data_5JEV # _entry.id 5JEV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5JEV WWPDB D_1000220377 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5JEV _pdbx_database_status.recvd_initial_deposition_date 2016-04-19 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _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 'Hall, J.P.' 1 'Cardin, C.J.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 44 _citation.language ? _citation.page_first 9472 _citation.page_last 9482 _citation.title ;Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes. ; _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkw753 _citation.pdbx_database_id_PubMed 27599841 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hall, J.P.' 1 primary 'Keane, P.M.' 2 primary 'Beer, H.' 3 primary 'Buchner, K.' 4 primary 'Winter, G.' 5 primary 'Sorensen, T.L.' 6 primary 'Cardin, D.J.' 7 primary 'Brazier, J.A.' 8 primary 'Cardin, C.J.' 9 # _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 5JEV _cell.details ? _cell.formula_units_Z ? _cell.length_a 48.720 _cell.length_a_esd ? _cell.length_b 48.720 _cell.length_b_esd ? _cell.length_c 29.960 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JEV _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3') ; 3045.992 1 ? ? ? ? 2 non-polymer syn 'Delta-Ru(phen)2(dppz) complex' 743.779 2 ? ? ? ? 3 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 1 ? ? ? ? 4 water nat water 18.015 67 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DT)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TCGGCGCCGA _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 DT n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DA 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 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5JEV _struct_ref.pdbx_db_accession 5JEV _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 5JEV _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5JEV _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _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 10 # 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 0TN non-polymer . 'Delta-Ru(phen)2(dppz) complex' ? 'C42 H26 N8 Ru' 743.779 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 # _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 5JEV _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.92 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 57.85 _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 5.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;1uL 2mM d(TCGGCGCCGA), 1uL 2mM del-[Ru(phen)2(dppz)]2+, 6uL of a solution containing 10% (V/V) 2-methyl-2,4-pentanediol, 40mM Na-cacodylate, 20mM Cobalt hexammine, 12mM NaCl and 80mM KCl. ; _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 2012-12-14 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'dual Si(111)' _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 0.8266 _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 I02' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.8266 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5JEV _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 0.99 _reflns.d_resolution_low 22.61 _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 19226 _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 -3 _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 94.