data_4E87 # _entry.id 4E87 # _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 4E87 NDB NA1693 RCSB RCSB071291 WWPDB D_1000071291 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2013-04-24 _pdbx_database_PDB_obs_spr.pdb_id 4JD8 _pdbx_database_PDB_obs_spr.replace_pdb_id 4E87 _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 4DX4 'Lower resolution model' unspecified PDB 4E7Y . unspecified PDB 4E8S . unspecified PDB 4E8X . unspecified PDB 4E95 . unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 4E87 _pdbx_database_status.recvd_initial_deposition_date 2012-03-19 _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 'Hall, J.P.' 1 'Ruiz-Morte, S.' 2 'Winter, G' 3 'Cardin, C.J.' 4 # _citation.id primary _citation.title 'Cooperativity in the DNA binding of ruthenium light switch complexes' _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 'Hall, J.P.' 1 primary 'Winter, G.' 2 primary 'Ruiz-Morte, S.' 3 primary 'Kelly, J.' 4 primary 'Cardin, C.J.' 5 # _cell.entry_id 4E87 _cell.length_a 37.370 _cell.length_b 37.370 _cell.length_c 53.020 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 4E87 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _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(*AP*TP*GP*CP*AP*T)-3'" 1808.229 2 ? ? ? ? 2 non-polymer syn 'Delta-Ru(phen)2(dppz) complex' 743.779 2 ? ? ? ? 3 water nat water 18.015 40 ? ? ? ? # _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 '(DA)(DT)(DG)(DC)(DA)(DT)' _entity_poly.pdbx_seq_one_letter_code_can ATGCAT _entity_poly.pdbx_strand_id A,B _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 DA n 1 2 DT n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 DT 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 4E87 _struct_ref.pdbx_db_accession 4E87 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ATGCAT _struct_ref.pdbx_db_isoform ? # 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 4E87 A 1 ? 6 ? 4E87 1 ? 6 ? 1 6 2 1 4E87 B 1 ? 6 ? 4E87 1 ? 6 ? 1 6 # 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 # _exptl.entry_id 4E87 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.96 _exptl_crystal.density_percent_sol 58.38 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.3 _exptl_crystal_grow.pdbx_details ;1ul 4mM rac-Ru(phen)2(dppz).Cl2, 1ul 2mM oligonucleotide, 8ul 40mM Sodium cacodylate, 12mM Spermine-HCl, 20mM BaCl2, 2% 2-methyl-2,4-pentanediol, 80mM NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _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 crystal 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 1.6531 _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 1.6531 # _reflns.entry_id 4E87 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 27.63 _reflns.d_resolution_high 1.94 _reflns.number_obs 3397 _reflns.number_all 3417 _reflns.percent_possible_obs 99.4 _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 1.94 _reflns_shell.d_res_low 1.99 _reflns_shell.percent_possible_all 96.9 _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 4E87 _refine.ls_number_reflns_obs 2868 _refine.ls_number_reflns_all 3018 _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 27.63 _refine.ls_d_res_high 1.95 _refine.ls_percent_reflns_obs 95.74 _refine.ls_R_factor_obs 0.18199 _refine.ls_R_factor_all 0.17854 _refine.ls_R_factor_R_work 0.1785 _refine.ls_R_factor_R_free 0.20888 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.8 _refine.ls_number_reflns_R_free 347 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.957 _refine.correlation_coeff_Fo_to_Fc_free 0.945 _refine.B_iso_mean 24.401 _refine.aniso_B[1][1] -0.26 _refine.aniso_B[2][2] -0.26 _refine.aniso_B[3][3] 0.39 _refine.aniso_B[1][2] -0.13 _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 0.196 _refine.pdbx_overall_ESU_R_Free 0.157 _refine.overall_SU_ML 0.095 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 3.333 _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 240 _refine_hist.pdbx_number_atoms_ligand 102 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 382 _refine_hist.d_res_high 1.95 _refine_hist.d_res_low 27.63 # 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 0.024 0.014 ? 396 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 3.161 1.917 ? 628 ? '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 0.088 0.200 ? 36 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.031 0.020 ? 232 ? '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 1.950 _refine_ls_shell.d_res_low 2.001 _refine_ls_shell.number_reflns_R_work 153 _refine_ls_shell.R_factor_R_work 0.238 _refine_ls_shell.percent_reflns_obs 81.55 _refine_ls_shell.R_factor_R_free 0.302 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 15 _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 4E87 _struct.title 'Racemic-[Ru(phen)2(dppz)]2+ bound to synthetic DNA' _struct.pdbx_descriptor "5'-D(*AP*TP*GP*CP*AP*T)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4E87 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Intercalation, DNA, racemic-[Ru(phen)2(dppz)]2+, Delta-[Ru(phen)2(dppz)]2+' # 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 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _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 hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 1 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 1 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 2 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 2 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 3 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 4 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 5 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 5 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 6 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 6 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 ? ? ? ? 9 'BINDING SITE FOR RESIDUE 0TN A 101' AC2 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE 0TN B 101' # 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 9 DT A 2 ? DT A 2 . ? 1_555 ? 2 AC1 9 DG A 3 ? DG A 3 . ? 1_555 ? 3 AC1 9 DC A 4 ? DC A 4 . ? 1_555 ? 4 AC1 9 DA A 5 ? DA A 5 . ? 6_665 ? 5 AC1 9 DT A 6 ? DT A 6 . ? 6_665 ? 6 AC1 9 DA B 1 ? DA B 1 . ? 6_665 ? 7 AC1 9 DC B 4 ? DC B 4 . ? 1_555 ? 8 AC1 9 DA B 5 ? DA B 5 . ? 1_555 ? 9 AC1 9 DT B 6 ? DT B 6 . ? 1_555 ? 10 AC2 7 DA A 1 ? DA A 1 . ? 2_665 ? 11 AC2 7 DC A 4 ? DC A 4 . ? 1_555 ? 12 AC2 7 DA A 5 ? DA A 5 . ? 1_555 ? 13 AC2 7 DT A 6 ? DT A 6 . ? 1_555 ? 14 AC2 7 DT B 2 ? DT B 2 . ? 1_555 ? 15 AC2 7 DG B 3 ? DG B 3 . ? 1_555 ? 16 AC2 7 DT B 6 ? DT B 6 . ? 2_665 ? # _database_PDB_matrix.entry_id 4E87 _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 4E87 _atom_sites.fract_transf_matrix[1][1] 0.026759 _atom_sites.fract_transf_matrix[1][2] 0.015450 _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] 0.030899 _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] 0.018861 _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 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 DA 1 1 1 DA DA A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n B 1 1 DA 1 1 1 DA DA B . n B 1 2 DT 2 2 2 DT DT B . n B 1 3 DG 3 3 3 DG DG B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 DT 6 6 6 DT DT B . 