data_3PBX # _entry.id 3PBX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 3PBX pdb_00003pbx 10.2210/pdb3pbx/pdb NDB NA0823 ? ? RCSB RCSB062203 ? ? WWPDB D_1000062203 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3GOO _pdbx_database_related.details 'Structure bound to the Holliday junction sequence d(TCGGCGCCGA)' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3PBX _pdbx_database_status.recvd_initial_deposition_date 2010-10-21 _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.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Naseer, A.' 1 ? 'Cardin, C.J.' 2 ? # _citation.id primary _citation.title 'Strontium bound to the sequence d(CCGGCGCCGG)' _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 'Naseer, A.' 1 ? primary 'Cardin, C.J.' 2 ? # _cell.entry_id 3PBX _cell.length_a 64.890 _cell.length_b 25.001 _cell.length_c 37.044 _cell.angle_alpha 90.00 _cell.angle_beta 110.01 _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 3PBX _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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 DNA 3046.980 2 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 57 ? ? ? ? # _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)(DC)(DG)(DC)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGGCGCCGG _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 DC n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DG 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 'Chemically synthesized' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3PBX _struct_ref.pdbx_db_accession 3PBX _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code CCGGCGCCGG _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 3PBX A 1 ? 10 ? 3PBX 1 ? 10 ? 1 10 2 1 3PBX B 1 ? 10 ? 3PBX 11 ? 20 ? 11 20 # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # _exptl.entry_id 3PBX _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.32 _exptl_crystal.density_percent_sol 46.90 _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 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details 'SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K' _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 'OXFORD SAPPHIRE CCD' _diffrn_detector.pdbx_collection_date 2007-02-10 _diffrn_detector.details 'multi-graded optics' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'SEALED TUBE' _diffrn_source.type 'OXFORD DIFFRACTION ENHANCE ULTRA' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3PBX _reflns.observed_criterion_sigma_I 1.00 _reflns.observed_criterion_sigma_F 1.00 _reflns.d_resolution_low 14.866 _reflns.d_resolution_high 1.879 _reflns.number_obs 3706 _reflns.number_all 4705 _reflns.percent_possible_obs 78.550 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 27.446 _reflns.pdbx_redundancy 2.1 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.879 _reflns_shell.d_res_low 1.927 _reflns_shell.percent_possible_all ? _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3PBX _refine.ls_number_reflns_obs 3531 _refine.ls_number_reflns_all ? _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 14.86 _refine.ls_d_res_high 1.879 _refine.ls_percent_reflns_obs 78.55 _refine.ls_R_factor_obs 0.25440 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.25080 _refine.ls_R_factor_R_free 0.32701 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 175 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.872 _refine.B_iso_mean 27.446 _refine.aniso_B[1][1] -3.38 _refine.aniso_B[2][2] 3.36 _refine.aniso_B[3][3] 0.23 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.31 _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 ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 3GOJ _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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_Free 0.245 _refine.overall_SU_ML 0.153 _refine.overall_SU_B 5.747 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R 0.273 _refine.pdbx_diffrn_id 1 _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 404 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 57 _refine_hist.number_atoms_total 463 _refine_hist.d_res_high 1.879 _refine_hist.d_res_low 14.86 # 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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.021 0.021 ? 