data_4RE7 # _entry.id 4RE7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4RE7 pdb_00004re7 10.2210/pdb4re7/pdb NDB NA3179 ? ? RCSB RCSB087235 ? ? WWPDB D_1000087235 ? ? # 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 2015-09-30 2 'Structure model' 1 1 2017-11-22 3 'Structure model' 1 2 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' software 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_software.classification' 2 2 'Structure model' '_software.name' 3 2 'Structure model' '_software.version' 4 3 'Structure model' '_database_2.pdbx_DOI' 5 3 'Structure model' '_database_2.pdbx_database_accession' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 3 'Structure model' '_struct_conn.pdbx_dist_value' 17 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 18 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 19 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 21 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 22 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RE7 _pdbx_database_status.recvd_initial_deposition_date 2014-09-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3QRN 'Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCGCCGA)' unspecified PDB 4QIO 'Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCGCCIA)' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hall, J.P.' 1 'Cardin, C.J.' 2 # _citation.id primary _citation.title 'The effects of DNA modification on the binding of polypyridyl ruthenium 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 _citation_author.identifier_ORCID primary 'Hall, J.P.' 1 ? primary 'Gurung, S.P.' 2 ? primary 'Beer, H.' 3 ? primary 'Buchner, K.' 4 ? primary 'Cardin, D.J.' 5 ? primary 'Brazier, J.A.' 6 ? primary 'Cardin, C.J.' 7 ? # 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*IP*GP*CP*GP*CP*CP*GP*A)-3'" 3030.979 1 ? ? ? ? 2 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 3 non-polymer syn 'Ru(tap)2(dppz) complex' 747.732 1 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # _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)(DI)(DG)(DC)(DG)(DC)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TCIGCGCCGA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'BARIUM ION' BA 3 'Ru(tap)2(dppz) complex' RKL 4 water HOH # 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 DI 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 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 # 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 DI 3 3 3 DI DI 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 BA 1 101 1 BA BA A . C 3 RKL 1 102 11 RKL RKL A . D 4 HOH 1 201 2 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal GDA 'data collection' . ? 1 SHELXCD phasing . ? 2 SHELXE 'model building' . ? 3 PHENIX refinement '(phenix.refine: 1.8.4_1496)' ? 4 XDS 'data reduction' . ? 5 SCALA 'data scaling' . ? 6 # _cell.entry_id 4RE7 _cell.length_a 47.830 _cell.length_b 47.830 _cell.length_c 32.110 _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 4RE7 _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 ? # _exptl.entry_id 4RE7 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.03 _exptl_crystal.density_percent_sol 59.40 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details ;1 uL 2 mM oligonucleotide (double HPLC-purified) + 1 uL 2 mM lambda-[Ru(TAP)2(dppz)]Cl2 + 6 uL 10% v/v MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine tetrahydrochloride, 80 mM sodium chloride, 20 mM barium chloride equilibrated against 1 mL 35% v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K ; _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 PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2014-07-10 _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 'double 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 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I02' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I02 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 4RE7 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 47.83 _reflns.d_resolution_high 2.18 _reflns.number_obs 2012 _reflns.number_all 2012 _reflns.percent_possible_obs 94.1 _reflns.pdbx_Rmerge_I_obs 0.137 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 11.