data_5NDI # _entry.id 5NDI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.284 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5NDI WWPDB D_1200003929 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5NDI _pdbx_database_status.recvd_initial_deposition_date 2017-03-08 _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 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 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5NDI _cell.details ? _cell.formula_units_Z ? _cell.length_a 47.476 _cell.length_a_esd ? _cell.length_b 48.185 _cell.length_b_esd ? _cell.length_c 153.066 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 16 _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 5NDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _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(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)-3') ; 6485.775 4 ? ? ? ? 2 non-polymer syn GUANIDINE 59.070 4 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 4 ? ? ? ? # _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 'UUUGCAGGACGACCUG(CBV)AAA' _entity_poly.pdbx_seq_one_letter_code_can UUUGCAGGACGACCUGCAAA _entity_poly.pdbx_strand_id A,B,C,D _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 U n 1 3 U n 1 4 G n 1 5 C n 1 6 A n 1 7 G n 1 8 G n 1 9 A n 1 10 C n 1 11 G n 1 12 A n 1 13 C n 1 14 C n 1 15 U n 1 16 G n 1 17 CBV n 1 18 A n 1 19 A n 1 20 A 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 20 _pdbx_entity_src_syn.organism_scientific 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5NDI _struct_ref.pdbx_db_accession 5NDI _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 5NDI A 1 ? 20 ? 5NDI 1 ? 20 ? 1 20 2 1 5NDI B 1 ? 20 ? 5NDI 1 ? 20 ? 1 20 3 1 5NDI C 1 ? 20 ? 5NDI 1 ? 20 ? 1 20 4 1 5NDI D 1 ? 20 ? 5NDI 1 ? 20 ? 1 20 # 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 GAI non-polymer . GUANIDINE ? 'C H5 N3' 59.070 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 5NDI _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 3.37 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.55 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _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 Chloride, 0.05 M MES pH 5.6, 2.0 M Lithium Sulfate monohydrate ; _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 2017-02-20 # _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 0.92011 _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 I04' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.92011 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I04 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate 53.66 _reflns.entry_id 5NDI _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.57 _reflns.d_resolution_low 51.02 _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 20792 _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 1.1 _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 5.38 _reflns.pdbx_Rmerge_I_obs 0.082 _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 0.038 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.998 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.57 _reflns_shell.d_res_low 2.61 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all 588 _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 99.3 _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 1.46 _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 5.3 _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 0.69 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.50 _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 5NDI _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.570 _refine.ls_d_res_low 40.344 _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 20792 _refine.ls_number_reflns_R_free 1034 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.13 _refine.ls_percent_reflns_R_free 4.97 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1901 _refine.ls_R_factor_R_free 0.2380 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1876 _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 29.49 _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 0.52 _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 1704 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 1725 _refine_hist.d_res_high 2.570 _refine_hist.d_res_low 40.344 # 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' ? 0.007 ? 1916 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.244 ? 