data_3UYA # _entry.id 3UYA # _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 3UYA NDB NA1476 RCSB RCSB069360 WWPDB D_1000069360 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2015-04-29 _pdbx_database_PDB_obs_spr.pdb_id 3UYB _pdbx_database_PDB_obs_spr.replace_pdb_id 3UYA _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 3QRN 'X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA)at high resolution.' unspecified PDB 3QF8 'X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA) at medium resolution.' unspecified PDB 3GOM 'Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4.' unspecified PDB 3UYB . unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 3UYA _pdbx_database_status.recvd_initial_deposition_date 2011-12-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 'Niyazi, H.N.' 1 'Texeira, S.C.M.' 2 'Mitchell, E.P.' 3 'Cardin, J.C.' 4 'Forsyth, V.T.' 5 # _citation.id primary _citation.title 'Crystal structure of lambda-[Ru(TAP)2(dppz)]2+ with d(CCGGTACCGG)2 displaying kinking of DNA via semiintercalation.' _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 'Niyazi, H.N.' 1 primary ;O'Sullivan, K. ; 2 primary 'Texeira, S.C.M.' 3 primary 'Mitchell, E.P.' 4 primary 'Kelly, J.M.' 5 primary 'Cardin, J.C.' 6 primary 'Forsyth, V.T.' 7 # _cell.entry_id 3UYA _cell.length_a 54.229 _cell.length_b 54.229 _cell.length_c 28.854 _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 3UYA _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(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'" 3045.992 1 ? ? ? ? 2 non-polymer syn 'Ru(tap)2(dppz) complex' 747.732 2 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 water nat water 18.015 45 ? ? ? ? # _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 '(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGGTACCGG _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 DC n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DG n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3UYA _struct_ref.pdbx_db_accession 3UYA _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3UYA _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 3UYA _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 RKL non-polymer . 'Ru(tap)2(dppz) complex' ? 'C38 H22 N12 Ru 2' 747.732 # _exptl.entry_id 3UYA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.48 _exptl_crystal.density_percent_sol 64.68 _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 7.0 _exptl_crystal_grow.pdbx_details ;10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(CCGGTACCGG), 1mM lambda-[Ru(tap)2dppz)Cl2, pH 7.0, 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 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2011-06-12 _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 '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 1.65312 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.65312 # _reflns.entry_id 3UYA _reflns.observed_criterion_sigma_I 1.9 _reflns.observed_criterion_sigma_F 1.9 _reflns.d_resolution_low 38.35 _reflns.d_resolution_high 1.90 _reflns.number_obs 3581 _reflns.number_all ? _reflns.percent_possible_obs 96.9 _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 1.90 _reflns_shell.d_res_low 2.0 _reflns_shell.percent_possible_all 81.1 _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_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3UYA _refine.ls_number_reflns_obs 3581 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.90 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.35 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 95.09 _refine.ls_R_factor_obs 0.14536 _refine.ls_R_factor_all 0.1472 _refine.ls_R_factor_R_work 0.14207 _refine.ls_R_factor_R_free 0.21099 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.2 _refine.ls_number_reflns_R_free 148 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.970 _refine.correlation_coeff_Fo_to_Fc_free 0.933 _refine.B_iso_mean 24.115 _refine.aniso_B[1][1] -0.09 _refine.aniso_B[2][2] -0.09 _refine.aniso_B[3][3] 0.17 _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' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.443 _refine.pdbx_overall_ESU_R_Free 0.135 _refine.overall_SU_ML 0.087 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 6.545 _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 103 _refine_hist.number_atoms_solvent 45 _refine_hist.number_atoms_total 350 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 38.35 # 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 0.019 0.014 ? 