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.5 _reflns.pdbx_Rmerge_I_obs 0.031 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 19.9 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.00 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 0.99 _reflns_shell.d_res_low 1.02 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.9 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 92.2 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.833 _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 6.7 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _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 5JEV _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 0.990 _refine.ls_d_res_low 18.901 _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 19198 _refine.ls_number_reflns_R_free 1804 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 90.03 _refine.ls_percent_reflns_R_free 5.22 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1242 _refine.ls_R_factor_R_free 0.1410 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1233 _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 THROUGHOUT _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 12.52 _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 0.05 _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 202 _refine_hist.pdbx_number_atoms_ligand 109 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 378 _refine_hist.d_res_high 0.990 _refine_hist.d_res_low 18.901 # 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' ? 0.013 ? 475 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 2.325 ? 761 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 27.801 ? 158 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.076 ? 58 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.021 ? 21 ? 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' 0.9900 1.0168 . . 135 2545 91.00 . . . 0.2531 . 0.2690 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0168 1.0467 . . 159 2498 90.00 . . . 0.2229 . 0.2306 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0467 1.0805 . . 158 2499 90.00 . . . 0.1879 . 0.1866 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0805 1.1191 . . 136 2556 91.00 . . . 0.1765 . 0.1596 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.1191 1.1639 . . 163 2512 91.00 . . . 0.1396 . 0.1289 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.1639 1.2168 . . 148 2572 91.00 . . . 0.1560 . 0.1124 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2168 1.2810 . . 128 2526 90.00 . . . 0.1135 . 0.0958 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2810 1.3612 . . 164 2532 91.00 . . . 0.1074 . 0.0922 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.3612 1.4663 . . 120 2568 92.00 . . . 0.1040 . 0.0859 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.4663 1.6138 . . 121 2555 91.00 . . . 0.0998 . 0.0819 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.6138 1.8471 . . 130 2529 90.00 . . . 0.1237 . 0.0917 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.8471 2.3265 . . 115 2484 88.00 . . . 0.1410 . 0.1289 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.3265 18.9042 . . 127 2376 85.00 . . . 0.1533 . 0.1420 . . . . . . . . . . # _struct.entry_id 5JEV _struct.title 'del-[Ru(phen)2(dppz]2+ bound to d(TCGGCGCCGA) with Cobalt hexammine' _struct.pdbx_descriptor ;DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*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 5JEV _struct_keywords.text 'DNA, Ruthenium, cross-linking, DNA probe' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? D NCO . CO ? ? ? 1_555 E HOH . O ? ? A NCO 103 A HOH 202 1_555 ? ? ? ? ? ? ? 2.486 ? metalc2 metalc ? ? D NCO . CO ? ? ? 1_555 E HOH . O ? ? A NCO 103 A HOH 201 1_555 ? ? ? ? ? ? ? 2.419 ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 A ? A DC 2 A DG 9 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 A ? A DC 2 A DG 9 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 A ? A DC 2 A DG 9 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DA 10 N1 A ? A DG 3 A DA 10 8_664 ? ? ? ? ? ? TYPE_10_PAIR ? ? hydrog8 hydrog ? ? A DG 3 N3 ? ? ? 