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 10.5 _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 2.18 _reflns_shell.d_res_low 2.24 _reflns_shell.percent_possible_all 93.0 _reflns_shell.Rmerge_I_obs 1.122 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.9 _reflns_shell.pdbx_redundancy 10.7 _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 4RE7 _refine.ls_number_reflns_obs 2000 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.94 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 33.821 _refine.ls_d_res_high 2.181 _refine.ls_percent_reflns_obs 93.44 _refine.ls_R_factor_obs 0.1950 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1925 _refine.ls_R_factor_R_free 0.2417 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.57 _refine.ls_number_reflns_R_free 159 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.22 _refine.pdbx_overall_phase_error 45.48 _refine.overall_SU_B ? _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 201 _refine_hist.pdbx_number_atoms_ligand 52 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 254 _refine_hist.d_res_high 2.181 _refine_hist.d_res_low 33.821 # 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 f_bond_d 0.005 ? ? 289 ? 'X-RAY DIFFRACTION' f_angle_d 1.915 ? ? 454 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 28.048 ? ? 97 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.027 ? ? 38 ? 'X-RAY DIFFRACTION' f_plane_restr 0.002 ? ? 13 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.181 _refine_ls_shell.d_res_low 33.825 _refine_ls_shell.number_reflns_R_work 3318 _refine_ls_shell.R_factor_R_work 0.1925 _refine_ls_shell.percent_reflns_obs 93.0 _refine_ls_shell.R_factor_R_free 0.2417 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 159 _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' # _database_PDB_matrix.entry_id 4RE7 _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 # _struct.entry_id 4RE7 _struct.title 'Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCIGCGCCGA)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RE7 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'inosine, kinking, ruthenium, 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4RE7 _struct_ref.pdbx_db_accession 4RE7 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code TCIGCGCCGA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RE7 _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 4RE7 _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 # _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 # 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)' 1930 ? 1 MORE -23 ? 1 'SSA (A^2)' 4940 ? # _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 # 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_554 y,x,-z-1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -32.1100000000 # _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 _struct_conn.pdbx_role metalc1 metalc ? ? A DI 3 N7 ? ? ? 1_555 B BA . BA ? ? A DI 3 A BA 101 1_555 ? ? ? ? ? ? ? 2.906 ? ? metalc2 metalc ? ? A DG 4 O6 ? ? ? 1_555 B BA . BA ? ? A DG 4 A BA 101 1_555 ? ? ? ? ? ? ? 2.804 ? ? hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 A DA 10 N1 ? ? A DT 1 A DA 10 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 A DA 10 N6 ? ? A DT 1 A DA 10 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DI 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DI 3 A DC 8 7_554 ? ? ? ? ? ? 