362 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 3.354 1.985 ? 580 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.087 0.200 ? 32 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.025 0.020 ? 211 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 7.646 3.000 ? 362 ? 'X-RAY DIFFRACTION' r_sphericity_free 27.121 5.000 ? 26 ? 'X-RAY DIFFRACTION' r_sphericity_bonded 16.654 5.000 ? 331 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.900 _refine_ls_shell.d_res_low 1.950 _refine_ls_shell.number_reflns_R_work 152 _refine_ls_shell.R_factor_R_work 0.143 _refine_ls_shell.percent_reflns_obs 66.26 _refine_ls_shell.R_factor_R_free 0.472 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 9 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3UYA _struct.title 'X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(CCGGTACCGG)' _struct.pdbx_descriptor "5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3UYA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA-Ruthenium complex, Semiintercalation, intercalation, Minor groove interaction, 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 ? # _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 ? ? D BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 11 A HOH 20 1_555 ? ? ? ? ? ? ? 2.835 ? metalc2 metalc ? ? A DT 5 O4 ? ? ? 1_555 D BA . BA ? ? A DT 5 A BA 11 1_555 ? ? ? ? ? ? ? 2.856 ? metalc3 metalc ? ? D BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 11 A HOH 34 1_555 ? ? ? ? ? ? ? 2.886 ? metalc4 metalc ? ? A DG 4 O6 ? ? ? 1_555 D BA . BA ? ? A DG 4 A BA 11 1_555 ? ? ? ? ? ? ? 2.931 ? metalc5 metalc ? ? D BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 11 A HOH 14 1_555 ? ? ? ? ? ? ? 2.934 ? metalc6 metalc ? ? D BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 11 A HOH 19 1_555 ? ? ? ? ? ? ? 2.994 ? metalc7 metalc ? ? D BA . BA ? ? ? 1_555 E HOH . O ? ? A BA 11 A HOH 29 1_555 ? ? ? ? ? ? ? 3.059 ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DT 5 N3 ? ? ? 1_555 A DA 6 N1 ? ? A DT 5 A DA 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 5 O4 ? ? ? 1_555 A DA 6 N6 ? ? A DT 5 A DA 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 A DT 5 N3 ? ? A DA 6 A DT 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DT 5 O4 ? ? A DA 6 A DT 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 7_555 ? ? ? ? ? ? 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 ? ? ? ? 11 'BINDING SITE FOR RESIDUE RKL A 13' AC2 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE RKL A 12' AC3 Software ? ? ? ? 8 'BINDING SITE FOR RESIDUE BA A 11' # 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 11 DC A 1 ? DC A 1 . ? 4_545 ? 2 AC1 11 DC A 2 ? DC A 2 . ? 4_545 ? 3 AC1 11 DG A 4 ? DG A 4 . ? 7_555 ? 4 AC1 11 DT A 5 ? DT A 5 . ? 7_555 ? 5 AC1 11 DT A 5 ? DT A 5 . ? 1_555 ? 6 AC1 11 DA A 6 ? DA A 6 . ? 1_555 ? 7 AC1 11 DA A 6 ? DA A 6 . ? 7_555 ? 8 AC1 11 DC A 7 ? DC A 7 . ? 1_555 ? 9 AC1 11 DC A 7 ? DC A 7 . ? 7_555 ? 10 AC1 11 HOH E . ? HOH A 16 . ? 7_555 ? 11 AC1 11 HOH E . ? HOH A 46 . ? 4_545 ? 12 AC2 11 DC A 1 ? DC A 1 . ? 4_545 ? 13 AC2 11 DC A 2 ? DC A 2 . ? 4_545 ? 14 AC2 11 DG A 3 ? DG A 3 . ? 1_555 ? 15 AC2 11 DG A 3 ? DG A 3 . ? 4_545 ? 16 AC2 11 DG A 4 ? DG A 4 . ? 1_555 ? 17 AC2 11 DC A 7 ? DC A 7 . ? 7_555 ? 18 AC2 11 DC A 8 ? DC A 8 . ? 7_555 ? 19 AC2 11 DG A 9 ? DG A 9 . ? 6_545 ? 20 AC2 11 DG A 10 ? DG A 10 . ? 6_545 ? 21 AC2 11 HOH E . ? HOH A 28 . ? 1_555 ? 22 AC2 11 HOH E . ? HOH A 48 . ? 1_555 ? 23 AC3 8 DG A 3 ? DG A 3 . ? 1_555 ? 24 AC3 8 DG A 4 ? DG A 4 . ? 1_555 ? 25 AC3 8 DT A 5 ? DT A 5 . ? 1_555 ? 26 AC3 8 HOH E . ? HOH A 14 . ? 1_555 ? 27 AC3 8 HOH E . ? HOH A 19 . ? 1_555 ? 28 AC3 8 HOH E . ? HOH A 20 . ? 1_555 ? 29 AC3 8 HOH E . ? HOH A 29 . ? 1_555 ? 