1_555 A DA 10 N6 A ? A DG 3 A DA 10 8_664 ? ? ? ? ? ? TYPE_10_PAIR ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 A ? A DG 4 A DC 7 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 A ? A DG 4 A DC 7 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 A ? A DG 4 A DC 7 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 6 N1 A ? A DC 5 A DG 6 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 6 O6 A ? A DC 5 A DG 6 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 6 N2 A ? A DC 5 A DG 6 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DG 6 N1 A ? ? 1_555 A DC 5 N3 ? ? A DG 6 A DC 5 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DG 6 N2 A ? ? 1_555 A DC 5 O2 ? ? A DG 6 A DC 5 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DG 6 O6 A ? ? 1_555 A DC 5 N4 ? ? A DG 6 A DC 5 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 7 N3 A ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 7 N4 A ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 7 O2 A ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DG 9 N1 A ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A DG 9 N2 A ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A DG 9 O6 A ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 8_664 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A DA 10 N1 A ? ? 1_555 A DG 3 N2 ? ? A DA 10 A DG 3 8_664 ? ? ? ? ? ? TYPE_10_PAIR ? ? hydrog28 hydrog ? ? A DA 10 N6 A ? ? 1_555 A DG 3 N3 ? ? A DA 10 A DG 3 8_664 ? ? ? ? ? ? TYPE_10_PAIR ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A 0TN 101 ? 6 'binding site for residue 0TN A 101' AC2 Software A 0TN 102 ? 8 'binding site for residue 0TN A 102' AC3 Software A NCO 103 ? 9 'binding site for residue NCO A 103' # 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 6 DT A 1 ? DT A 1 . ? 3_655 ? 2 AC1 6 DT A 1 ? DT A 1 . ? 2_675 ? 3 AC1 6 DC A 2 ? DC A 2 . ? 1_555 ? 4 AC1 6 DG A 3 ? DG A 3 . ? 1_555 ? 5 AC1 6 DG A 9 ? DG A 9 . ? 8_664 ? 6 AC1 6 DA A 10 ? DA A 10 . ? 8_664 ? 7 AC2 8 DG A 3 ? DG A 3 . ? 1_555 ? 8 AC2 8 DG A 4 ? DG A 4 . ? 1_555 ? 9 AC2 8 DC A 7 ? DC A 7 . ? 2_575 ? 10 AC2 8 DC A 7 ? DC A 7 . ? 8_664 ? 11 AC2 8 DC A 8 ? DC A 8 . ? 2_575 ? 12 AC2 8 DC A 8 ? DC A 8 . ? 8_664 ? 13 AC2 8 DG A 9 ? DG A 9 . ? 8_664 ? 14 AC2 8 DA A 10 ? DA A 10 . ? 8_664 ? 15 AC3 9 DC A 2 ? DC A 2 . ? 1_555 ? 16 AC3 9 DG A 3 ? DG A 3 . ? 1_555 ? 17 AC3 9 DG A 4 ? DG A 4 . ? 1_555 ? 18 AC3 9 DC A 5 ? DC A 5 . ? 8_664 ? 19 AC3 9 DG A 6 ? DG A 6 . ? 8_664 ? 20 AC3 9 DC A 7 ? DC A 7 . ? 8_664 ? 21 AC3 9 HOH E . ? HOH A 201 . ? 1_555 ? 22 AC3 9 HOH E . ? HOH A 202 . ? 1_555 ? 23 AC3 9 HOH E . ? HOH A 207 . ? 8_664 ? # _atom_sites.entry_id 5JEV _atom_sites.fract_transf_matrix[1][1] 0.020525 _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] 0.020525 _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] 0.033378 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CO H N O P RU # 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 DT 1 1 1 DT DT A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DA 10 10 10 DA DA 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 0TN 1 101 2 0TN 0TN A . C 2 0TN 1 102 3 0TN 0TN A . D 3 NCO 1 103 1 NCO NCO A . E 4 HOH 1 201 97 HOH HOH A . E 4 HOH 2 202 99 HOH HOH A . E 4 HOH 3 203 94 HOH HOH A . E 4 HOH 4 204 60 HOH HOH A . E 4 HOH 5 205 86 HOH HOH A . E 4 HOH 6 206 30 HOH HOH A . E 4 HOH 7 207 76 HOH HOH A . E 4 HOH 8 208 27 HOH HOH A . E 4 HOH 9 209 19 HOH HOH A . E 4 HOH 10 210 6 HOH HOH A . E 4 HOH 11 211 57 HOH HOH A . E 4 HOH 12 212 35 HOH HOH A . E 4 HOH 13 213 13 HOH HOH A . E 4 HOH 14 214 16 HOH HOH A . E 4 HOH 15 215 37 HOH HOH A . E 4 HOH 16 216 12 HOH HOH A . E 4 HOH 17 217 79 HOH HOH A . E 4 HOH 18 218 74 HOH HOH A . E 4 HOH 19 219 38 HOH HOH A . E 4 HOH 20 220 78 HOH HOH A . E 4 HOH 21 221 84 HOH HOH A . E 4 HOH 22 222 5 HOH HOH A . E 4 HOH 23 223 17 HOH HOH A . E 4 HOH 24 224 100 HOH HOH A . E 4 HOH 25 225 43 HOH HOH A . E 4 HOH 26 226 66 HOH HOH A . E 4 HOH 27 227 18 HOH HOH A . E 4 HOH 28 228 41 HOH HOH A . E 4 HOH 29 229 64 HOH HOH A . E 4 HOH 30 230 15 HOH HOH A . E 4 HOH 31 231 2 HOH HOH A . E 4 HOH 32 232 22 HOH HOH