452 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.666 3.000 ? 694 'X-RAY DIFFRACTION' ? r_chiral_restr 0.150 0.200 ? 78 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.015 0.020 ? 210 'X-RAY DIFFRACTION' ? r_nbd_refined 0.259 0.200 ? 130 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.344 0.200 ? 245 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.389 0.200 ? 36 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.172 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.106 0.200 ? 34 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.434 0.200 ? 25 'X-RAY DIFFRACTION' ? r_scbond_it 3.007 3.000 ? 546 'X-RAY DIFFRACTION' ? r_scangle_it 4.016 4.500 ? 694 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.879 _refine_ls_shell.d_res_low 1.927 _refine_ls_shell.number_reflns_R_work 25 _refine_ls_shell.R_factor_R_work 0.477 _refine_ls_shell.percent_reflns_obs 7.69 _refine_ls_shell.R_factor_R_free 0.454 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 2 _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 3PBX _struct.title 'Strontium bound to the sequence d(CCGGCGCCGG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3PBX _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Holliday junction (higher order DNA structure), Intermediate formed in Homologous recombination, 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 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? C SR . SR ? ? ? 1_555 F HOH . O ? ? B SR 22 B HOH 69 1_555 ? ? ? ? ? ? ? 2.798 ? ? metalc2 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 27 B HOH 42 1_555 ? ? ? ? ? ? ? 2.177 ? ? metalc3 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? B NA 27 B HOH 43 1_555 ? ? ? ? ? ? ? 2.463 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 15 1_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 B SR 22 ? 3 'BINDING SITE FOR RESIDUE SR B 22' AC2 Software B NA 27 ? 2 'BINDING SITE FOR RESIDUE NA B 27' # 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 3 HOH E . ? HOH A 23 . ? 2_556 ? 2 AC1 3 HOH E . ? HOH A 24 . ? 2_556 ? 3 AC1 3 HOH F . ? HOH B 69 . ? 1_555 ? 4 AC2 2 HOH F . ? HOH B 42 . ? 1_555 ? 5 AC2 2 HOH F . ? HOH B 43 . ? 1_555 ? # _database_PDB_matrix.entry_id 3PBX _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 3PBX _atom_sites.fract_transf_matrix[1][1] 0.015411 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005611 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.039998 _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] 0.028728 _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 NA O P SR # 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 C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DG 4 14 14 DG G B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DG 6 16 16 DG G B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 DG G 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 SR 1 22 22 SR SR B . D 3 NA 1 27 27 NA NA B . E 4 HOH 1 21 21 HOH HOH A . E 4 HOH 2 23 23 HOH HOH A . E 4 HOH 3 24 24 HOH HOH A . E 4 HOH 4 30 30 HOH HOH A . E 4 HOH 5 31 31 HOH HOH A . E 4 HOH 6 34 34 HOH HOH A . E 4 HOH 7 35 35 HOH HOH A . E 4 HOH 8 36 36 HOH HOH A . E 4 HOH 9 38 38 HOH HOH A . E 4 HOH 10 39 39 HOH HOH A . E 4 HOH 11 48 48 HOH HOH A . E 4 HOH 12 53 53 HOH HOH A . E 4 HOH 13 57 57 HOH HOH A . E 4 HOH 14 62 62 HOH HOH A . E 4 HOH 15 66 66 HOH HOH A . E 4 HOH 16 67 67 HOH HOH A . E 4 HOH 17 70 70 HOH HOH A . E 4 HOH 18 74 74 HOH HOH A . F 4 HOH 1 26 26 HOH HOH B . F 4 HOH 2 28 28 HOH HOH B . F 4 HOH 3 29 29 HOH HOH B . F 4 HOH 4 32 32 HOH HOH B . F 4 HOH 5 37 37 HOH HOH B . F 4 HOH 6 40 40 HOH HOH B . F 4 HOH 7 41 41 HOH HOH B . F 4 HOH 8 42 42 HOH HOH B . F 4 HOH 9 43 43 HOH HOH B . F 4 HOH 10 44 44 HOH HOH B . F 4 HOH 11 45 45 HOH HOH B . F 4 HOH 12 46 46 HOH HOH B . F 4 HOH 13 47 47 HOH HOH B . F 4 HOH 14 49 49 HOH HOH B . F 4 HOH 15 50 50 HOH HOH B . F 4 HOH 16 51 51 HOH HOH B . F 4 HOH 17 52 52 HOH HOH B . F 4 HOH 18 54 54 HOH HOH B . F 4 HOH 19 55 55 HOH HOH B . F 4 HOH 20 56 56 HOH HOH B . F 4 HOH 21 59 59 HOH HOH B . F 4 HOH 22 60 60 HOH HOH B . F 4 HOH 23 61 61 HOH HOH B . F 4 HOH 24 63 63 HOH HOH B . F 4 HOH 25 64 64 HOH HOH B . F 4 HOH 26 65 65 HOH HOH B . F 4 HOH 27 68 68 HOH HOH B . F 4 HOH 28 69 69 HOH HOH B . F 4 HOH 29 71 71 HOH HOH B . F 4 HOH 30 72 72 HOH HOH B . F 4 HOH 31 73 73 HOH HOH B . F 4 HOH 32 75 75 HOH HOH B . F 4 HOH 33 76 76 HOH HOH B . F 4 HOH 34 77 77 HOH HOH B . F 4 HOH 35 78 78 HOH HOH B . F 4 HOH 36 79 79 HOH HOH B . F 4 HOH 37 80 80 HOH HOH B . F 4 HOH 38 81 81 HOH HOH B . F 4 HOH 39 82 82 HOH HOH B . # _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,F # 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)' 3610 ? 1 MORE -79 ? 1 'SSA (A^2)' 6630 ? # 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' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -12.6758694828 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.8077616180 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 36 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id O _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id F _pdbx_struct_conn_angle.ptnr1_label_comp_id HOH _pdbx_struct_conn_angle.ptnr1_label_seq_id . _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id B _pdbx_struct_conn_angle.ptnr1_auth_comp_id HOH _pdbx_struct_conn_angle.ptnr1_auth_seq_id 42 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id NA _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id D _pdbx_struct_conn_angle.ptnr2_label_comp_id NA _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id B _pdbx_struct_conn_angle.ptnr2_auth_comp_id NA _pdbx_struct_conn_angle.ptnr2_auth_seq_id 27 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id O _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id F _pdbx_struct_conn_angle.ptnr3_label_comp_id HOH _pdbx_struct_conn_angle.ptnr3_label_seq_id . _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id B _pdbx_struct_conn_angle.ptnr3_auth_comp_id HOH _pdbx_struct_conn_angle.ptnr3_auth_seq_id 43 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 79.4 _pdbx_struct_conn_angle.value_esd ? # 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 2011-02-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2023-09-06 # _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' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Refinement description' 4 3 'Structure model' 'Structure summary' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' 'Refinement description' # 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 3 'Structure model' audit_author 2 3 'Structure model' citation_author 3 3 'Structure model' software 4 4 'Structure model' chem_comp_atom 5 4 'Structure model' chem_comp_bond 6 4 'Structure model' database_2 7 4 'Structure model' pdbx_initial_refinement_model 8 4 'Structure model' struct_conn 9 4 '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 3 'Structure model' '_audit_author.name' 2 3 'Structure model' '_citation_author.name' 3 3 'Structure model' '_software.name' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_struct_conn.pdbx_dist_value' 7 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrysalisPro 'data collection' Red ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.2.0005 ? 3 CrysalisPro 'data reduction' Red ? 4 CrysalisPro 'data scaling' Red ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N3 B DG 16 ? ? O B HOH 29 ? ? 1.83 2 1 O2 B DC 15 ? ? O B HOH 75 ? ? 