data_4DX4 # _entry.id 4DX4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4DX4 NDB NA1651 RCSB RCSB070892 WWPDB D_1000070892 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2017-03-08 _pdbx_database_PDB_obs_spr.pdb_id 4E8S _pdbx_database_PDB_obs_spr.replace_pdb_id 4DX4 _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3QF8 . unspecified PDB 3QRN . unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 4DX4 _pdbx_database_status.recvd_initial_deposition_date 2012-02-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 'Ruiz Morte, S.' 1 'Hall, J.P.' 2 'Cardin, C.J.' 3 # _citation.id primary _citation.title 'Lambda-[Ru(TAP)2(DPPZ-(Me2))]2+ Bound to Synthetic DNA Oligomer' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ruiz Morte, S.' 1 primary 'Hall, J.P.' 2 primary 'Cardin, C.J.' 3 primary 'Kelly, J.M.' 4 primary ;O'Sullivan, K. ; 5 # _cell.entry_id 4DX4 _cell.length_a 42.480 _cell.length_b 42.480 _cell.length_c 39.730 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4DX4 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # 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 "5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'" 3045.992 1 ? ? ? ? 2 non-polymer syn "(11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)" 775.785 1 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 5 water nat water 18.015 82 ? ? ? ? # _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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'DNA purchased from ATDbio' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4DX4 _struct_ref.pdbx_db_accession 4DX4 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code TCGGCGCCGA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4DX4 _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 4DX4 _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 BA non-polymer . 'BARIUM ION' ? 'Ba 2' 137.327 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 RML non-polymer . "(11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)" 'Lambda-[Ru(1,4,5,8-tetraazaphenanthrene)2(11,12-dimethyl-dipyridophenazine)]2+' 'C40 H26 N12 Ru 2' 775.785 # _exptl.entry_id 4DX4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.94 _exptl_crystal.density_percent_sol 58.19 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 278 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_details ;6 ul of 10% MPD, 40mM Na Cacodylate, 12mM Spermine, 80mM Potassium Chloride, 20mM Barium Chloride. 1 ul of 1mM DNA duplex. 1ul of 2mM Lambda-[Ru(TAP)2(dppz(Me)2)]Cl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2012-02-08 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Dual Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I04' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I04 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 4DX4 _reflns.observed_criterion_sigma_I 3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.031 _reflns.d_resolution_high 1.51 _reflns.number_obs 6127 _reflns.number_all 6127 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.51 _reflns_shell.d_res_low 1.59 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4DX4 _refine.ls_number_reflns_obs 5813 _refine.ls_number_reflns_all 5824 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.031 _refine.ls_d_res_high 1.51 _refine.ls_percent_reflns_obs 99.80 _refine.ls_R_factor_obs 0.14235 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.14086 _refine.ls_R_factor_R_free 0.17304 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 279 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.973 _refine.correlation_coeff_Fo_to_Fc_free 0.963 _refine.B_iso_mean 18.946 _refine.aniso_B[1][1] -0.22 _refine.aniso_B[2][2] -0.22 _refine.aniso_B[3][3] 0.43 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] -0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.060 _refine.pdbx_overall_ESU_R_Free 0.064 _refine.overall_SU_ML 0.039 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.027 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _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 55 _refine_hist.number_atoms_solvent 82 _refine_hist.number_atoms_total 339 _refine_hist.d_res_high 1.51 _refine_hist.d_res_low 30.031 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.040 0.013 ? 