2980 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 10.459 ? 912 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.044 ? 392 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.007 ? 84 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.5699 2.7054 . . 132 2662 89.00 . . . 0.4694 . 0.4640 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.7054 2.8748 . . 154 2782 96.00 . . . 0.4307 . 0.4127 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.8748 3.0967 . . 166 2816 97.00 . . . 0.3304 . 0.2939 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0967 3.4082 . . 150 2872 97.00 . . . 0.3123 . 0.2158 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.4082 3.9011 . . 136 2835 97.00 . . . 0.2700 . 0.1794 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.9011 4.9135 . . 146 2895 98.00 . . . 0.1819 . 0.1482 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.9135 40.3491 . . 150 2896 99.00 . . . 0.1651 . 0.1276 . . . . . . . . . . # _struct.entry_id 5NDI _struct.title 'The structure of the E.coli guanidine II riboswitch P1 stem-loop' _struct.pdbx_descriptor ;RNA (5'-R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)-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 5NDI _struct_keywords.text 'guanidine II riboswitch, stem-loop, tetra loop, dimer, 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 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 2 ? I N N 2 ? J N N 4 ? 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 covale1 covale both ? A G 16 "O3'" ? ? ? 1_555 A CBV 17 P ? ? A G 16 A CBV 17 1_555 ? ? ? ? ? ? ? 1.600 ? covale2 covale one ? A CBV 17 "O3'" ? ? ? 1_555 A A 18 P ? ? A CBV 17 A A 18 1_555 ? ? ? ? ? ? ? 1.592 ? covale3 covale both ? B G 16 "O3'" ? ? ? 1_555 B CBV 17 P ? ? B G 16 B CBV 17 1_555 ? ? ? ? ? ? ? 1.607 ? covale4 covale one ? B CBV 17 "O3'" ? ? ? 1_555 B A 18 P ? ? B CBV 17 B A 18 1_555 ? ? ? ? ? ? ? 1.603 ? covale5 covale both ? C G 16 "O3'" ? ? ? 1_555 C CBV 17 P ? ? C G 16 C CBV 17 1_555 ? ? ? ? ? ? ? 1.606 ? covale6 covale one ? C CBV 17 "O3'" ? ? ? 1_555 C A 18 P ? ? C CBV 17 C A 18 1_555 ? ? ? ? ? ? ? 1.595 ? covale7 covale both ? D G 16 "O3'" ? ? ? 1_555 D CBV 17 P ? ? D G 16 D CBV 17 1_555 ? ? ? ? ? ? ? 1.610 ? covale8 covale one ? D CBV 17 "O3'" ? ? ? 1_555 D A 18 P ? ? D CBV 17 D A 18 1_555 ? ? ? ? ? ? ? 1.602 ? hydrog1 hydrog ? ? A U 1 N3 ? ? ? 1_555 A A 20 N1 ? ? A U 1 A A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A U 1 O4 ? ? ? 1_555 A A 20 N6 ? ? A U 1 A A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 19 N1 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 19 N6 ? ? A U 2 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 3 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 3 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 A CBV 17 N3 ? ? A G 4 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 A CBV 17 O2 ? ? A G 4 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 A CBV 17 N4 ? ? A G 4 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 5 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 5 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 5 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 15 N3 ? ? A A 6 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 15 O4 ? ? A A 6 A U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 8 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 8 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 8 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A A 9 N6 ? ? ? 1_555 B C 13 O2 ? ? A A 9 B C 13 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 11 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 11 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 11 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A C 13 O2 ? ? ? 1_555 B A 9 N6 ? ? A C 13 B A 9 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? hydrog29 hydrog ? ? B U 1 N3 ? ? ? 1_555 B A 20 N1 ? ? B U 1 B A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? B U 1 O4 ? ? ? 1_555 B A 20 N6 ? ? B U 1 B A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? B U 2 N3 ? ? ? 1_555 B A 19 N1 ? ? B U 2 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog32 hydrog ? ? B U 2 O4 ? ? ? 1_555 B A 19 N6 ? ? B U 2 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog33 hydrog ? ? B U 3 N3 ? ? ? 1_555 B A 18 N1 ? ? B U 3 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog34 hydrog ? ? B U 3 O4 ? ? ? 