data_3TOK # _entry.id 3TOK # _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 3TOK pdb_00003tok 10.2210/pdb3tok/pdb NDB NA1297 ? ? RCSB RCSB067727 ? ? WWPDB D_1000067727 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2ORG . unspecified PDB 2ORF . unspecified PDB 2ORH . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3TOK _pdbx_database_status.recvd_initial_deposition_date 2011-09-05 _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_ _audit_author.name _audit_author.pdbx_ordinal 'Carter, M.' 1 'Ho, P.S.' 2 # _citation.id primary _citation.title 'Assaying the Energies of Biological Halogen Bonds' _citation.journal_abbrev 'CRYST.GROWTH DES.' _citation.journal_volume 11 _citation.page_first 5087 _citation.page_last 5095 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1528-7483 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI 10.1021/cg200991v # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Carter, M.' 1 ? primary 'Ho, P.S.' 2 ? # _cell.entry_id 3TOK _cell.length_a 65.36 _cell.length_b 24.60 _cell.length_c 37.41 _cell.angle_alpha 90.00 _cell.angle_beta 110.76 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3TOK _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 (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3') ; 3029.994 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3') ; 3061.003 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 128 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DA)(DT)(DA)(DC)(DC)(DG)(DG)' CCGATACCGG A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DG)(DT)(DA)(DT)(DC)(DG)(DG)' CCGGTATCGG B ? # 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 DA 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 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DG n 2 5 DT n 2 6 DA n 2 7 DT n 2 8 DC n 2 9 DG n 2 10 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'Synthetic construct' 2 1 sample ? ? ? ? ? 'Synthetic construct' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3TOK 3TOK 1 ? CCGATACCGG ? 2 PDB 3TOK 3TOK 2 ? CCGGTATCGG ? # 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 3TOK A 1 ? 10 ? 3TOK 1 ? 10 ? 1 10 2 2 3TOK B 1 ? 10 ? 3TOK 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # _exptl.entry_id 3TOK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.31 _exptl_crystal.density_percent_sol 46.76 _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 298.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;25mM Sodium Calcodylate, 10mM Calcuim Chloride, 1.1mM Spermine, and 0.35mM of each DNA strand, pH 7.0, vapor diffusion, sitting drop,temperature 298K, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K ; # _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 NOIR-1 _diffrn_detector.pdbx_collection_date 2009-06-24 _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 'Rosenbaum-rock SI(111) sagitally focused monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 4.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 4.2.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3TOK _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 40 _reflns.d_resolution_high 1.5 _reflns.number_obs 10026 _reflns.number_all ? _reflns.percent_possible_obs 97.98 _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.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3TOK _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 5299 _refine.ls_number_reflns_all 5886 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 40 _refine.ls_d_res_high 1.74 _refine.ls_percent_reflns_obs 88.8 _refine.ls_R_factor_obs 0.22042 _refine.ls_R_factor_all 0.2357 _refine.ls_R_factor_R_work 0.2339 _refine.ls_R_factor_R_free 0.2913 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 297 _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 2ORG _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_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 1 _refine_hist.number_atoms_solvent 128 _refine_hist.number_atoms_total 533 _refine_hist.d_res_high 1.74 _refine_hist.d_res_low 40 # 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 c_bond_d 1.343 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d 1.900 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.74 _refine_ls_shell.d_res_low 1.84 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work ? _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 3TOK _struct.title 'Assaying the energies of biological halogen bonds.