30 AC3 8 HOH E . ? HOH A 34 . ? 1_555 ? # _database_PDB_matrix.entry_id 3UYA _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 3UYA _atom_sites.fract_transf_matrix[1][1] 0.018440 _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] 0.018440 _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] 0.034657 _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 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 DC 1 1 1 DC DC 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 DT 5 5 5 DT DT A . n A 1 6 DA 6 6 6 DA DA 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 DG 10 10 10 DG DG 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 RKL 1 13 13 RKL RKL A . C 2 RKL 1 12 12 RKL RKL A . D 3 BA 1 11 1 BA BA A . E 4 HOH 1 14 1 HOH HOH A . E 4 HOH 2 15 15 HOH HOH A . E 4 HOH 3 16 16 HOH HOH A . E 4 HOH 4 17 17 HOH HOH A . E 4 HOH 5 18 18 HOH HOH A . E 4 HOH 6 19 2 HOH HOH A . E 4 HOH 7 20 3 HOH HOH A . E 4 HOH 8 21 21 HOH HOH A . E 4 HOH 9 22 22 HOH HOH A . E 4 HOH 10 23 23 HOH HOH A . E 4 HOH 11 24 24 HOH HOH A . E 4 HOH 12 25 25 HOH HOH A . E 4 HOH 13 26 26 HOH HOH A . E 4 HOH 14 27 27 HOH HOH A . E 4 HOH 15 28 28 HOH HOH A . E 4 HOH 16 29 4 HOH HOH A . E 4 HOH 17 30 30 HOH HOH A . E 4 HOH 18 31 31 HOH HOH A . E 4 HOH 19 32 32 HOH HOH A . E 4 HOH 20 33 33 HOH HOH A . E 4 HOH 21 34 5 HOH HOH A . E 4 HOH 22 35 6 HOH HOH A . E 4 HOH 23 36 7 HOH HOH A . E 4 HOH 24 37 37 HOH HOH A . E 4 HOH 25 38 38 HOH HOH A . E 4 HOH 26 39 39 HOH HOH A . E 4 HOH 27 40 40 HOH HOH A . E 4 HOH 28 41 41 HOH HOH A . E 4 HOH 29 42 42 HOH HOH A . E 4 HOH 30 43 43 HOH HOH A . E 4 HOH 31 44 44 HOH HOH A . E 4 HOH 32 45 45 HOH HOH A . E 4 HOH 33 46 46 HOH HOH A . E 4 HOH 34 47 47 HOH HOH A . E 4 HOH 35 48 48 HOH HOH A . E 4 HOH 36 49 49 HOH HOH A . E 4 HOH 37 50 50 HOH HOH A . E 4 HOH 38 51 51 HOH HOH A . E 4 HOH 39 52 52 HOH HOH A . E 4 HOH 40 53 53 HOH HOH A . E 4 HOH 41 54 54 HOH HOH A . E 4 HOH 42 55 9 HOH HOH A . E 4 HOH 43 56 11 HOH HOH A . E 4 HOH 44 57 12 HOH HOH A . E 4 HOH 45 58 13 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)' 980 ? 1 MORE -5 ? 1 'SSA (A^2)' 4560 ? # 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' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O4 ? A DT 5 ? A DT 5 ? 1_555 116.4 ? 2 O ? E HOH . ? A HOH 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 34 ? 1_555 75.0 ? 3 O4 ? A DT 5 ? A DT 5 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 34 ? 1_555 150.2 ? 4 O ? E HOH . ? A HOH 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 69.8 ? 5 O4 ? A DT 5 ? A DT 5 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 67.8 ? 6 O ? E HOH . ? A HOH 34 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O6 ? A DG 4 ? A DG 4 ? 1_555 139.1 ? 7 O ? E HOH . ? A HOH 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 14 ? 1_555 68.0 ? 8 O4 ? A DT 5 ? A DT 5 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 14 ? 1_555 70.6 ? 9 O ? E HOH . ? A HOH 34 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 14 ? 1_555 91.0 ? 10 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 14 ? 1_555 94.6 ? 11 O ? E HOH . ? A HOH 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 137.5 ? 12 O4 ? A DT 5 ? A DT 5 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 106.0 ? 13 O ? E HOH . ? A HOH 34 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 69.4 ? 14 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 128.3 ? 15 O ? E HOH . ? A HOH 14 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 19 ? 1_555 133.4 ? 16 O ? E HOH . ? A HOH 20 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 122.6 ? 17 O4 ? A DT 5 ? A DT 5 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 75.4 ? 18 O ? E HOH . ? A HOH 34 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 75.5 ? 19 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 142.2 ? 20 O ? E HOH . ? A HOH 14 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 64.4 ? 21 O ? E HOH . ? A HOH 19 ? 