1_555 B A 18 N6 ? ? B U 3 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog35 hydrog ? ? B G 4 N1 ? ? ? 1_555 B CBV 17 N3 ? ? B G 4 B CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog36 hydrog ? ? B G 4 N2 ? ? ? 1_555 B CBV 17 O2 ? ? B G 4 B CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog37 hydrog ? ? B G 4 O6 ? ? ? 1_555 B CBV 17 N4 ? ? B G 4 B CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog38 hydrog ? ? B C 5 N3 ? ? ? 1_555 B G 16 N1 ? ? B C 5 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog39 hydrog ? ? B C 5 N4 ? ? ? 1_555 B G 16 O6 ? ? B C 5 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog40 hydrog ? ? B C 5 O2 ? ? ? 1_555 B G 16 N2 ? ? B C 5 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog41 hydrog ? ? B A 6 N1 ? ? ? 1_555 B U 15 N3 ? ? B A 6 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog42 hydrog ? ? B A 6 N6 ? ? ? 1_555 B U 15 O4 ? ? B A 6 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog43 hydrog ? ? B G 7 N1 ? ? ? 1_555 B C 14 N3 ? ? B G 7 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog44 hydrog ? ? B G 7 N2 ? ? ? 1_555 B C 14 O2 ? ? B G 7 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog45 hydrog ? ? B G 7 O6 ? ? ? 1_555 B C 14 N4 ? ? B G 7 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog46 hydrog ? ? B G 8 N1 ? ? ? 1_555 B C 13 N3 ? ? B G 8 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog47 hydrog ? ? B G 8 N2 ? ? ? 1_555 B C 13 O2 ? ? B G 8 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog48 hydrog ? ? B G 8 O6 ? ? ? 1_555 B C 13 N4 ? ? B G 8 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog49 hydrog ? ? C U 1 N3 ? ? ? 1_555 C A 20 N1 ? ? C U 1 C A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog50 hydrog ? ? C U 1 O4 ? ? ? 1_555 C A 20 N6 ? ? C U 1 C A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog51 hydrog ? ? C U 2 N3 ? ? ? 1_555 C A 19 N1 ? ? C U 2 C A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog52 hydrog ? ? C U 2 O4 ? ? ? 1_555 C A 19 N6 ? ? C U 2 C A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog53 hydrog ? ? C U 3 N3 ? ? ? 1_555 C A 18 N1 ? ? C U 3 C A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog54 hydrog ? ? C U 3 O4 ? ? ? 1_555 C A 18 N6 ? ? C U 3 C A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog55 hydrog ? ? C G 4 N1 ? ? ? 1_555 C CBV 17 N3 ? ? C G 4 C CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog56 hydrog ? ? C G 4 N2 ? ? ? 1_555 C CBV 17 O2 ? ? C G 4 C CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog57 hydrog ? ? C G 4 O6 ? ? ? 1_555 C CBV 17 N4 ? ? C G 4 C CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog58 hydrog ? ? C C 5 N3 ? ? ? 1_555 C G 16 N1 ? ? C C 5 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog59 hydrog ? ? C C 5 N4 ? ? ? 1_555 C G 16 O6 ? ? C C 5 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog60 hydrog ? ? C C 5 O2 ? ? ? 1_555 C G 16 N2 ? ? C C 5 C G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog61 hydrog ? ? C A 6 N1 ? ? ? 1_555 C U 15 N3 ? ? C A 6 C U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog62 hydrog ? ? C A 6 N6 ? ? ? 1_555 C U 15 O4 ? ? C A 6 C U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog63 hydrog ? ? C G 7 N1 ? ? ? 1_555 C C 14 N3 ? ? C G 7 C C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog64 hydrog ? ? C G 7 N2 ? ? ? 1_555 C C 14 O2 ? ? C G 7 C C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog65 hydrog ? ? C G 7 O6 ? ? ? 1_555 C C 14 N4 ? ? C G 7 C C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog66 hydrog ? ? C G 8 N1 ? ? ? 1_555 C C 13 N3 ? ? C G 8 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog67 hydrog ? ? C G 8 N2 ? ? ? 1_555 C C 13 O2 ? ? C G 8 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog68 hydrog ? ? C G 8 O6 ? ? ? 1_555 C C 13 N4 ? ? C G 8 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog69 hydrog ? ? C A 9 N6 ? ? ? 1_555 D C 13 O2 ? ? C A 9 D C 13 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? hydrog70 hydrog ? ? C C 10 N3 ? ? ? 1_555 D G 11 N1 ? ? C C 10 D G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog71 hydrog ? ? C C 10 N4 ? ? ? 1_555 D G 11 O6 ? ? C C 10 D G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog72 hydrog ? ? C C 10 O2 ? ? ? 1_555 D G 11 N2 ? ? C C 10 D G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog73 hydrog ? ? C G 11 N1 ? ? ? 1_555 D C 10 N3 ? ? C G 11 D C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog74 hydrog ? ? C G 11 N2 ? ? ? 