'DI-DC PAIR' ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 5 A DG 6 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 5 A DG 6 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 5 A DG 6 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 6 A DC 5 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 6 A DC 5 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 6 A DC 5 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DI 3 O6 ? ? A DC 8 A DI 3 7_554 ? ? ? ? ? ? 'DC-DI PAIR' ? ? ? hydrog20 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 10 N1 ? ? ? 1_555 A DT 1 N3 ? ? A DA 10 A DT 1 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 10 N6 ? ? ? 1_555 A DT 1 O4 ? ? A DA 10 A DT 1 7_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id N7 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id DI _pdbx_struct_conn_angle.ptnr1_label_seq_id 3 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id DI _pdbx_struct_conn_angle.ptnr1_auth_seq_id 3 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id BA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id B _pdbx_struct_conn_angle.ptnr2_label_comp_id BA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id BA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 101 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id O6 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id DG _pdbx_struct_conn_angle.ptnr3_label_seq_id 4 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id DG _pdbx_struct_conn_angle.ptnr3_auth_seq_id 4 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 75.2 _pdbx_struct_conn_angle.value_esd ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A BA 101 ? 2 'BINDING SITE FOR RESIDUE BA A 101' AC2 Software A RKL 102 ? 10 'BINDING SITE FOR RESIDUE RKL A 102' # 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 2 DI A 3 ? DI A 3 . ? 1_555 ? 2 AC1 2 DG A 4 ? DG A 4 . ? 1_555 ? 3 AC2 10 DT A 1 ? DT A 1 . ? 6_454 ? 4 AC2 10 DC A 2 ? DC A 2 . ? 6_454 ? 5 AC2 10 DI A 3 ? DI A 3 . ? 6_454 ? 6 AC2 10 DI A 3 ? DI A 3 . ? 7_554 ? 7 AC2 10 DG A 4 ? DG A 4 . ? 7_554 ? 8 AC2 10 DC A 7 ? DC A 7 . ? 1_555 ? 9 AC2 10 DC A 8 ? DC A 8 . ? 1_555 ? 10 AC2 10 DG A 9 ? DG A 9 . ? 4_455 ? 11 AC2 10 DA A 10 ? DA A 10 . ? 2_565 ? 12 AC2 10 DA A 10 ? DA A 10 . ? 4_455 ? # _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 10.5399 _pdbx_refine_tls.origin_y 11.9227 _pdbx_refine_tls.origin_z -19.6956 _pdbx_refine_tls.T[1][1] 0.7892 _pdbx_refine_tls.T[2][2] 0.7835 _pdbx_refine_tls.T[3][3] 0.5859 _pdbx_refine_tls.T[1][2] 0.0531 _pdbx_refine_tls.T[1][3] -0.0091 _pdbx_refine_tls.T[2][3] -0.0285 _pdbx_refine_tls.L[1][1] 4.9133 _pdbx_refine_tls.L[2][2] 6.1569 _pdbx_refine_tls.L[3][3] 1.8969 _pdbx_refine_tls.L[1][2] -2.1317 _pdbx_refine_tls.L[1][3] 2.0699 _pdbx_refine_tls.L[2][3] -2.6301 _pdbx_refine_tls.S[1][1] -0.0704 _pdbx_refine_tls.S[1][2] 0.2214 _pdbx_refine_tls.S[1][3] -0.7320 _pdbx_refine_tls.S[2][1] -0.3011 _pdbx_refine_tls.S[2][2] 0.2186 _pdbx_refine_tls.S[2][3] 0.1891 _pdbx_refine_tls.S[3][1] -0.2632 _pdbx_refine_tls.S[3][2] -0.1487 _pdbx_refine_tls.S[3][3] -0.0333 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ;chain 'A' ; # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal BA BA BA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DI OP3 O N N 109 DI P P N N 110 DI OP1 O N N 111 DI OP2 O N N 112 DI "O5'" O N N 113 DI "C5'" C N N 114 DI "C4'" C N R 115 DI "O4'" O N N 116 DI "C3'" C N S 117 DI "O3'" O N N 118 DI "C2'" C N N 119 DI "C1'" C N R 120 DI N9 N Y N 121 DI C8 C Y N 122 DI N7 N Y N 123 DI C5 C Y N 124 DI C6 C N N 125 DI O6 O N N 126 DI N1 N N N 127 DI C2 C N N 128 DI N3 N N N 129 DI C4 C Y N 130 DI HOP3 H N N 131 DI HOP2 H N N 132 DI "H5'" H N N 133 DI "H5''" H N N 134 DI "H4'" H N N 135 DI "H3'" H N N 136 DI "HO3'" H N N 137 DI "H2'" H N N 138 DI "H2''" H N N 139 DI "H1'" H