1.96 3 1 O A HOH 30 ? ? O B HOH 32 ? ? 1.96 4 1 O6 B DG 20 ? ? O B HOH 82 ? ? 2.03 5 1 OP2 B DC 17 ? ? O B HOH 80 ? ? 2.03 6 1 N3 B DG 19 ? ? O B HOH 54 ? ? 2.05 7 1 N3 B DG 20 ? ? O B HOH 72 ? ? 2.10 8 1 OP1 B DC 15 ? ? O B HOH 41 ? ? 2.14 9 1 O2 A DC 5 ? ? O A HOH 39 ? ? 2.18 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O B HOH 64 ? ? 1_555 O B HOH 65 ? ? 4_456 1.49 2 1 O B HOH 73 ? ? 1_555 O B HOH 77 ? ? 3_555 1.98 3 1 O B HOH 73 ? ? 1_555 O B HOH 82 ? ? 3_555 2.18 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.375 1.419 -0.044 0.006 N 2 1 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.364 1.419 -0.055 0.006 N 3 1 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.373 1.419 -0.046 0.006 N 4 1 "O3'" A DC 5 ? ? "C3'" A DC 5 ? ? 1.374 1.419 -0.045 0.006 N 5 1 "O3'" A DG 6 ? ? "C3'" A DG 6 ? ? 1.374 1.419 -0.045 0.006 N 6 1 "O3'" A DC 7 ? ? "C3'" A DC 7 ? ? 1.340 1.419 -0.079 0.006 N 7 1 "O3'" B DC 11 ? ? "C3'" B DC 11 ? ? 1.380 1.419 -0.039 0.006 N 8 1 C8 B DG 13 ? ? N9 B DG 13 ? ? 1.427 1.374 0.053 0.007 N 9 1 "O3'" B DC 15 ? ? "C3'" B DC 15 ? ? 1.357 1.419 -0.062 0.006 N 10 1 N1 B DC 15 ? ? C6 B DC 15 ? ? 1.330 1.367 -0.037 0.006 N 11 1 "C5'" B DG 20 ? ? "C4'" B DG 20 ? ? 1.555 1.512 0.043 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 100.70 104.50 -3.80 0.40 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 115.75 108.30 7.45 0.30 N 3 1 C2 A DC 1 ? ? N3 A DC 1 ? ? C4 A DC 1 ? ? 123.57 119.90 3.67 0.50 N 4 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 123.84 118.90 4.94 0.60 N 5 1 "O3'" A DC 1 ? ? P A DC 2 ? ? "O5'" A DC 2 ? ? 115.54 104.00 11.54 1.90 Y 6 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 100.70 104.50 -3.80 0.40 N 7 1 "C1'" A DC 2 ? ? "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 115.16 110.30 4.86 0.70 N 8 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 99.58 105.90 -6.32 0.80 N 9 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 102.25 108.00 -5.75 0.70 N 10 1 "O5'" A DG 3 ? ? P A DG 3 ? ? OP2 A DG 3 ? ? 98.43 105.70 -7.27 0.90 N 11 1 "O5'" A DG 3 ? ? "C5'" A DG 3 ? ? "C4'" A DG 3 ? ? 100.87 109.40 -8.53 0.80 N 12 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 102.89 109.40 -6.51 0.80 N 13 1 C5 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 132.45 128.60 3.85 0.60 N 14 1 "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? 99.18 104.50 -5.32 0.40 N 15 1 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 108.94 103.10 5.84 0.90 N 16 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 100.74 108.00 -7.26 0.70 N 17 1 C6 A DC 5 ? ? N1 A DC 5 ? ? C2 A DC 5 ? ? 123.13 120.30 2.83 0.40 N 18 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 102.86 108.00 -5.14 0.70 N 19 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 124.81 119.90 4.91 0.60 N 20 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 123.05 128.60 -5.55 0.60 N 21 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 112.00 108.30 3.70 0.30 N 22 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? "C2'" A DC 8 ? ? 100.16 105.90 -5.74 0.80 N 23 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 103.57 108.00 -4.43 0.70 N 24 1 "O5'" A DG 9 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 100.11 105.70 -5.59 0.90 N 25 1 "O5'" A DG 9 ? ? "C5'" A DG 9 ? ? "C4'" A DG 9 ? ? 104.59 109.40 -4.81 0.80 N 26 1 P A DG 9 ? ? "O5'" A DG 9 ? ? "C5'" A DG 9 ? ? 131.46 120.90 10.56 1.60 N 27 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 115.41 119.90 -4.49 0.60 N 28 1 "O5'" A DG 10 ? ? P A DG 10 ? ? OP2 A DG 10 ? ? 99.72 105.70 -5.98 0.90 N 29 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 100.87 108.00 -7.13 0.70 N 30 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 100.80 108.00 -7.20 0.70 N 31 1 "C3'" B DC 12 ? ? "O3'" B DC 12 ? ? P B DG 13 ? ? 127.35 119.70 7.65 1.20 Y 32 1 OP1 B DG 13 ? ? P B DG 13 ? ? OP2 B DG 13 ? ? 