292 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 3.021 1.751 ? 460 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.105 0.200 ? 30 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.034 0.020 ? 160 ? 'X-RAY DIFFRACTION' r_gen_planes_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.51 _refine_ls_shell.d_res_low 1.547 _refine_ls_shell.number_reflns_R_work 348 _refine_ls_shell.R_factor_R_work 0.201 _refine_ls_shell.percent_reflns_obs 99.45 _refine_ls_shell.R_factor_R_free 0.227 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4DX4 _struct.title 'Lambda-[Ru(TAP)2(DPPZ-(Me2))]2+ Bound to Synthetic DNA Oligomer' _struct.pdbx_descriptor "5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4DX4 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, Lambda-[Ru(TAP)2(DPPZ-(Me2))]2+, 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 3 ? D N N 4 ? E N N 5 ? # _struct_biol.id 1 _struct_biol.details ? # 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 ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 202 1_555 ? ? ? ? ? ? ? 2.774 ? metalc2 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 203 1_555 ? ? ? ? ? ? ? 2.782 ? metalc3 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 206 1_555 ? ? ? ? ? ? ? 2.810 ? metalc4 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 204 1_555 ? ? ? ? ? ? ? 2.836 ? metalc5 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 201 1_555 ? ? ? ? ? ? ? 2.845 ? metalc6 metalc ? ? A DG 4 O6 ? ? ? 1_555 C BA . BA ? ? A DG 4 A BA 102 1_555 ? ? ? ? ? ? ? 2.849 ? metalc7 metalc ? ? C BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 102 A HOH 205 1_555 ? ? ? ? ? ? ? 2.899 ? metalc8 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 103 A HOH 215 1_555 ? ? ? ? ? ? ? 3.006 ? metalc9 metalc ? ? A DG 3 N7 ? ? ? 1_555 C BA . BA ? ? A DG 3 A BA 102 1_555 ? ? ? ? ? ? ? 2.978 ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 5 A DG 6 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 5 A DG 6 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 5 A DG 6 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 6 A DC 5 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 6 A DC 5 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 6 A DC 5 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 8_445 ? ? ? ? ? ? WATSON-CRICK ? ? # 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 ? ? ? ? 13 'BINDING SITE FOR RESIDUE RML A 101' AC2 Software ? ? ? ? 8 'BINDING SITE FOR RESIDUE BA A 102' AC3 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE NA 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 13 DT A 1 ? DT A 1 . ? 6_535 ? 2 AC1 13 DC A 2 ? DC A 2 . ? 6_535 ? 3 AC1 13 DG A 3 ? DG A 3 . ? 6_535 ? 4 AC1 13 DG A 3 ? DG A 3 . ? 8_445 ? 5 AC1 13 DG A 4 ? DG A 4 . ? 8_445 ? 6 AC1 13 DC A 5 ? DC A 5 . ? 8_445 ? 7 AC1 13 DC A 7 ? DC A 7 . ? 1_555 ? 8 AC1 13 DC A 8 ? DC A 8 . ? 1_555 ? 9 AC1 13 DG A 9 ? DG A 9 . ? 3_444 ? 10 AC1 13 DA A 10 ? DA A 10 . ? 1_555 ? 11 AC1 13 HOH E . ? HOH A 210 . ? 1_555 ? 12 AC1 13 HOH E . ? HOH A 236 . ? 6_535 ? 13 AC1 13 HOH E . ? HOH A 237 . ? 1_555 ? 14 AC2 8 DG A 3 ? DG A 3 . ? 1_555 ? 15 AC2 8 DG A 4 ? DG A 4 . ? 1_555 ? 16 AC2 8 HOH E . ? HOH A 201 . ? 1_555 ? 17 AC2 8 HOH E . ? HOH A 202 . ? 1_555 ? 18 AC2 8 HOH E . ? HOH A 203 . ? 1_555 ? 19 AC2 8 HOH E . ? HOH A 204 . ? 1_555 ? 20 AC2 8 HOH E . ? HOH A 205 . ? 1_555 ? 21 AC2 8 HOH E . ? HOH A 206 . ? 1_555 ? 22 AC3 4 DG A 4 ? DG A 4 . ? 1_555 ? 23 AC3 4 DC A 5 ? DC A 5 . ? 1_555 ? 24 AC3 4 HOH E . ? HOH A 205 . ? 8_445 ? 25 AC3 4 HOH E . ? HOH A 215 . ? 