1_555 D C 10 O2 ? ? C G 11 D C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog75 hydrog ? ? C G 11 O6 ? ? ? 1_555 D C 10 N4 ? ? C G 11 D C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog76 hydrog ? ? C C 13 O2 ? ? ? 1_555 D A 9 N6 ? ? C C 13 D A 9 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? hydrog77 hydrog ? ? D U 1 N3 ? ? ? 1_555 D A 20 N1 ? ? D U 1 D A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog78 hydrog ? ? D U 1 O4 ? ? ? 1_555 D A 20 N6 ? ? D U 1 D A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog79 hydrog ? ? D U 2 N3 ? ? ? 1_555 D A 19 N1 ? ? D U 2 D A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog80 hydrog ? ? D U 2 O4 ? ? ? 1_555 D A 19 N6 ? ? D U 2 D A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog81 hydrog ? ? D U 3 N3 ? ? ? 1_555 D A 18 N1 ? ? D U 3 D A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog82 hydrog ? ? D U 3 O4 ? ? ? 1_555 D A 18 N6 ? ? D U 3 D A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog83 hydrog ? ? D G 4 N1 ? ? ? 1_555 D CBV 17 N3 ? ? D G 4 D CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog84 hydrog ? ? D G 4 N2 ? ? ? 1_555 D CBV 17 O2 ? ? D G 4 D CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog85 hydrog ? ? D G 4 O6 ? ? ? 1_555 D CBV 17 N4 ? ? D G 4 D CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog86 hydrog ? ? D C 5 N3 ? ? ? 1_555 D G 16 N1 ? ? D C 5 D G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog87 hydrog ? ? D C 5 N4 ? ? ? 1_555 D G 16 O6 ? ? D C 5 D G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog88 hydrog ? ? D C 5 O2 ? ? ? 1_555 D G 16 N2 ? ? D C 5 D G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog89 hydrog ? ? D A 6 N1 ? ? ? 1_555 D U 15 N3 ? ? D A 6 D U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog90 hydrog ? ? D A 6 N6 ? ? ? 1_555 D U 15 O4 ? ? D A 6 D U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog91 hydrog ? ? D G 7 N1 ? ? ? 1_555 D C 14 N3 ? ? D G 7 D C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog92 hydrog ? ? D G 7 N2 ? ? ? 1_555 D C 14 O2 ? ? D G 7 D C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog93 hydrog ? ? D G 7 O6 ? ? ? 1_555 D C 14 N4 ? ? D G 7 D C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog94 hydrog ? ? D G 8 N1 ? ? ? 1_555 D C 13 N3 ? ? D G 8 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog95 hydrog ? ? D G 8 N2 ? ? ? 1_555 D C 13 O2 ? ? D G 8 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog96 hydrog ? ? D G 8 O6 ? ? ? 1_555 D C 13 N4 ? ? D G 8 D C 13 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 A GAI 101 ? 4 'binding site for residue GAI A 101' AC2 Software B GAI 101 ? 4 'binding site for residue GAI B 101' AC3 Software B NA 102 ? 1 'binding site for residue NA B 102' AC4 Software C GAI 101 ? 4 'binding site for residue GAI C 101' AC5 Software D GAI 101 ? 4 'binding site for residue GAI D 101' AC6 Software B G 16 ? 9 'binding site for Di-nucleotide G B 16 and CBV B 17' AC7 Software B CBV 17 ? 7 'binding site for Di-nucleotide CBV B 17 and A B 18' AC8 Software C G 16 ? 7 'binding site for Di-nucleotide G C 16 and CBV C 17' AC9 Software C CBV 17 ? 6 'binding site for Di-nucleotide CBV C 17 and A C 18' AD1 Software D G 16 ? 6 'binding site for Di-nucleotide G D 16 and CBV D 17' AD2 Software D CBV 17 ? 7 'binding site for Di-nucleotide CBV D 17 and A D 18' # 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 8 ? G A 8 . ? 1_555 ? 2 AC1 4 A A 9 ? A A 9 . ? 1_555 ? 3 AC1 4 C A 10 ? C A 10 . ? 1_555 ? 4 AC1 4 G A 11 ? G A 11 . ? 1_555 ? 5 AC2 4 G B 8 ? G B 8 . ? 1_555 ? 6 AC2 4 A B 9 ? A B 9 . ? 1_555 ? 7 AC2 4 C B 10 ? C B 10 . ? 1_555 ? 8 AC2 4 G B 11 ? G B 11 . ? 1_555 ? 9 AC3 1 G B 8 ? G B 8 . ? 1_555 ? 10 AC4 4 G C 8 ? G C 8 . ? 1_555 ? 11 AC4 4 A C 9 ? A C 9 . ? 1_555 ? 12 AC4 4 C C 10 ? C C 10 . ? 1_555 ? 13 AC4 4 G C 11 ? G C 11 . ? 1_555 ? 14 AC5 4 G D 8 ? G D 8 . ? 1_555 ? 15 AC5 4 A D 9 ? A D 9 . ? 1_555 ? 16 AC5 4 C D 10 ? C D 10 . ? 1_555 ? 17 AC5 4 G D 11 ? G D 11 . ? 1_555 ? 18 AC6 9 G A 7 ? G A 7 . ? 3_545 ? 19 AC6 9 G A 8 ? G A 8 . ? 3_545 ? 20 AC6 9 G B 4 ? G B 4 . ? 1_555 ? 21 AC6 9 C B 5 ? C B 5 . ? 1_555 ? 22 AC6 9 A B 6 ? A B 6 . ? 1_555 ? 23 AC6 9 U B 15 ? U B 15 . ? 1_555 ? 24 AC6 9 A B 18 ? A B 18 . ? 1_555 ? 25 AC6 9 HOH K . ? HOH B 202 . ? 1_555 ? 26 AC6 9 HOH K . ? HOH B 203 . ? 1_555 ? 27 AC7 7 G A 8 ? G A 8 . ? 3_545 ? 28 AC7 7 U B 3 ? U B 3 . ? 1_555 ? 29 AC7 7 G B 4 ? G B 4 . ? 1_555 ? 