129.95 119.60 10.35 1.50 N 33 1 "O5'" B DG 13 ? ? P B DG 13 ? ? OP2 B DG 13 ? ? 92.15 105.70 -13.55 0.90 N 34 1 C6 B DG 13 ? ? N1 B DG 13 ? ? C2 B DG 13 ? ? 120.13 125.10 -4.97 0.60 N 35 1 C5 B DG 13 ? ? C6 B DG 13 ? ? N1 B DG 13 ? ? 115.58 111.50 4.08 0.50 N 36 1 C5 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 123.70 128.60 -4.90 0.60 N 37 1 C6 B DG 14 ? ? C5 B DG 14 ? ? N7 B DG 14 ? ? 126.75 130.40 -3.65 0.60 N 38 1 N1 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 124.93 119.90 5.03 0.60 N 39 1 C5 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 122.47 128.60 -6.13 0.60 N 40 1 OP1 B DC 15 ? ? P B DC 15 ? ? OP2 B DC 15 ? ? 128.92 119.60 9.32 1.50 N 41 1 "O5'" B DC 15 ? ? P B DC 15 ? ? OP1 B DC 15 ? ? 97.01 105.70 -8.69 0.90 N 42 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 103.66 108.00 -4.34 0.70 N 43 1 C2 B DC 15 ? ? N3 B DC 15 ? ? C4 B DC 15 ? ? 116.24 119.90 -3.66 0.50 N 44 1 C4 B DC 15 ? ? C5 B DC 15 ? ? C6 B DC 15 ? ? 121.57 117.40 4.17 0.50 N 45 1 C5 B DC 15 ? ? C6 B DC 15 ? ? N1 B DC 15 ? ? 117.99 121.00 -3.01 0.50 N 46 1 N3 B DC 15 ? ? C4 B DC 15 ? ? N4 B DC 15 ? ? 122.50 118.00 4.50 0.70 N 47 1 C5 B DC 15 ? ? C4 B DC 15 ? ? N4 B DC 15 ? ? 115.30 120.20 -4.90 0.70 N 48 1 "O4'" B DG 16 ? ? "C1'" B DG 16 ? ? N9 B DG 16 ? ? 110.10 108.30 1.80 0.30 N 49 1 "C3'" B DG 16 ? ? "O3'" B DG 16 ? ? P B DC 17 ? ? 132.78 119.70 13.08 1.20 Y 50 1 P B DC 17 ? ? "O5'" B DC 17 ? ? "C5'" B DC 17 ? ? 103.42 120.90 -17.48 1.60 N 51 1 C4 B DC 17 ? ? C5 B DC 17 ? ? C6 B DC 17 ? ? 114.04 117.40 -3.36 0.50 N 52 1 "C5'" B DG 19 ? ? "C4'" B DG 19 ? ? "O4'" B DG 19 ? ? 119.00 109.80 9.20 1.10 N 53 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 111.42 108.30 3.12 0.30 N 54 1 C5 B DG 19 ? ? N7 B DG 19 ? ? C8 B DG 19 ? ? 101.26 104.30 -3.04 0.50 N 55 1 C5 B DG 19 ? ? C6 B DG 19 ? ? O6 B DG 19 ? ? 123.80 128.60 -4.80 0.60 N 56 1 "O4'" B DG 20 ? ? "C4'" B DG 20 ? ? "C3'" B DG 20 ? ? 99.23 104.50 -5.27 0.40 N 57 1 "C5'" B DG 20 ? ? "C4'" B DG 20 ? ? "C3'" B DG 20 ? ? 123.44 115.70 7.74 1.20 N 58 1 "C5'" B DG 20 ? ? "C4'" B DG 20 ? ? "O4'" B DG 20 ? ? 116.89 109.80 7.09 1.10 N 59 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 110.16 108.30 1.86 0.30 N # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 NA NA NA N N 75 SR SR SR N N 76 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 # _ndb_struct_conf_na.entry_id 3PBX _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 10 1_555 0.818 -0.419 0.059 2.187 -10.491 -2.589 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.031 -0.338 0.213 0.168 -5.665 -7.453 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.560 -0.169 0.268 -0.448 -0.733 2.947 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -0.159 -0.194 0.328 0.717 -9.423 0.468 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DC 5 1_555 B DG 6 1_555 -0.758 0.005 0.224 -2.703 -6.034 -5.317 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.346 -0.139 0.301 6.816 -8.003 -4.059 6 A_DG6:DC15_B A 6 ? B 15 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.325 1.971 3.505 4.043 2.440 37.514 2.698 0.068 3.635 3.776 -6.256 37.800 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.023 2.667 3.356 -1.269 -2.062 37.008 4.470 -0.206 3.205 -3.244 1.996 37.085 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DG 4 1_555 B DC 7 1_555 -0.543 1.426 3.496 -2.851 2.306 37.525 1.882 0.439 3.604 3.575 4.418 37.698 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DC 5 1_555 B DG 6 1_555 -0.139 0.378 3.399 1.914 -1.491 36.022 0.828 0.504 3.369 -2.408 -3.091 36.101 4 AA_DG4DC5:DG16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DC 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 0.072 0.724 3.157 -0.112 3.388 33.082 0.713 -0.144 3.213 5.931 0.196 33.251 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 'SODIUM ION' NA 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3GOJ _pdbx_initial_refinement_model.details ? #