1_555 ? # _database_PDB_matrix.entry_id 4DX4 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4DX4 _atom_sites.fract_transf_matrix[1][1] 0.023540 _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] 0.023540 _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] 0.025170 _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 BA C N NA 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 RML 1 101 1 RML RML A . C 3 BA 1 102 1 BA BA A . D 4 NA 1 103 1 NA NA A . E 5 HOH 1 201 1 HOH HOH A . E 5 HOH 2 202 2 HOH HOH A . E 5 HOH 3 203 3 HOH HOH A . E 5 HOH 4 204 4 HOH HOH A . E 5 HOH 5 205 5 HOH HOH A . E 5 HOH 6 206 6 HOH HOH A . E 5 HOH 7 207 7 HOH HOH A . E 5 HOH 8 208 8 HOH HOH A . E 5 HOH 9 209 9 HOH HOH A . E 5 HOH 10 210 10 HOH HOH A . E 5 HOH 11 211 11 HOH HOH A . E 5 HOH 12 212 12 HOH HOH A . E 5 HOH 13 213 13 HOH HOH A . E 5 HOH 14 214 14 HOH HOH A . E 5 HOH 15 215 15 HOH HOH A . E 5 HOH 16 216 16 HOH HOH A . E 5 HOH 17 217 17 HOH HOH A . E 5 HOH 18 218 18 HOH HOH A . E 5 HOH 19 219 19 HOH HOH A . E 5 HOH 20 220 20 HOH HOH A . E 5 HOH 21 221 21 HOH HOH A . E 5 HOH 22 222 22 HOH HOH A . E 5 HOH 23 223 23 HOH HOH A . E 5 HOH 24 224 24 HOH HOH A . E 5 HOH 25 225 25 HOH HOH A . E 5 HOH 26 226 26 HOH HOH A . E 5 HOH 27 227 27 HOH HOH A . E 5 HOH 28 228 28 HOH HOH A . E 5 HOH 29 229 29 HOH HOH A . E 5 HOH 30 230 30 HOH HOH A . E 5 HOH 31 231 31 HOH HOH A . E 5 HOH 32 232 32 HOH HOH A . E 5 HOH 33 233 33 HOH HOH A . E 5 HOH 34 234 34 HOH HOH A . E 5 HOH 35 235 35 HOH HOH A . E 5 HOH 36 236 36 HOH HOH A . E 5 HOH 37 237 37 HOH HOH A . E 5 HOH 38 238 38 HOH HOH A . E 5 HOH 39 239 39 HOH HOH A . E 5 HOH 40 240 40 HOH HOH A . E 5 HOH 41 241 41 HOH HOH A . E 5 HOH 42 242 42 HOH HOH A . E 5 HOH 43 243 43 HOH HOH A . E 5 HOH 44 244 44 HOH HOH A . E 5 HOH 45 245 45 HOH HOH A . E 5 HOH 46 246 46 HOH HOH A . E 5 HOH 47 247 47 HOH HOH A . E 5 HOH 48 248 48 HOH HOH A . E 5 HOH 49 249 49 HOH HOH A . E 5 HOH 50 250 50 HOH HOH A . E 5 HOH 51 251 51 HOH HOH A . E 5 HOH 52 252 52 HOH HOH A . E 5 HOH 53 253 53 HOH HOH A . E 5 HOH 54 254 54 HOH HOH A . E 5 HOH 55 255 55 HOH HOH A . E 5 HOH 56 256 56 HOH HOH A . E 5 HOH 57 257 57 HOH HOH A . E 5 HOH 58 258 58 HOH HOH A . E 5 HOH 59 259 59 HOH HOH A . E 5 HOH 60 260 60 HOH HOH A . E 5 HOH 61 261 61 HOH HOH A . E 5 HOH 62 262 62 HOH HOH A . E 5 HOH 63 263 63 HOH HOH A . E 5 HOH 64 264 64 HOH HOH A . E 5 HOH 65 265 65 HOH HOH A . E 5 HOH 66 266 66 HOH HOH A . E 5 HOH 67 267 67 HOH HOH A . E 5 HOH 68 268 68 HOH HOH A . E 5 HOH 69 269 69 HOH HOH A . E 5 HOH 70 270 70 HOH HOH A . E 5 HOH 71 271 71 HOH HOH A . E 5 HOH 72 272 72 HOH HOH A . E 5 HOH 73 273 73 HOH HOH A . E 5 HOH 74 274 74 HOH HOH A . E 5 HOH 75 275 75 HOH HOH A . E 5 HOH 76 276 76 HOH HOH A . E 5 HOH 77 277 77 HOH HOH A . E 5 HOH 78 278 78 HOH HOH A . E 5 HOH 79 279 79 HOH HOH A . E 5 HOH 80 280 80 HOH HOH A . E 5 HOH 81 281 81 HOH HOH A . E 5 HOH 82 282 82 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 760 ? 1 MORE -4 ? 1 'SSA (A^2)' 4260 ? # 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_445 -y-1,-x-1,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 -42.4800000000 -1.0000000000 0.0000000000 0.0000000000 -42.4800000000 0.0000000000 0.0000000000 -1.0000000000 19.8650000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 278 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 203 ? 1_555 75.0 ? 2 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 71.5 ? 3 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 206 ? 1_555 76.0 ? 4 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 137.5 ? 5 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 83.3 ? 6 O ? E HOH . ? A HOH 206 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 204 ? 1_555 68.0 ? 7 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 68.1 ? 8 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 138.9 ? 9 O ? E HOH . ? A HOH 206 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 107.6 ? 10 O ? E HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 201 ? 1_555 136.9 ? 11 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 137.5 ? 12 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 71.6 ? 13 O ? E HOH . ? A HOH 206 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 123.0 ? 14 O ? E HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 62.7 ? 15 O ? E HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 127.7 ? 16 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 113.0 ? 