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3TOK _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA Holliday Junction, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ;The asymmetric unit contains two DNA strands. The biological unit is deposited as four strands, containing two pairs of symmetry related alternative conformations ; # 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 ? ? B DC 2 O2 A ? ? 1_555 C NA . NA ? ? B DC 12 B NA 101 1_555 ? ? ? ? ? ? ? 2.901 ? ? metalc2 metalc ? ? B DG 3 "O4'" A ? ? 1_555 C NA . NA ? ? B DG 13 B NA 101 1_555 ? ? ? ? ? ? ? 3.013 ? ? metalc3 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? B NA 101 B HOH 204 1_555 ? ? ? ? ? ? ? 2.744 ? ? metalc4 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? B NA 101 B HOH 208 1_555 ? ? ? ? ? ? ? 2.986 ? ? metalc5 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? B NA 101 B HOH 238 1_555 ? ? ? ? ? ? ? 2.997 ? ? metalc6 metalc ? ? C NA . NA ? ? ? 1_555 E HOH . O ? ? B NA 101 B HOH 240 1_555 ? ? ? ? ? ? ? 2.671 ? ? hydrog1 hydrog ? ? A DC 1 N3 A ? ? 1_555 B DG 10 N1 A ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 A ? ? 1_555 B DG 10 O6 A ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 A ? ? 1_555 B DG 10 N2 A ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 A ? ? 1_555 B DG 9 N1 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 A ? ? 1_555 B DG 9 O6 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 A ? ? 1_555 B DG 9 N2 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 A ? ? 1_555 B DC 8 N3 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 A ? ? 1_555 B DC 8 O2 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 A ? ? 1_555 B DC 8 N4 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 A ? ? 1_555 B DT 7 N3 A ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 A ? ? 1_555 B DT 7 O4 A ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 A ? ? 1_555 B DA 6 N1 A ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 A ? ? 1_555 B DA 6 N6 A ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N1 A ? ? 1_555 B DT 5 N3 A ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 A ? ? 1_555 B DT 5 O4 A ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id NA _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 8 _struct_site.details 'BINDING SITE FOR RESIDUE NA B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 8 DC A 2 ? DC A 2 . ? 2_657 ? 2 AC1 8 DG A 3 ? DG A 3 . ? 2_657 ? 3 AC1 8 DC B 2 ? DC B 12 . ? 1_555 ? 4 AC1 8 DG B 3 ? DG B 13 . ? 1_555 ? 5 AC1 8 HOH E . ? HOH B 204 . ? 1_555 ? 6 AC1 8 HOH E . ? HOH B 208 . ? 1_555 ? 7 AC1 8 HOH E . ? HOH B 238 . ? 1_555 ? 8 AC1 8 HOH E . ? HOH B 240 . ? 1_555 ? # _database_PDB_matrix.entry_id 3TOK _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 3TOK _atom_sites.fract_transf_matrix[1][1] 0.015298 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005805 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040634 _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] 0.028583 _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 # 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 DA 4 4 4 DA DA 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 B 2 1 DC 1 11 11 DC DC B . n B 2 2 DC 2 12 12 DC DC B . n B 2 3 DG 3 13 13 DG DG B . n B 2 4 DG 4 14 14 DG DG B . n B 2 5 DT 5 15 15 DT DT B . n B 2 6 DA 6 16 16 DA DA B . n B 2 7 DT 7 17 17 DT DT B . n B 2 8 DC 8 18 18 DC DC B . n B 2 9 DG 9 19 19 DG DG B . n B 2 10 DG 10 20 20 DG DG 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 3 NA 1 101 45 NA NA B . D 4 HOH 1 101 43 HOH HOH A . D 4 HOH 2 102 44 HOH HOH A . D 4 HOH 3 103 48 HOH HOH A . D 4 HOH 4 104 62 HOH HOH A . D 4 HOH 5 105 70 HOH HOH A . D 4 HOH 6 106 71 HOH HOH A . D 4 HOH 7 107 75 HOH HOH A . D 4 HOH 8 108 81 HOH HOH A . D 4 HOH 9 109 82 HOH HOH A . D 4 HOH 10 110 83 HOH HOH A . D 4 HOH 11 111 85 HOH HOH A . D 4 HOH 12 112 87 HOH HOH A . D 4 HOH 13 113 88 HOH HOH A . D 4 HOH 14 114 89 HOH HOH A . D 4 HOH 15 115 91 HOH HOH A . D 4 HOH 16 116 92 HOH HOH A . D 4 HOH 17 117 96 HOH HOH A . D 4 HOH 18 118 97 HOH HOH A . D 4 HOH 19 119 99 HOH HOH A . D 4 HOH 20 120 102 HOH HOH A . D 4 HOH 21 121 106 HOH HOH A . D 4 HOH 22 122 109 HOH HOH A . D 4 