30 AC7 7 G B 16 ? G B 16 . ? 1_555 ? 31 AC7 7 A B 19 ? A B 19 . ? 1_555 ? 32 AC7 7 HOH K . ? HOH B 202 . ? 1_555 ? 33 AC7 7 HOH K . ? HOH B 203 . ? 1_555 ? 34 AC8 7 G C 4 ? G C 4 . ? 1_555 ? 35 AC8 7 C C 5 ? C C 5 . ? 1_555 ? 36 AC8 7 A C 6 ? A C 6 . ? 1_555 ? 37 AC8 7 U C 15 ? U C 15 . ? 1_555 ? 38 AC8 7 A C 18 ? A C 18 . ? 1_555 ? 39 AC8 7 G D 7 ? G D 7 . ? 4_566 ? 40 AC8 7 G D 8 ? G D 8 . ? 4_566 ? 41 AC9 6 U C 3 ? U C 3 . ? 1_555 ? 42 AC9 6 G C 4 ? G C 4 . ? 1_555 ? 43 AC9 6 C C 5 ? C C 5 . ? 1_555 ? 44 AC9 6 G C 16 ? G C 16 . ? 1_555 ? 45 AC9 6 A C 19 ? A C 19 . ? 1_555 ? 46 AC9 6 G D 8 ? G D 8 . ? 4_566 ? 47 AD1 6 G C 8 ? G C 8 . ? 4_466 ? 48 AD1 6 G D 4 ? G D 4 . ? 1_555 ? 49 AD1 6 C D 5 ? C D 5 . ? 1_555 ? 50 AD1 6 A D 6 ? A D 6 . ? 1_555 ? 51 AD1 6 U D 15 ? U D 15 . ? 1_555 ? 52 AD1 6 A D 18 ? A D 18 . ? 1_555 ? 53 AD2 7 U B 2 ? U B 2 . ? 1_465 ? 54 AD2 7 G C 8 ? G C 8 . ? 4_466 ? 55 AD2 7 U D 3 ? U D 3 . ? 1_555 ? 56 AD2 7 G D 4 ? G D 4 . ? 1_555 ? 57 AD2 7 C D 5 ? C D 5 . ? 1_555 ? 58 AD2 7 G D 16 ? G D 16 . ? 1_555 ? 59 AD2 7 A D 19 ? A D 19 . ? 1_555 ? # _atom_sites.entry_id 5NDI _atom_sites.fract_transf_matrix[1][1] 0.021063 _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] 0.020753 _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] 0.006533 _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 U 1 1 1 U U A . n A 1 2 U 2 2 2 U U 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 C 5 5 5 C C A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n A 1 8 G 8 8 8 G G A . n A 1 9 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A 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 U 15 15 15 U U A . n A 1 16 G 16 16 16 G G A . n A 1 17 CBV 17 17 17 CBV CBV A . n A 1 18 A 18 18 18 A A A . n A 1 19 A 19 19 19 A A A . n A 1 20 A 20 20 20 A A A . n B 1 1 U 1 1 1 U U B . n B 1 2 U 2 2 2 U U B . n B 1 3 U 3 3 3 U U B . n B 1 4 G 4 4 4 G G B . n B 1 5 C 5 5 5 C C B . n B 1 6 A 6 6 6 A A B . n B 1 7 G 7 7 7 G G B . n B 1 8 G 8 8 8 G G B . n B 1 9 A 9 9 9 A A B . n B 1 10 C 10 10 10 C C B . n B 1 11 G 11 11 11 G G B . n B 1 12 A 12 12 12 A A B . n B 1 13 C 13 13 13 C C B . n B 1 14 C 14 14 14 C C B . n B 1 15 U 15 15 15 U U B . n B 1 16 G 16 16 16 G G B . n B 1 17 CBV 17 17 17 CBV CBV B . n B 1 18 A 18 18 18 A A B . n B 1 19 A 19 19 19 A A B . n B 1 20 A 20 20 20 A A B . n C 1 1 U 1 1 1 U U C . n C 1 2 U 2 2 2 U U C . n C 1 3 U 3 3 3 U U C . n C 1 4 G 4 4 4 G G C . n C 1 5 C 5 5 5 C C C . n C 1 6 A 6 6 6 A A C . n C 1 7 G 7 7 7 G G C . n C 1 8 G 8 8 8 G G C . n C 1 9 A 9 9 9 A A C . n C 1 10 C 10 10 10 C C C . n C 1 11 G 11 11 11 G G C . n C 1 12 A 12 12 12 A A C . n C 1 13 C 13 13 13 C C C . n C 1 14 C 14 14 14 C C C . n C 1 15 U 15 15 15 U U C . n C 1 16 G 16 16 16 G G C . n C 1 17 CBV 17 17 17 CBV CBV C . n C 1 18 A 18 18 18 A A C . n C 1 19 A 19 19 19 A A C . n C 1 20 A 20 20 20 A A C . n D 1 1 U 1 1 1 U U D . n D 1 2 U 2 2 2 U U D . n D 1 3 U 3 3 3 U U D . n D 1 4 G 4 4 4 G G D . n D 1 5 C 5 5 5 C C D . n D 1 6 A 6 6 6 A A D . n D 1 7 G 7 7 7 G G D . n D 1 8 G 8 8 8 G G D . n D 1 9 A 9 9 9 A A D . n D 1 10 C 10 10 10 C C D . n D 1 11 G 11 11 11 G G D . n D 1 12 A 12 12 12 A A D . n D 1 13 C 13 13 13 C C D . n D 1 14 C 14 14 14 C C D . n D 1 15 U 15 15 15 U U D . n D 1 16 G 16 16 16 G G D . n D 1 17 CBV 17 17 17 CBV CBV D . n D 1 18 A 18 18 18 A A D . n D 1 19 A 19 19 19 A A D . n D 1 20 A 20 20 20 A A D . 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 E 2 GAI 1 101 3 GAI GAI A . F 2 GAI 1 101 2 GAI GAI B . G 3 NA 1 102 1 NA NA B . H 2 GAI 1 101 4 GAI GAI C . I 2 GAI 1 101 1 GAI GAI D . J 4 HOH 1 201 2 HOH HOH A . K 4 HOH 1 201 3 HOH HOH B . K 4 HOH 2 202 4 HOH HOH B . K 4 HOH 3 203 1 HOH HOH B . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 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,E,F,G,J,K 2 1 C,D,H,I # _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 2017-05-31 2 'Structure model' 1 1 2017-07-05 3 'Structure model' 1 2 2017-08-30 # _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' # 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 # 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' # 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 -3.7590 16.2206 48.6564 0.7336 0.5561 0.5211 -0.0085 -0.0885 -0.0831 1.6652 3.4965 3.8987 0.5659 1.7150 3.1383 0.4842 -0.1576 -0.1556 0.2167 -0.5557 0.3505 1.1403 -0.3240 0.0396 'X-RAY DIFFRACTION' 2 ? refined -0.4941 20.8495 48.0448 0.8500 0.5724 0.6231 -0.0587 -0.0636 -0.0517 2.7830 6.7420 2.2777 -2.3741 -0.3902 1.6542 0.2285 -0.2474 0.0364 -0.7059 -0.0692 0.1731 0.1306 -0.0501 -0.0883 'X-RAY DIFFRACTION' 3 ? refined 9.3794 -3.7099 47.5839 0.8000 0.6205 0.5988 0.0201 -0.1500 0.0264 0.9672 2.8796 2.3089 -0.8476 0.3177 -0.5698 -0.0339 -0.1494 0.1501 -0.1951 0.1713 -0.1107 -0.1501 0.2244 -0.2252 'X-RAY DIFFRACTION' 4 ? refined 6.3597 -8.2776 48.2317 0.8824 0.5924 0.6178 -0.0140 -0.0839 0.0557 2.7725 7.7067 1.5836 -3.1050 2.1483 -1.6550 -0.1649 -0.1535 0.0367 -0.5774 0.2529 0.4843 -0.2753 0.1103 -0.0755 'X-RAY DIFFRACTION' 5 ? refined 0.7263 19.3356 69.2243 0.8922 0.6966 0.5877 -0.0048 0.0868 -0.0017 1.0871 1.9065 1.0351 0.3446 0.5763 -0.9663 0.0948 0.0929 -0.2198 -0.0664 0.1210 0.3940 0.2740 0.0323 -0.1935 'X-RAY DIFFRACTION' 6 ? refined -10.9510 26.0396 78.4856 0.6547 1.0577 0.6893 0.0472 0.1095 -0.0183 1.2004 1.9843 3.9588 1.5454 0.5856 0.8227 -0.0185 -0.4464 0.0077 0.2586 -0.3934 0.4360 0.5703 0.2020 0.3343 'X-RAY DIFFRACTION' 7 ? refined -9.0872 27.4171 69.3864 0.6515 0.8438 0.6283 0.0535 0.0593 -0.0657 7.6646 4.3694 5.7430 -0.9084 -2.1748 -4.2016 -0.0026 0.0266 -0.0138 -0.6717 -0.1462 -0.1892 0.5805 0.5606 0.0119 'X-RAY DIFFRACTION' 8 ? refined 6.4773 23.3284 74.3290 0.7292 0.9813 0.6533 0.1301 0.0759 0.0743 1.9310 3.4930 3.1792 -0.0449 -0.2260 3.1039 0.3301 -0.3377 0.5669 -0.1386 -0.3611 -0.6486 0.9747 0.1786 0.0061 'X-RAY DIFFRACTION' 9 ? refined -32.0088 29.4583 61.6777 0.5165 0.8710 0.4946 0.1230 -0.0161 0.0661 5.8066 7.1318 5.4963 3.9510 -1.4576 -0.5402 -0.0339 -0.6875 -0.0891 0.4965 -0.4288 -0.7456 0.4829 1.3097 0.6648 'X-RAY DIFFRACTION' 10 ? refined -21.0787 33.2525 69.0415 0.5850 0.9759 0.6253 -0.0351 -0.0822 -0.0879 7.2306 4.0433 3.1719 1.3113 0.7685 -2.5660 -0.1756 0.1643 0.1219 -0.3913 0.2641 0.3167 0.1802 0.2759 -0.1537 'X-RAY DIFFRACTION' 11 ? refined -37.4088 34.1039 66.6342 0.5239 0.8428 0.5981 -0.0602 0.0369 -0.0689 4.2255 3.4406 6.4561 1.0843 5.0533 0.1304 -0.0500 -1.1937 0.3627 -0.1308 -0.7007 0.1221 -0.2359 -0.3973 0.7394 # 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 20 ) ; 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? ;chain 'B' and (resid 1 through 10 ) ; 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? ;chain 'B' and (resid 11 through 20 ) ; 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? ;chain 'C' and (resid 1 through 5 ) ; 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? ;chain 'C' and (resid 6 through 10 ) ; 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? ;chain 'C' and (resid 11 through 15 ) ; 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? ;chain 'C' and (resid 16 through 20 ) ; 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? ;chain 'D' and (resid 1 through 5 ) ; 'X-RAY DIFFRACTION' 10 10 ? ? ? ? ? ? ? ? ? ;chain 'D' and (resid 6 through 15 ) ; 'X-RAY DIFFRACTION' 11 11 ? ? ? ? ? ? ? ? ? ;chain 'D' and (resid 16 through 20 ) ; # 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 G 16 ? ? O2P A CBV 17 ? ? 0.47 2 1 "O3'" C G 16 ? ? O3P C CBV 17 ? ? 0.51 3 1 "O3'" D G 16 ? ? O3P D CBV 17 ? ? 0.68 4 1 "O3'" B G 16 ? ? O2P B CBV 17 ? ? 0.69 5 1 "HO3'" A CBV 17 ? ? P A A 18 ? ? 0.77 6 1 "HO3'" B CBV 17 ? ? P B A 18 ? ? 0.78 7 1 "HO3'" C CBV 17 ? ? P C A 18 ? ? 0.78 8 1 "HO3'" D CBV 17 ? ? P D A 18 ? ? 0.82 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5NDI 'double helix' 5NDI 'a-form double helix' 5NDI 'hairpin loop' 5NDI '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 U 1 1_555 A A 20 1_555 -0.096 -0.094 0.574 -3.327 -16.152 -1.088 1 A_U1:A20_A A 1 ? A 20 ? 20 1 1 A U 2 1_555 A A 19 1_555 -0.204 -0.158 0.421 -2.250 -14.316 0.868 2 A_U2:A19_A A 2 ? A 19 ? 20 1 1 A U 3 1_555 A A 18 1_555 -0.027 -0.152 0.136 -1.158 -11.139 0.361 3 A_U3:A18_A A 3 ? A 18 ? 20 1 1 A G 4 1_555 A CBV 17 1_555 -0.067 -0.038 -0.039 -1.873 -9.714 2.446 4 A_G4:CBV17_A A 4 ? A 17 ? 19 1 1 A C 5 1_555 A G 16 1_555 0.129 -0.159 0.238 2.418 -6.520 1.222 5 A_C5:G16_A A 5 ? A 16 ? 19 1 1 A A 6 1_555 A U 15 1_555 0.052 -0.186 0.091 1.885 -4.333 -0.512 6 A_A6:U15_A A 6 ? A 15 ? 20 1 1 A G 7 1_555 A C 14 1_555 -0.171 -0.271 0.046 2.364 -3.427 -0.047 7 A_G7:C14_A A 7 ? A 14 ? 19 1 1 A G 8 1_555 A C 13 1_555 -0.071 -0.116 -0.193 2.945 -0.392 1.398 8 A_G8:C13_A A 8 ? A 13 ? 19 1 1 B C 10 1_555 A G 11 1_555 0.124 -0.185 0.033 9.864 -12.478 -1.029 9 B_C10:G11_A B 10 ? A 11 ? 19 1 1 B G 11 1_555 A C 10 1_555 -0.117 -0.159 0.269 -5.479 -15.555 0.947 10 B_G11:C10_A B 11 ? A 10 ? 