17 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 147.3 ? 18 O ? E HOH . ? A HOH 206 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 77.1 ? 19 O ? E HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 69.6 ? 20 O ? E HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 67.8 ? 21 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 O ? E HOH . ? A HOH 205 ? 1_555 109.2 ? 22 O ? E HOH . ? A HOH 202 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 73.2 ? 23 O ? E HOH . ? A HOH 203 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 76.1 ? 24 O ? E HOH . ? A HOH 206 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 139.4 ? 25 O ? E HOH . ? A HOH 204 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 136.1 ? 26 O ? E HOH . ? A HOH 201 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 76.4 ? 27 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 74.0 ? 28 O ? E HOH . ? A HOH 205 ? 1_555 BA ? C BA . ? A BA 102 ? 1_555 N7 ? A DG 3 ? A DG 3 ? 1_555 136.3 ? # 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 2013-03-06 2 'Structure model' 1 1 2017-03-08 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group Other # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal GDA 'data collection' . ? 1 SHELXC/D/E 'model building' . ? 2 REFMAC refinement 5.6.0117 ? 3 MOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 SHELXC/D/E phasing . ? 6 # 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 P A DG 4 ? ? OP2 A DG 4 ? ? 1.370 1.485 -0.115 0.017 N 2 1 P A DC 7 ? ? OP2 A DC 7 ? ? 1.331 1.485 -0.154 0.017 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DC _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 5 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.078 _pdbx_validate_planes.type 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 4DX4 _ndb_struct_conf_na.feature '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_445 0.154 -0.062 0.221 -11.110 8.544 0.842 1 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 8_445 -0.223 -0.055 0.183 23.459 -5.704 -0.622 2 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 8_445 -0.203 -0.168 -0.093 -8.455 1.798 -1.469 3 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DC 5 1_555 A DG 6 8_445 0.245 -0.051 0.272 -4.835 -6.091 0.409 4 A_DC5:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A DC 5 8_445 -0.245 -0.051 0.272 4.835 -6.091 0.409 5 A_DG6:DC5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 8_445 0.203 -0.168 -0.093 8.455 1.798 -1.469 6 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DG 3 8_445 0.223 -0.055 0.183 -23.459 -5.704 -0.622 7 A_DC8:DG3_A A 8 ? A 3 ? 19 1 1 A DG 9 1_555 A DC 2 8_445 -0.154 -0.062 0.221 11.110 8.544 0.842 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_445 A DG 3 1_555 A DC 8 8_445 -0.449 1.681 2.648 2.229 3.988 19.131 3.278 2.232 2.865 11.784 -6.585 19.664 1 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 8_445 A DG 4 1_555 A DC 7 8_445 -0.125 0.821 5.178 -2.196 51.935 15.655 -5.157 -0.119 2.337 74.326 3.143 54.131 2 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 8_445 A DC 5 1_555 A DG 6 8_445 -0.878 0.125 3.267 -3.718 -2.564 38.641 0.502 0.862 3.319 -3.858 5.596 38.894 3 AA_DG4DC5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 5 1_555 A DG 6 8_445 A DG 6 1_555 A DC 5 8_445 0.000 0.793 3.285 0.000 20.311 27.188 -2.226 0.000 3.122 37.311 0.000 33.822 4 AA_DC5DG6:DC5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DC 5 8_445 A DC 7 1_555 A DG 4 8_445 0.878 0.125 3.267 3.718 -2.564 38.641 0.502 -0.862 3.319 -3.858 -5.596 38.894 5 AA_DG6DC7:DG4DC5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 8_445 A DC 8 1_555 A DG 3 8_445 0.125 0.821 5.178 2.196 51.935 15.655 -5.157 0.119 2.337 74.326 -3.143 54.131 6 AA_DC7DC8:DG3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DC 8 1_555 A DG 3 8_445 A DG 9 1_555 A DC 2 8_445 0.449 1.681 2.648 -2.229 3.988 19.131 3.278 -2.232 2.865 11.784 6.585 19.664 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 "(11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)" RML 3 'BARIUM ION' BA 4 'SODIUM ION' NA 5 water HOH #