A . E 4 HOH 33 233 67 HOH HOH A . E 4 HOH 34 234 33 HOH HOH A . E 4 HOH 35 235 103 HOH HOH A . E 4 HOH 36 236 24 HOH HOH A . E 4 HOH 37 237 14 HOH HOH A . E 4 HOH 38 238 96 HOH HOH A . E 4 HOH 39 239 36 HOH HOH A . E 4 HOH 40 240 92 HOH HOH A . E 4 HOH 41 241 20 HOH HOH A . E 4 HOH 42 242 101 HOH HOH A . E 4 HOH 43 243 9 HOH HOH A . E 4 HOH 44 244 10 HOH HOH A . E 4 HOH 45 245 7 HOH HOH A . E 4 HOH 46 246 87 HOH HOH A . E 4 HOH 47 247 21 HOH HOH A . E 4 HOH 48 248 73 HOH HOH A . E 4 HOH 49 249 95 HOH HOH A . E 4 HOH 50 250 61 HOH HOH A . E 4 HOH 51 251 3 HOH HOH A . E 4 HOH 52 252 42 HOH HOH A . E 4 HOH 53 253 4 HOH HOH A . E 4 HOH 54 254 28 HOH HOH A . E 4 HOH 55 255 102 HOH HOH A . E 4 HOH 56 256 81 HOH HOH A . E 4 HOH 57 257 56 HOH HOH A . E 4 HOH 58 258 68 HOH HOH A . E 4 HOH 59 259 91 HOH HOH A . E 4 HOH 60 260 85 HOH HOH A . E 4 HOH 61 261 65 HOH HOH A . E 4 HOH 62 262 93 HOH HOH A . E 4 HOH 63 263 55 HOH HOH A . E 4 HOH 64 264 8 HOH HOH A . E 4 HOH 65 265 90 HOH HOH A . E 4 HOH 66 266 89 HOH HOH A . E 4 HOH 67 267 88 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 1 2 A,B,C,D,E # 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' 8_664 -y+1,-x+1,-z-1/2 0.0000000000 -1.0000000000 0.0000000000 48.7200000000 -1.0000000000 0.0000000000 0.0000000000 48.7200000000 0.0000000000 0.0000000000 -1.0000000000 -14.9800000000 # 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 HOH 221 ? E HOH . 2 1 A HOH 267 ? E 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 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N1 ? D NCO . ? A NCO 103 ? 1_555 98.7 ? 2 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N2 ? D NCO . ? A NCO 103 ? 1_555 82.7 ? 3 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N2 ? D NCO . ? A NCO 103 ? 1_555 176.9 ? 4 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 103 ? 1_555 130.2 ? 5 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 103 ? 1_555 89.4 ? 6 N2 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N3 ? D NCO . ? A NCO 103 ? 1_555 91.8 ? 7 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N4 ? D NCO . ? A NCO 103 ? 1_555 43.0 ? 8 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N4 ? D NCO . ? A NCO 103 ? 1_555 90.4 ? 9 N2 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N4 ? D NCO . ? A NCO 103 ? 1_555 92.5 ? 10 N3 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N4 ? D NCO . ? A NCO 103 ? 1_555 88.3 ? 11 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N5 ? D NCO . ? A NCO 103 ? 1_555 47.4 ? 12 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N5 ? D NCO . ? A NCO 103 ? 1_555 92.8 ? 13 N2 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N5 ? D NCO . ? A NCO 103 ? 1_555 86.1 ? 14 N3 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N5 ? D NCO . ? A NCO 103 ? 1_555 177.0 ? 15 N4 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N5 ? D NCO . ? A NCO 103 ? 1_555 89.7 ? 16 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 139.1 ? 17 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 90.5 ? 18 N2 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 86.6 ? 19 N3 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 89.4 ? 20 N4 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 177.5 ? 21 N5 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 N6 ? D NCO . ? A NCO 103 ? 1_555 92.6 ? 22 O ? E HOH . ? A HOH 202 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 90.1 ? 23 N1 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 97.3 ? 24 N2 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 79.9 ? 25 N3 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 137.7 ? 26 N4 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 133.1 ? 27 N5 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 44.0 ? 28 N6 ? D NCO . ? A NCO 103 ? 