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 C 2 0TN 1 101 1 0TN KPD A . D 2 0TN 1 101 1 0TN RKP B . E 3 HOH 1 201 1 HOH HOH A . E 3 HOH 2 202 2 HOH HOH A . E 3 HOH 3 203 3 HOH HOH A . E 3 HOH 4 204 4 HOH HOH A . E 3 HOH 5 205 6 HOH HOH A . E 3 HOH 6 206 7 HOH HOH A . E 3 HOH 7 207 10 HOH HOH A . E 3 HOH 8 208 13 HOH HOH A . E 3 HOH 9 209 16 HOH HOH A . E 3 HOH 10 210 17 HOH HOH A . E 3 HOH 11 211 19 HOH HOH A . E 3 HOH 12 212 20 HOH HOH A . E 3 HOH 13 213 22 HOH HOH A . E 3 HOH 14 214 24 HOH HOH A . E 3 HOH 15 215 28 HOH HOH A . E 3 HOH 16 216 29 HOH HOH A . E 3 HOH 17 217 31 HOH HOH A . E 3 HOH 18 218 35 HOH HOH A . E 3 HOH 19 219 36 HOH HOH A . E 3 HOH 20 220 37 HOH HOH A . E 3 HOH 21 221 38 HOH HOH A . E 3 HOH 22 222 40 HOH HOH A . F 3 HOH 1 201 23 HOH HOH B . F 3 HOH 2 202 5 HOH HOH B . F 3 HOH 3 203 8 HOH HOH B . F 3 HOH 4 204 9 HOH HOH B . F 3 HOH 5 205 11 HOH HOH B . F 3 HOH 6 206 12 HOH HOH B . F 3 HOH 7 207 14 HOH HOH B . F 3 HOH 8 208 15 HOH HOH B . F 3 HOH 9 209 18 HOH HOH B . F 3 HOH 10 210 21 HOH HOH B . F 3 HOH 11 211 25 HOH HOH B . F 3 HOH 12 212 26 HOH HOH B . F 3 HOH 13 213 27 HOH HOH B . F 3 HOH 14 214 30 HOH HOH B . F 3 HOH 15 215 32 HOH HOH B . F 3 HOH 16 216 33 HOH HOH B . F 3 HOH 17 217 34 HOH HOH B . F 3 HOH 18 218 39 HOH HOH B . # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 2013-03-20 2 'Structure model' 1 1 2013-04-24 # 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 ? # 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 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 SHELXC/D/E phasing . ? 6 # 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 "O3'" A DG 3 ? ? P A DC 4 ? ? OP2 A DC 4 ? ? 117.33 110.50 6.83 1.10 Y 2 1 "C1'" A DT 6 ? ? "O4'" A DT 6 ? ? "C4'" A DT 6 ? ? 103.46 110.10 -6.64 1.00 N # _ndb_struct_conf_na.entry_id 4E87 _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 DA 1 1_555 B DT 6 1_555 0.099 -0.151 0.097 -9.276 0.830 1.158 1 A_DA1:DT6_B A 1 ? B 6 ? 20 1 1 A DT 2 1_555 B DA 5 1_555 -0.026 -0.100 0.080 14.568 9.307 3.094 2 A_DT2:DA5_B A 2 ? B 5 ? 20 1 1 A DG 3 1_555 B DC 4 1_555 -0.392 -0.088 -0.291 -1.341 9.876 -0.512 3 A_DG3:DC4_B A 3 ? B 4 ? 19 1 1 A DC 4 1_555 B DG 3 1_555 0.377 -0.190 -0.322 16.778 2.099 -1.101 4 A_DC4:DG3_B A 4 ? B 3 ? 19 1 1 A DA 5 1_555 B DT 2 1_555 0.179 -0.103 -0.028 -11.617 16.125 7.960 5 A_DA5:DT2_B A 5 ? B 2 ? 20 1 1 A DT 6 1_555 B DA 1 1_555 -0.140 -0.125 -0.427 12.854 8.046 3.817 6 A_DT6:DA1_B A 6 ? B 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 DA 1 1_555 B DT 6 1_555 A DT 2 1_555 B DA 5 1_555 1.024 0.224 2.869 0.403 3.123 28.757 -0.162 -1.972 2.891 6.265 -0.808 28.926 1 AA_DA1DT2:DA5DT6_BB A 1 ? B 6 ? A 2 ? B 5 ? 1 A DT 2 1_555 B DA 5 1_555 A DG 3 1_555 B DC 4 1_555 0.767 1.921 6.875 12.674 2.835 25.625 2.476 4.723 6.676 5.932 -26.514 28.679 2 AA_DT2DG3:DC4DA5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DG 3 1_555 B DC 4 1_555 A DC 4 1_555 B DG 3 1_555 -0.208 0.016 2.914 1.499 6.161 22.873 -1.774 0.947 2.802 15.165 -3.690 23.724 3 AA_DG3DC4:DG3DC4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DC 4 1_555 B DG 3 1_555 A DA 5 1_555 B DT 2 1_555 -1.758 1.860 6.874 -11.292 5.460 22.232 0.622 -3.446 7.171 12.921 26.723 25.488 4 AA_DC4DA5:DT2DG3_BB A 4 ? B 3 ? A 5 ? B 2 ? 1 A DA 5 1_555 B DT 2 1_555 A DT 6 1_555 B DA 1 1_555 -0.619 0.119 2.819 4.091 6.428 14.574 -3.343 4.559 2.395 23.368 -14.872 16.436 5 AA_DA5DT6:DA1DT2_BB A 5 ? B 2 ? A 6 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'Delta-Ru(phen)2(dppz) complex' 0TN 3 water HOH #