 SO4 104 ? E SO4 . 2 1 A NA 105 ? F NA . 3 1 A NA 106 ? G NA . 4 1 A HOH 202 ? J HOH . 5 1 A HOH 212 ? J HOH . # 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 "O3'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O2'" ? A G 5 ? A G 5 ? 1_555 54.1 ? 2 "O3'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O3'" ? A G 5 ? A G 5 ? 1_555 0.0 ? 3 "O2'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O3'" ? A G 5 ? A G 5 ? 1_555 54.1 ? 4 "O3'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O2'" ? A G 5 ? A G 5 ? 1_555 54.1 ? 5 "O2'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O2'" ? A G 5 ? A G 5 ? 1_555 0.0 ? 6 "O3'" ? A G 5 ? A G 5 ? 1_555 NA ? G NA . ? A NA 106 ? 1_555 "O2'" ? A G 5 ? A G 5 ? 1_555 54.1 ? 7 "O2'" ? A A 16 ? A A 16 ? 1_555 NA ? F NA . ? A NA 105 ? 1_555 "O2'" ? A A 16 ? A A 16 ? 1_555 0.0 ? 8 "O2'" ? A CBV 17 ? A CBV 17 ? 1_555 NA ? I NA . ? A NA 108 ? 1_555 O1P ? A CBV 17 ? A CBV 17 ? 1_555 53.7 ? 9 OP1 ? A C 18 ? A C 18 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 O2P ? A CBV 17 ? A CBV 17 ? 1_555 93.7 ? # 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' 2 0 2019-03-20 5 'Structure model' 2 1 2019-07-10 # _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' 'Atomic model' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Structure summary' 7 5 'Structure model' 'Data collection' # 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' atom_site 4 4 'Structure model' diffrn_source 5 4 'Structure model' pdbx_struct_assembly 6 4 'Structure model' pdbx_struct_assembly_gen 7 4 'Structure model' pdbx_struct_assembly_prop 8 4 'Structure model' pdbx_struct_oper_list 9 4 'Structure model' struct_keywords 10 5 'Structure model' diffrn_source # 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' '_atom_site.occupancy' 7 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 8 4 'Structure model' '_pdbx_struct_assembly.details' 9 4 'Structure model' '_pdbx_struct_assembly.method_details' 10 4 'Structure model' '_pdbx_struct_assembly.oligomeric_count' 11 4 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 12 4 'Structure model' '_struct_keywords.text' 13 5 'Structure model' '_diffrn_source.pdbx_synchrotron_site' # 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 -18.2016 21.1106 15.0547 0.3703 0.3166 0.2735 -0.0244 -0.0073 -0.0310 1.4022 2.6346 3.3235 0.6054 0.1862 -2.4182 0.0666 -0.1776 0.0489 0.3431 0.0665 -0.1653 -0.2237 0.2343 -0.1781 'X-RAY DIFFRACTION' 2 ? refined -16.1060 18.4951 8.7348 0.2747 0.3474 0.2637 -0.0465 0.0015 0.0328 2.1619 3.9579 5.0536 -2.8644 3.1027 -3.8482 -0.1176 0.4122 0.2470 0.2913 -0.1378 -0.1156 -0.5118 0.7143 0.2006 # 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 ? ? 0.36 2 1 HN42 A CBV 17 ? ? O4 A SO4 103 ? ? 1.55 3 1 "C3'" A A 16 ? ? O3P A CBV 17 ? ? 1.77 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 215 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 226 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 10_455 _pdbx_validate_symm_contact.dist 1.92 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5NEP 'a-form double helix' 5NEP 'hairpin loop' 5NEP '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 -0.209 -0.103 -0.048 -4.941 -1.771 -0.719 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A CBV 17 1_555 -0.273 -0.166 -0.011 -3.053 -12.470 1.602 2 A_G2:CBV17_A A 2 ? A 17 ? 19 1 1 A U 3 1_555 A A 16 1_555 0.040 -0.112 0.120 -0.579 -12.389 4.082 3 A_U3:A16_A A 3 ? A 16 ? 20 1 1 A G 4 1_555 A C 15 1_555 -0.338 -0.098 -0.181 -5.421 -9.397 1.831 4 A_G4:C15_A A 4 ? A 15 ? 19 1 1 A G 5 1_555 A C 14 1_555 -0.260 -0.167 -0.251 -9.759 -9.901 -2.893 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A G 6 1_555 A C 13 1_555 -0.211 -0.134 -0.100 -7.248 -5.915 -1.746 6 A_G6:C13_A A 6 ? A 13 ? 19 1 1 A G 7 1_555 A C 12 1_555 -0.096 -0.088 -0.118 -2.336 0.158 -1.931 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 0.363 -1.946 3.256 1.618 2.807 29.422 -4.386 -0.377 3.076 5.505 -3.174 29.596 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 0.297 -1.713 3.221 -0.811 2.404 33.133 -3.384 -0.651 3.085 4.208 1.420 33.227 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 -0.385 -1.652 3.311 1.820 11.715 30.137 -4.872 0.988 2.486 21.513 -3.342 32.335 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 0.261 -2.011 3.390 1.962 8.553 28.596 -5.590 -0.118 2.700 16.822 -3.858 29.885 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 0.530 -1.930 3.245 1.721 4.028 30.817 -4.335 -0.673 2.999 7.531 -3.219 31.120 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 0.059 -2.216 3.202 0.804 2.384 28.035 -5.088 0.058 3.008 4.908 -1.655 28.145 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 1-METHYLGUANIDINE MGX 3 'SULFATE ION' SO4 4 'SODIUM ION' NA 5 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 ? #