1_555 CO ? D NCO . ? A NCO 103 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 49.0 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2016-09-14 2 'Structure model' 1 1 2016-09-21 3 'Structure model' 1 2 2016-09-28 4 'Structure model' 1 3 2016-11-09 # _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' 'Database references' 3 4 'Structure model' 'Database references' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.10.1_2155: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXDE ? ? ? . 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 5 # 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 O A HOH 256 ? ? O A HOH 259 ? ? 1.62 2 1 O2 A DT 1 ? B O A HOH 203 ? ? 1.80 3 1 O A HOH 218 ? ? O A HOH 240 ? ? 1.92 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 "HO3'" A DA 10 ? A 1_555 O A HOH 206 ? ? 6_463 1.47 2 1 C7 A DT 1 ? B 1_555 O A HOH 253 ? ? 2_674 2.03 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C5 A DT 1 ? B C6 A DT 1 ? B 1.295 1.339 -0.044 0.007 N 2 1 C6 A DT 1 ? B N1 A DT 1 ? B 1.326 1.378 -0.052 0.007 N 3 1 C5 A DT 1 ? B C7 A DT 1 ? B 1.392 1.496 -0.104 0.006 N 4 1 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.367 1.419 -0.052 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N3 A DT 1 ? B C4 A DT 1 ? B O4 A DT 1 ? B 123.55 119.90 3.65 0.60 N 2 1 "O4'" A DG 9 ? A "C1'" A DG 9 ? A N9 A DG 9 ? A 110.28 108.30 1.98 0.30 N # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 264 ? . 5.91 2 1 O ? A HOH 265 ? . 5.98 3 1 O ? A HOH 266 ? . 6.01 4 1 O ? A HOH 267 ? . 6.84 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5JEV 'double helix' 5JEV 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 2 1_555 A DG 9 8_664 0.146 -0.145 0.210 -6.196 -8.087 -1.090 1 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 8_664 -0.153 -0.094 0.331 15.669 -2.833 -1.092 2 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 8_664 -0.129 -0.094 -0.033 -10.796 -7.145 -1.217 3 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DC 5 1_555 A DG 6 8_664 0.117 -0.164 0.006 2.459 -5.716 -0.769 4 A_DC5:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A DC 5 8_664 -0.117 -0.164 0.006 -2.459 -5.716 -0.769 5 A_DG6:DC5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 8_664 0.129 -0.094 -0.033 10.796 -7.145 -1.217 6 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DG 3 8_664 0.153 -0.094 0.331 -15.669 -2.833 -1.092 7 A_DC8:DG3_A A 8 ? A 3 ? 19 1 1 A DG 9 1_555 A DC 2 8_664 -0.146 -0.145 0.210 6.196 -8.087 -1.090 8 A_DG9:DC2_A A 9 ? A 2 ? 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 DC 2 1_555 A DG 9 8_664 A DG 3 1_555 A DC 8 8_664 0.070 0.365 2.829 3.700 3.176 30.773 0.151 0.486 2.840 5.938 -6.917 31.148 1 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 8_664 A DG 4 1_555 A DC 7 8_664 -0.519 0.110 5.273 0.701 48.604 23.600 -5.143 0.650 2.478 65.632 -0.947 53.720 2 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 8_664 A DC 5 1_555 A DG 6 8_664 0.144 -0.113 3.076 -2.659 2.495 28.933 -0.734 -0.830 3.030 4.968 5.295 29.157 3 AA_DG4DC5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 5 1_555 A DG 6 8_664 A DG 6 1_555 A DC 5 8_664 0.000 0.504 3.239 0.000 3.158 39.014 0.376 0.000 3.268 4.719 0.000 39.137 4 AA_DC5DG6:DC5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DC 5 8_664 A DC 7 1_555 A DG 4 8_664 -0.144 -0.113 3.076 2.659 2.495 28.933 -0.734 0.830 3.030 4.968 -5.295 29.157 5 AA_DG6DC7:DG4DC5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 8_664 A DC 8 1_555 A DG 3 8_664 0.519 0.110 5.273 -0.701 48.604 23.600 -5.143 -0.650 2.478 65.632 0.947 53.720 6 AA_DC7DC8:DG3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DC 8 1_555 A DG 3 8_664 A DG 9 1_555 A DC 2 8_664 -0.070 0.365 2.829 -3.700 3.176 30.773 0.151 -0.486 2.840 5.938 6.917 31.148 7 AA_DC8DG9:DC2DG3_AA A 8 ? A 3 ? A 9 ? A 2 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'Delta-Ru(phen)2(dppz) complex' 0TN 3 'COBALT HEXAMMINE(III)' NCO 4 water HOH #