N N 140 DI H8 H N N 141 DI H1 H N N 142 DI H2 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 RKL RU RU N N 183 RKL C1 C Y N 184 RKL N1 N Y N 185 RKL C2 C Y N 186 RKL N2 N Y N 187 RKL C3 C Y N 188 RKL N3 N Y N 189 RKL C4 C Y N 190 RKL N4 N Y N 191 RKL C5 C Y N 192 RKL N5 N Y N 193 RKL C6 C Y N 194 RKL N6 N Y N 195 RKL C7 C Y N 196 RKL N7 N Y N 197 RKL C8 C Y N 198 RKL N8 N Y N 199 RKL C9 C Y N 200 RKL N9 N Y N 201 RKL C10 C Y N 202 RKL N10 N Y N 203 RKL C11 C Y N 204 RKL N11 N Y N 205 RKL C12 C Y N 206 RKL N12 N Y N 207 RKL C13 C Y N 208 RKL C14 C Y N 209 RKL C15 C Y N 210 RKL C16 C Y N 211 RKL C17 C Y N 212 RKL C18 C Y N 213 RKL C19 C Y N 214 RKL C20 C Y N 215 RKL C21 C Y N 216 RKL C22 C Y N 217 RKL C23 C Y N 218 RKL C24 C Y N 219 RKL C25 C Y N 220 RKL C26 C Y N 221 RKL C27 C Y N 222 RKL C28 C Y N 223 RKL C29 C Y N 224 RKL C30 C Y N 225 RKL C31 C Y N 226 RKL C32 C Y N 227 RKL C33 C Y N 228 RKL C34 C Y N 229 RKL C35 C Y N 230 RKL C36 C Y N 231 RKL C37 C Y N 232 RKL C38 C Y N 233 RKL H2 H N N 234 RKL H3 H N N 235 RKL H4 H N N 236 RKL H9 H N N 237 RKL H11 H N N 238 RKL H12 H N N 239 RKL H14 H N N 240 RKL H16 H N N 241 RKL H17 H N N 242 RKL H18 H N N 243 RKL H20 H N N 244 RKL H21 H N N 245 RKL H23 H N N 246 RKL H24 H N N 247 RKL H27 H N N 248 RKL H28 H N N 249 RKL H30 H N N 250 RKL H31 H N N 251 RKL H33 H N N 252 RKL H34 H N N 253 RKL H37 H N N 254 RKL H38 H N N 255 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DI OP3 P sing N N 113 DI OP3 HOP3 sing N N 114 DI P OP1 doub N N 115 DI P OP2 sing N N 116 DI P "O5'" sing N N 117 DI OP2 HOP2 sing N N 118 DI "O5'" "C5'" sing N N 119 DI "C5'" "C4'" sing N N 120 DI "C5'" "H5'" sing N N 121 DI "C5'" "H5''" sing N N 122 DI "C4'" "O4'" sing N N 123 DI "C4'" "C3'" sing N N 124 DI "C4'" "H4'" sing N N 125 DI "O4'" "C1'" sing N N 126 DI "C3'" "O3'" sing N N 127 DI "C3'" "C2'" sing N N 128 DI "C3'" "H3'" sing N N 129 DI "O3'" "HO3'" sing N N 130 DI "C2'" "C1'" sing N N 131 DI "C2'" "H2'" sing N N 132 DI "C2'" "H2''" sing N N 133 DI "C1'" N9 sing N N 134 DI "C1'" "H1'" sing N N 135 DI N9 C8 sing Y N 136 DI N9 C4 sing Y N 137 DI C8 N7 doub Y N 138 DI C8 H8 sing N N 139 DI N7 C5 sing Y N 140 DI C5 C6 sing N N 141 DI C5 C4 doub Y N 142 DI C6 O6 doub N N 143 DI C6 N1 sing N N 144 DI N1 C2 sing N N 145 DI N1 H1 sing N N 146 DI C2 N3 doub N N 147 DI C2 H2 sing N N 148 DI N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 RKL RU N1 sing N N 189 RKL RU N2 sing N N 190 RKL RU N5 sing N N 191 RKL RU N8 sing N N 192 RKL RU N9 sing N N 193 RKL RU N12 sing N N 194 RKL C1 N2 doub Y N 195 RKL C1 C5 sing Y N 196 RKL C1 C10 sing Y N 197 RKL N1 C10 doub Y N 198 RKL N1 C12 sing Y N 199 RKL C2 N2 sing Y N 200 RKL C2 C3 doub Y N 201 RKL C2 H2 sing N N 202 RKL C3 C4 sing Y N 203 RKL C3 H3 sing N N 204 RKL N3 C6 doub Y N 205 RKL N3 C15 sing Y N 206 RKL C4 C5 doub Y N 207 RKL C4 H4 sing N N 208 RKL N4 C7 doub Y N 209 RKL N4 C13 sing Y N 210 RKL C5 C6 sing Y N 211 RKL N5 C19 doub Y N 212 RKL N5 C20 sing Y N 213 RKL C6 C7 sing Y N 214 RKL N6 C21 sing Y N 215 RKL N6 C22 doub Y N 216 RKL C7 C8 sing Y N 217 RKL N7 C25 doub Y N 218 RKL N7 C27 sing Y N 219 RKL C8 C9 doub Y N 220 RKL C8 C10 sing Y N 221 RKL N8 C26 doub Y N 222 RKL N8 C28 sing Y N 223 RKL C9 C11 sing Y N 224 RKL C9 H9 sing N N 225 RKL N9 C29 doub Y N 226 RKL N9 C30 sing Y N 227 RKL N10 C31 sing Y N 228 RKL N10 C32 doub Y N 229 RKL C11 C12 doub Y N 230 RKL C11 H11 sing N N 231 RKL N11 C35 doub Y N 232 RKL N11 C37 sing Y N 233 RKL C12 H12 sing N N 234 RKL N12 C36 doub Y N 235 RKL N12 C38 sing Y N 236 RKL C13 C14 sing Y N 237 RKL C13 C15 doub Y N 238 RKL C14 C18 doub Y N 239 RKL C14 H14 sing N N 240 RKL C15 C16 sing Y N 241 RKL C16 C17 doub Y N 242 RKL C16 H16 sing N N 243 RKL C17 C18 sing Y N 244 RKL C17 H17 sing N N 245 RKL C18 H18 sing N N 246 RKL C19 C22 sing Y N 247 RKL C19 C26 sing Y