1_555 BA ? D BA . ? A BA 11 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 69.8 ? # 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 2013-01-16 2 'Structure model' 1 1 2015-04-29 # 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 # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x -11.846 _pdbx_refine_tls.origin_y -15.071 _pdbx_refine_tls.origin_z 1.916 _pdbx_refine_tls.T[1][1] 0.0142 _pdbx_refine_tls.T[2][2] 0.0193 _pdbx_refine_tls.T[3][3] 0.0008 _pdbx_refine_tls.T[1][2] 0.0004 _pdbx_refine_tls.T[1][3] -0.0015 _pdbx_refine_tls.T[2][3] 0.0004 _pdbx_refine_tls.L[1][1] 0.0377 _pdbx_refine_tls.L[2][2] 0.0085 _pdbx_refine_tls.L[3][3] 0.1880 _pdbx_refine_tls.L[1][2] -0.0179 _pdbx_refine_tls.L[1][3] -0.0835 _pdbx_refine_tls.L[2][3] 0.0397 _pdbx_refine_tls.S[1][1] 0.0027 _pdbx_refine_tls.S[2][2] 0.0053 _pdbx_refine_tls.S[3][3] -0.0081 _pdbx_refine_tls.S[1][2] -0.0102 _pdbx_refine_tls.S[1][3] 0.0038 _pdbx_refine_tls.S[2][3] -0.0017 _pdbx_refine_tls.S[2][1] -0.0017 _pdbx_refine_tls.S[3][1] -0.0083 _pdbx_refine_tls.S[3][2] 0.0159 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 1 A 10 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 A 11 A 13 ? . . . . ? 'X-RAY DIFFRACTION' 3 1 A 14 A 58 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MxCuBE 'data collection' . ? 1 shelx_cde 'model building' . ? 2 REFMAC refinement 5.6.0117 ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 shelx_cde 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 DC 1 ? ? P A DC 2 ? A OP1 A DC 2 ? A 119.82 110.50 9.32 1.10 Y 2 1 "C1'" A DT 5 ? ? "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? 104.02 110.10 -6.08 1.00 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3UYA 'double helix' 3UYA '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 1 1_555 A DG 10 7_555 0.149 -0.179 -0.043 -8.510 21.160 10.018 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 7_555 0.191 -0.124 -0.024 -7.983 3.380 0.456 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 7_555 -0.233 -0.096 0.259 22.149 -6.668 -1.398 3 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 7_555 -0.371 -0.180 -0.126 -7.320 3.460 -0.288 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DT 5 1_555 A DA 6 7_555 0.093 -0.131 -0.404 17.058 12.267 5.789 5 A_DT5:DA6_A A 5 ? A 6 ? 20 1 1 A DC 1 1_555 A DG 10 1_555 0.149 -0.179 -0.043 -8.510 21.160 10.018 6 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 1_555 0.191 -0.124 -0.024 -7.983 3.380 0.456 7 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 1_555 -0.233 -0.096 0.259 22.149 -6.668 -1.398 8 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 1_555 -0.371 -0.180 -0.126 -7.320 3.460 -0.288 9 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DT 5 1_555 A DA 6 1_555 0.093 -0.131 -0.404 17.058 12.267 5.789 10 A_DT5:DA6_A A 5 ? A 6 ? 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 DC 1 1_555 A DG 10 7_555 A DC 2 1_555 A DG 9 7_555 -1.853 0.705 6.902 9.845 -18.187 26.396 7.169 6.440 4.568 -33.971 -18.389 33.419 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 7_555 A DG 3 1_555 A DC 8 7_555 -0.108 1.532 2.743 -1.585 4.182 22.599 2.542 -0.221 2.974 10.539 3.994 23.032 2 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 7_555 A DG 4 1_555 A DC 7 7_555 0.047 0.706 5.054 -0.891 49.621 17.520 -5.091 -0.159 2.404 71.758 1.289 52.445 3 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 7_555 A DT 5 1_555 A DA 6 7_555 0.723 0.020 2.713 0.114 8.790 16.490 -3.856 -2.178 2.412 28.189 -0.364 18.672 4 AA_DG4DT5:DA6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 1 1_555 A DG 10 1_555 A DC 2 1_555 A DG 9 1_555 -1.853 0.705 6.902 9.845 -18.187 26.396 7.169 6.440 4.568 -33.971 -18.389 33.419 5 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 1_555 A DG 3 1_555 A DC 8 1_555 -0.108 1.532 2.743 -1.585 4.182 22.600 2.542 -0.221 2.974 10.539 3.994 23.032 6 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 1_555 A DG 4 1_555 A DC 7 1_555 0.047 0.706 5.054 -0.891 49.621 17.520 -5.091 -0.159 2.404 71.758 1.289 52.445 7 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 1_555 A DT 5 1_555 A DA 6 1_555 0.723 0.020 2.713 0.114 8.790 16.490 -3.856 -2.178 2.412 28.189 -0.364 18.672 8 AA_DG4DT5:DA6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'Ru(tap)2(dppz) complex' RKL 3 'BARIUM ION' BA 4 water HOH #