19 1 1 B C 13 1_555 B G 8 1_555 0.093 -0.182 -0.081 2.680 -1.412 -2.332 11 B_C13:G8_B B 13 ? B 8 ? 19 1 1 B C 14 1_555 B G 7 1_555 0.139 -0.163 0.034 2.192 -3.651 2.453 12 B_C14:G7_B B 14 ? B 7 ? 19 1 1 B U 15 1_555 B A 6 1_555 -0.074 -0.239 0.197 1.490 -4.043 1.986 13 B_U15:A6_B B 15 ? B 6 ? 20 1 1 B G 16 1_555 B C 5 1_555 -0.155 -0.193 0.211 -1.682 -9.463 -0.149 14 B_G16:C5_B B 16 ? B 5 ? 19 1 1 B CBV 17 1_555 B G 4 1_555 -0.177 -0.011 0.035 -2.203 -11.118 -0.268 15 B_CBV17:G4_B B 17 ? B 4 ? 19 1 1 B A 18 1_555 B U 3 1_555 0.108 -0.082 -0.032 -2.467 -2.106 -2.751 16 B_A18:U3_B B 18 ? B 3 ? 20 1 1 B A 19 1_555 B U 2 1_555 0.120 -0.099 0.389 8.143 -3.765 3.715 17 B_A19:U2_B B 19 ? B 2 ? 20 1 1 B A 20 1_555 B U 1 1_555 0.097 -0.114 0.318 8.748 -15.271 1.931 18 B_A20:U1_B B 20 ? B 1 ? 20 1 1 C U 1 1_555 C A 20 1_555 -0.162 -0.188 0.200 -4.611 -9.842 -4.974 19 C_U1:A20_C C 1 ? C 20 ? 20 1 1 C U 2 1_555 C A 19 1_555 -0.167 -0.151 0.151 -6.241 -6.488 -0.301 20 C_U2:A19_C C 2 ? C 19 ? 20 1 1 C U 3 1_555 C A 18 1_555 -0.094 -0.181 0.326 -3.274 -6.626 -1.027 21 C_U3:A18_C C 3 ? C 18 ? 20 1 1 C G 4 1_555 C CBV 17 1_555 0.119 -0.009 -0.011 -2.954 -10.288 3.591 22 C_G4:CBV17_C C 4 ? C 17 ? 19 1 1 C C 5 1_555 C G 16 1_555 0.128 -0.111 0.225 -1.217 -7.998 0.628 23 C_C5:G16_C C 5 ? C 16 ? 19 1 1 C A 6 1_555 C U 15 1_555 0.085 -0.145 0.070 -0.488 -1.949 1.404 24 C_A6:U15_C C 6 ? C 15 ? 20 1 1 C G 7 1_555 C C 14 1_555 -0.112 -0.204 -0.036 -2.666 -3.540 1.110 25 C_G7:C14_C C 7 ? C 14 ? 19 1 1 C G 8 1_555 C C 13 1_555 -0.036 -0.118 -0.185 -3.002 -2.061 -0.424 26 C_G8:C13_C C 8 ? C 13 ? 19 1 1 D C 10 1_555 C G 11 1_555 0.184 -0.165 0.073 7.719 -14.226 1.032 27 D_C10:G11_C D 10 ? C 11 ? 19 1 1 D G 11 1_555 C C 10 1_555 -0.187 -0.130 0.118 -7.352 -14.095 -0.383 28 D_G11:C10_C D 11 ? C 10 ? 19 1 1 D C 13 1_555 D G 8 1_555 0.149 -0.141 -0.259 -2.070 0.651 0.422 29 D_C13:G8_D D 13 ? D 8 ? 19 1 1 D C 14 1_555 D G 7 1_555 0.205 -0.187 -0.017 -2.860 -4.934 1.020 30 D_C14:G7_D D 14 ? D 7 ? 19 1 1 D U 15 1_555 D A 6 1_555 -0.010 -0.051 0.096 1.175 -5.224 2.864 31 D_U15:A6_D D 15 ? D 6 ? 20 1 1 D G 16 1_555 D C 5 1_555 -0.177 -0.154 0.287 4.731 -9.483 1.741 32 D_G16:C5_D D 16 ? D 5 ? 19 1 1 D CBV 17 1_555 D G 4 1_555 -0.185 0.000 0.078 3.636 -13.546 1.982 33 D_CBV17:G4_D D 17 ? D 4 ? 19 1 1 D A 18 1_555 D U 3 1_555 -0.114 -0.023 0.054 -2.065 -4.531 0.736 34 D_A18:U3_D D 18 ? D 3 ? 20 1 1 D A 19 1_555 D U 2 1_555 0.031 -0.102 0.074 3.651 -10.506 1.502 35 D_A19:U2_D D 19 ? D 2 ? 20 1 1 D A 20 1_555 D U 1 1_555 0.057 -0.119 0.348 -1.355 -13.419 0.338 36 D_A20:U1_D D 20 ? D 1 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A U 1 1_555 A A 20 1_555 A U 2 1_555 A A 19 1_555 -0.088 -1.331 3.032 -3.145 5.305 35.541 -2.827 -0.259 2.808 8.611 5.104 36.055 1 AA_U1U2:A19A20_AA A 1 ? A 20 ? A 2 ? A 19 ? 1 A U 2 1_555 A A 19 1_555 A U 3 1_555 A A 18 1_555 -0.131 -1.228 3.114 -0.149 4.933 32.695 -2.931 0.208 2.903 8.701 0.262 33.055 2 AA_U2U3:A18A19_AA A 2 ? A 19 ? A 3 ? A 18 ? 1 A U 3 1_555 A A 18 1_555 A G 4 1_555 A CBV 17 1_555 -0.142 -1.311 3.153 0.595 10.299 31.405 -3.885 0.341 2.602 18.414 -1.063 33.015 3 AA_U3G4:CBV17A18_AA A 3 ? A 18 ? A 4 ? A 17 ? 1 A G 4 1_555 A CBV 17 1_555 A C 5 1_555 A G 16 1_555 0.180 -1.376 3.121 -2.944 4.827 34.628 -2.952 -0.706 2.885 8.043 4.906 35.072 4 AA_G4C5:G16CBV17_AA A 4 ? A 17 ? A 5 ? A 16 ? 1 A C 5 1_555 A G 16 1_555 A A 6 1_555 A U 15 1_555 -0.401 -1.762 3.061 -0.428 13.309 29.951 -5.034 0.651 2.113 24.298 0.781 32.716 5 AA_C5A6:U15G16_AA A 5 ? A 16 ? A 6 ? A 15 ? 1 A A 6 1_555 A U 15 1_555 A G 7 1_555 A C 14 1_555 0.253 -1.669 3.142 0.635 7.981 30.116 -4.477 -0.362 2.628 15.029 -1.195 31.139 6 AA_A6G7:C14U15_AA A 6 ? A 15 ? A 7 ? A 14 ? 1 A G 7 1_555 A C 14 1_555 A G 8 1_555 A C 13 1_555 0.519 -1.817 3.221 3.308 6.712 29.716 -4.678 -0.372 2.793 12.833 -6.325 30.624 7 AA_G7G8:C13C14_AA A 7 ? A 14 ? A 8 ? A 13 ? 1 A G 8 1_555 A C 13 1_555 B C 10 1_555 A G 11 1_555 -3.823 0.035 3.467 2.283 -3.058 112.823 0.058 2.322 3.415 -1.835 -1.370 112.865 8 AB_G8C10:G11C13_AA A 8 ? A 13 ? B 10 ? A 11 ? 1 B C 10 1_555 A G 11 1_555 B G 11 1_555 A C 10 1_555 0.325 -1.689 3.643 -0.146 7.234 35.337 -3.821 -0.547 3.245 11.765 0.237 36.047 9 BB_C10G11:C10G11_AA B 10 ? A 11 ? B 11 ? A 10 ? 1 B G 11 1_555 A C 10 1_555 B C 13 1_555 B G 8 1_555 3.866 0.121 3.314 -0.010 -0.956 113.606 0.083 -2.310 3.313 -0.571 0.006 113.608 10 BB_G11C13:G8C10_BA B 11 ? A 10 ? B 13 ? B 8 ? 