N 248 RKL C20 C21 doub Y N 249 RKL C20 H20 sing N N 250 RKL C21 H21 sing N N 251 RKL C22 C23 sing Y N 252 RKL C23 C24 doub Y N 253 RKL C23 H23 sing N N 254 RKL C24 C25 sing Y N 255 RKL C24 H24 sing N N 256 RKL C25 C26 sing Y N 257 RKL C27 C28 doub Y N 258 RKL C27 H27 sing N N 259 RKL C28 H28 sing N N 260 RKL C29 C32 sing Y N 261 RKL C29 C36 sing Y N 262 RKL C30 C31 doub Y N 263 RKL C30 H30 sing N N 264 RKL C31 H31 sing N N 265 RKL C32 C33 sing Y N 266 RKL C33 C34 doub Y N 267 RKL C33 H33 sing N N 268 RKL C34 C35 sing Y N 269 RKL C34 H34 sing N N 270 RKL C35 C36 sing Y N 271 RKL C37 C38 doub Y N 272 RKL C37 H37 sing N N 273 RKL C38 H38 sing N N 274 # _ndb_struct_conf_na.entry_id 4RE7 _ndb_struct_conf_na.feature '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 DT 1 1_555 A DA 10 7_554 -0.040 -0.159 -0.069 -14.457 9.389 9.915 1 A_DT1:DA10_A A 1 ? A 10 ? 20 1 1 A DC 2 1_555 A DG 9 7_554 0.622 0.201 0.185 -17.049 8.720 1.636 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DI 3 1_555 A DC 8 7_554 0.015 -0.086 0.138 30.845 -6.081 1.276 3 A_DI3:DC8_A A 3 ? A 8 ? ? 1 1 A DG 4 1_555 A DC 7 7_554 -0.500 -0.043 -0.107 -10.262 1.773 4.378 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DC 5 1_555 A DG 6 7_554 0.072 -0.277 0.671 1.527 -4.127 -1.900 5 A_DC5:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A DC 5 7_554 -0.072 -0.277 0.671 -1.527 -4.127 -1.900 6 A_DG6:DC5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 7_554 0.500 -0.043 -0.107 10.262 1.773 4.378 7 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DI 3 7_554 -0.015 -0.086 0.138 -30.845 -6.081 1.276 8 A_DC8:DI3_A A 8 ? A 3 ? ? 1 1 A DG 9 1_555 A DC 2 7_554 -0.622 0.201 0.185 17.049 8.720 1.636 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DA 10 1_555 A DT 1 7_554 0.040 -0.159 -0.069 14.457 9.389 9.915 10 A_DA10:DT1_A A 10 ? A 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 DT 1 1_555 A DA 10 7_554 A DC 2 1_555 A DG 9 7_554 -0.964 0.923 7.227 6.733 -12.200 28.693 6.430 4.377 5.984 -22.984 -12.685 31.833 1 AA_DT1DC2:DG9DA10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 7_554 A DI 3 1_555 A DC 8 7_554 0.242 1.532 2.332 2.809 8.812 19.976 1.245 0.248 2.759 23.823 -7.594 21.994 2 AA_DC2DI3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DI 3 1_555 A DC 8 7_554 A DG 4 1_555 A DC 7 7_554 0.324 0.728 5.140 -0.532 49.908 13.390 -5.465 -0.440 2.076 75.931 0.810 51.565 3 AA_DI3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 7_554 A DC 5 1_555 A DG 6 7_554 -1.007 0.266 3.115 -5.619 -1.865 36.503 0.665 0.852 3.213 -2.954 8.898 36.964 4 AA_DG4DC5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 5 1_555 A DG 6 7_554 A DG 6 1_555 A DC 5 7_554 0.000 0.794 4.569 0.000 39.224 23.779 -4.447 0.000 3.100 59.964 0.000 45.625 5 AA_DC5DG6:DC5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DC 5 7_554 A DC 7 1_555 A DG 4 7_554 1.007 0.266 3.115 5.619 -1.865 36.503 0.665 -0.852 3.213 -2.954 -8.898 36.964 6 AA_DG6DC7:DG4DC5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 7_554 A DC 8 1_555 A DI 3 7_554 -0.324 0.728 5.140 0.532 49.908 13.390 -5.465 0.440 2.076 75.931 -0.810 51.565 7 AA_DC7DC8:DI3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DC 8 1_555 A DI 3 7_554 A DG 9 1_555 A DC 2 7_554 -0.242 1.532 2.332 -2.809 8.812 19.976 1.245 -0.248 2.759 23.823 7.594 21.994 8 AA_DC8DG9:DC2DI3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 7_554 A DA 10 1_555 A DT 1 7_554 0.964 0.923 7.227 -6.733 -12.200 28.693 6.430 -4.377 5.984 -22.984 12.685 31.833 9 AA_DG9DA10:DT1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # _atom_sites.entry_id 4RE7 _atom_sites.fract_transf_matrix[1][1] 0.020907 _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] 0.020907 _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] 0.031143 _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_