1 B C 13 1_555 B G 8 1_555 B C 14 1_555 B G 7 1_555 -0.233 -1.891 3.172 -3.278 4.257 29.765 -4.431 -0.173 2.889 8.202 6.316 30.235 11 BB_C13C14:G7G8_BB B 13 ? B 8 ? B 14 ? B 7 ? 1 B C 14 1_555 B G 7 1_555 B U 15 1_555 B A 6 1_555 -0.303 -1.567 3.179 -0.764 6.350 32.057 -3.806 0.416 2.831 11.357 1.366 32.673 12 BB_C14U15:A6G7_BB B 14 ? B 7 ? B 15 ? B 6 ? 1 B U 15 1_555 B A 6 1_555 B G 16 1_555 B C 5 1_555 0.217 -1.624 3.060 0.902 11.091 31.246 -4.447 -0.251 2.367 19.821 -1.612 33.121 13 BB_U15G16:C5A6_BB B 15 ? B 6 ? B 16 ? B 5 ? 1 B G 16 1_555 B C 5 1_555 B CBV 17 1_555 B G 4 1_555 -0.264 -1.706 3.263 1.512 4.349 33.988 -3.552 0.676 3.014 7.397 -2.573 34.289 14 BB_G16CBV17:G4C5_BB B 16 ? B 5 ? B 17 ? B 4 ? 1 B CBV 17 1_555 B G 4 1_555 B A 18 1_555 B U 3 1_555 -0.235 -1.521 3.174 -0.827 12.318 32.034 -4.305 0.283 2.445 21.355 1.434 34.273 15 BB_CBV17A18:U3G4_BB B 17 ? B 4 ? B 18 ? B 3 ? 1 B A 18 1_555 B U 3 1_555 B A 19 1_555 B U 2 1_555 0.058 -0.968 3.072 -0.917 6.983 31.899 -2.823 -0.247 2.800 12.516 1.644 32.648 16 BB_A18A19:U2U3_BB B 18 ? B 3 ? B 19 ? B 2 ? 1 B A 19 1_555 B U 2 1_555 B A 20 1_555 B U 1 1_555 0.460 -0.846 3.209 3.390 14.828 34.741 -3.100 -0.299 2.674 23.490 -5.371 37.831 17 BB_A19A20:U1U2_BB B 19 ? B 2 ? B 20 ? B 1 ? 1 C U 1 1_555 C A 20 1_555 C U 2 1_555 C A 19 1_555 -0.329 -1.363 3.142 -1.275 10.845 34.326 -3.602 0.370 2.616 17.826 2.096 35.971 18 CC_U1U2:A19A20_CC C 1 ? C 20 ? C 2 ? C 19 ? 1 C U 2 1_555 C A 19 1_555 C U 3 1_555 C A 18 1_555 0.227 -1.132 3.143 -0.309 7.784 32.610 -3.145 -0.441 2.803 13.622 0.540 33.503 19 CC_U2U3:A18A19_CC C 2 ? C 19 ? C 3 ? C 18 ? 1 C U 3 1_555 C A 18 1_555 C G 4 1_555 C CBV 17 1_555 0.626 -1.338 2.997 3.779 16.230 32.441 -4.039 -0.562 2.165 26.948 -6.275 36.368 20 CC_U3G4:CBV17A18_CC C 3 ? C 18 ? C 4 ? C 17 ? 1 C G 4 1_555 C CBV 17 1_555 C C 5 1_555 C G 16 1_555 0.197 -1.737 3.157 -1.821 3.285 32.844 -3.573 -0.635 2.959 5.786 3.207 33.053 21 CC_G4C5:G16CBV17_CC C 4 ? C 17 ? C 5 ? C 16 ? 1 C C 5 1_555 C G 16 1_555 C A 6 1_555 C U 15 1_555 -0.193 -1.745 3.037 -0.292 8.714 30.167 -4.630 0.310 2.451 16.319 0.548 31.374 22 CC_C5A6:U15G16_CC C 5 ? C 16 ? C 6 ? C 15 ? 1 C A 6 1_555 C U 15 1_555 C G 7 1_555 C C 14 1_555 0.331 -1.714 3.224 0.654 7.473 31.292 -4.334 -0.488 2.757 13.610 -1.191 32.157 23 CC_A6G7:C14U15_CC C 6 ? C 15 ? C 7 ? C 14 ? 1 C G 7 1_555 C C 14 1_555 C G 8 1_555 C C 13 1_555 0.239 -1.913 3.183 3.234 3.706 31.114 -4.177 0.129 2.950 6.855 -5.983 31.491 24 CC_G7G8:C13C14_CC C 7 ? C 14 ? C 8 ? C 13 ? 1 C G 8 1_555 C C 13 1_555 D C 10 1_555 C G 11 1_555 -3.691 0.336 3.326 0.552 -2.277 111.675 0.230 2.236 3.309 -1.376 -0.334 111.691 25 CD_G8C10:G11C13_CC C 8 ? C 13 ? D 10 ? C 11 ? 1 D C 10 1_555 C G 11 1_555 D G 11 1_555 C C 10 1_555 -0.101 -1.589 3.636 0.071 7.085 35.407 -3.633 0.174 3.267 11.507 -0.115 36.087 26 DD_C10G11:C10G11_CC D 10 ? C 11 ? D 11 ? C 10 ? 1 D G 11 1_555 C C 10 1_555 D C 13 1_555 D G 8 1_555 3.810 0.107 3.443 1.277 -2.799 112.095 0.099 -2.280 3.469 -1.687 -0.770 112.123 27 DD_G11C13:G8C10_DC D 11 ? C 10 ? D 13 ? D 8 ? 1 D C 13 1_555 D G 8 1_555 D C 14 1_555 D G 7 1_555 -0.570 -1.813 3.243 -2.929 6.222 29.988 -4.571 0.533 2.859 11.829 5.569 30.749 28 DD_C13C14:G7G8_DD D 13 ? D 8 ? D 14 ? D 7 ? 1 D C 14 1_555 D G 7 1_555 D U 15 1_555 D A 6 1_555 0.067 -1.689 3.072 -0.947 7.358 29.825 -4.458 -0.290 2.587 14.025 1.804 30.713 29 DD_C14U15:A6G7_DD D 14 ? D 7 ? D 15 ? D 6 ? 1 D U 15 1_555 D A 6 1_555 D G 16 1_555 D C 5 1_555 0.160 -1.680 3.006 0.783 9.788 29.112 -4.790 -0.173 2.335 18.810 -1.505 30.690 30 DD_U15G16:C5A6_DD D 15 ? D 6 ? D 16 ? D 5 ? 1 D G 16 1_555 D C 5 1_555 D CBV 17 1_555 D G 4 1_555 -0.048 -1.643 3.213 1.146 4.412 32.948 -3.572 0.266 2.971 7.733 -2.008 33.254 31 DD_G16CBV17:G4C5_DD D 16 ? D 5 ? D 17 ? D 4 ? 1 D CBV 17 1_555 D G 4 1_555 D A 18 1_555 D U 3 1_555 -0.352 -1.619 3.230 0.533 10.446 33.919 -4.064 0.650 2.627 17.398 -0.888 35.450 32 DD_CBV17A18:U3G4_DD D 17 ? D 4 ? D 18 ? D 3 ? 1 D A 18 1_555 D U 3 1_555 D A 19 1_555 D U 2 1_555 0.753 -1.783 3.055 3.074 9.462 27.839 -5.228 -0.916 2.400 18.917 -6.146 29.530 33 DD_A18A19:U2U3_DD D 18 ? D 3 ? D 19 ? D 2 ? 1 D A 19 1_555 D U 2 1_555 D A 20 1_555 D U 1 1_555 0.205 -1.527 3.117 0.410 7.052 35.924 -3.315 -0.276 2.780 11.298 -0.656 36.589 34 DD_A19A20:U1U2_DD D 19 ? D 2 ? D 20 ? D 1 ? # _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 GUANIDINE GAI 3 'SODIUM ION' NA 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 ? #