HOH 23 123 114 HOH HOH A . D 4 HOH 24 124 119 HOH HOH A . D 4 HOH 25 125 121 HOH HOH A . D 4 HOH 26 126 125 HOH HOH A . D 4 HOH 27 127 128 HOH HOH A . D 4 HOH 28 128 133 HOH HOH A . D 4 HOH 29 129 134 HOH HOH A . D 4 HOH 30 130 141 HOH HOH A . D 4 HOH 31 131 143 HOH HOH A . D 4 HOH 32 132 145 HOH HOH A . D 4 HOH 33 133 146 HOH HOH A . D 4 HOH 34 134 147 HOH HOH A . D 4 HOH 35 135 151 HOH HOH A . D 4 HOH 36 136 154 HOH HOH A . D 4 HOH 37 137 157 HOH HOH A . D 4 HOH 38 138 159 HOH HOH A . D 4 HOH 39 139 161 HOH HOH A . D 4 HOH 40 140 162 HOH HOH A . D 4 HOH 41 141 164 HOH HOH A . D 4 HOH 42 142 168 HOH HOH A . D 4 HOH 43 143 171 HOH HOH A . D 4 HOH 44 144 173 HOH HOH A . D 4 HOH 45 145 174 HOH HOH A . D 4 HOH 46 146 176 HOH HOH A . D 4 HOH 47 147 177 HOH HOH A . D 4 HOH 48 148 178 HOH HOH A . D 4 HOH 49 149 180 HOH HOH A . D 4 HOH 50 150 204 HOH HOH A . D 4 HOH 51 151 206 HOH HOH A . D 4 HOH 52 152 169 HOH HOH A . E 4 HOH 1 201 120 HOH HOH B . E 4 HOH 2 202 155 HOH HOH B . E 4 HOH 3 203 163 HOH HOH B . E 4 HOH 4 204 41 HOH HOH B . E 4 HOH 5 205 42 HOH HOH B . E 4 HOH 6 206 46 HOH HOH B . E 4 HOH 7 207 47 HOH HOH B . E 4 HOH 8 208 49 HOH HOH B . E 4 HOH 9 209 50 HOH HOH B . E 4 HOH 10 210 51 HOH HOH B . E 4 HOH 11 211 52 HOH HOH B . E 4 HOH 12 212 53 HOH HOH B . E 4 HOH 13 213 54 HOH HOH B . E 4 HOH 14 214 55 HOH HOH B . E 4 HOH 15 215 56 HOH HOH B . E 4 HOH 16 216 57 HOH HOH B . E 4 HOH 17 217 58 HOH HOH B . E 4 HOH 18 218 59 HOH HOH B . E 4 HOH 19 219 61 HOH HOH B . E 4 HOH 20 220 63 HOH HOH B . E 4 HOH 21 221 65 HOH HOH B . E 4 HOH 22 222 68 HOH HOH B . E 4 HOH 23 223 69 HOH HOH B . E 4 HOH 24 224 72 HOH HOH B . E 4 HOH 25 225 73 HOH HOH B . E 4 HOH 26 226 74 HOH HOH B . E 4 HOH 27 227 76 HOH HOH B . E 4 HOH 28 228 77 HOH HOH B . E 4 HOH 29 229 78 HOH HOH B . E 4 HOH 30 230 79 HOH HOH B . E 4 HOH 31 231 80 HOH HOH B . E 4 HOH 32 232 84 HOH HOH B . E 4 HOH 33 233 86 HOH HOH B . E 4 HOH 34 234 90 HOH HOH B . E 4 HOH 35 235 93 HOH HOH B . E 4 HOH 36 236 95 HOH HOH B . E 4 HOH 37 237 98 HOH HOH B . E 4 HOH 38 238 100 HOH HOH B . E 4 HOH 39 239 103 HOH HOH B . E 4 HOH 40 240 104 HOH HOH B . E 4 HOH 41 241 105 HOH HOH B . E 4 HOH 42 242 108 HOH HOH B . E 4 HOH 43 243 113 HOH HOH B . E 4 HOH 44 244 115 HOH HOH B . E 4 HOH 45 245 118 HOH HOH B . E 4 HOH 46 246 124 HOH HOH B . E 4 HOH 47 247 126 HOH HOH B . E 4 HOH 48 248 129 HOH HOH B . E 4 HOH 49 249 130 HOH HOH B . E 4 HOH 50 250 131 HOH HOH B . E 4 HOH 51 251 132 HOH HOH B . E 4 HOH 52 252 135 HOH HOH B . E 4 HOH 53 253 137 HOH HOH B . E 4 HOH 54 254 138 HOH HOH B . E 4 HOH 55 255 139 HOH HOH B . E 4 HOH 56 256 140 HOH HOH B . E 4 HOH 57 257 142 HOH HOH B . E 4 HOH 58 258 144 HOH HOH B . E 4 HOH 59 259 148 HOH HOH B . E 4 HOH 60 260 149 HOH HOH B . E 4 HOH 61 261 150 HOH HOH B . E 4 HOH 62 262 152 HOH HOH B . E 4 HOH 63 263 153 HOH HOH B . E 4 HOH 64 264 156 HOH HOH B . E 4 HOH 65 265 158 HOH HOH B . E 4 HOH 66 266 160 HOH HOH B . E 4 HOH 67 267 165 HOH HOH B . E 4 HOH 68 268 166 HOH HOH B . E 4 HOH 69 269 167 HOH HOH B . E 4 HOH 70 270 170 HOH HOH B . E 4 HOH 71 271 172 HOH HOH B . E 4 HOH 72 272 175 HOH HOH B . E 4 HOH 73 273 179 HOH HOH B . E 4 HOH 74 274 181 HOH HOH B . E 4 HOH 75 275 182 HOH HOH B . E 4 HOH 76 276 205 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 # 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)' 3050 ? 1 MORE -32 ? 1 'SSA (A^2)' 6860 ? # 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_657 -x+1,y,-z+2 -1.0000000000 0.0000000000 0.0000000000 38.8397334277 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 69.9621887946 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B HOH 207 ? E HOH . 2 1 B HOH 274 ? E HOH . # 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 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 "O4'" A B DG 3 ? B DG 13 ? 1_555 121.5 ? 2 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 204 ? 1_555 120.3 ? 3 "O4'" A B DG 3 ? B DG 13 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 204 ? 1_555 109.1 ? 4 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 208 ? 1_555 107.8 ? 5 "O4'" A B DG 3 ? B DG 13 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 208 ? 1_555 80.5 ? 6 O ? E HOH . ? B HOH 204 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 208 ? 1_555 50.2 ? 7 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 238 ? 1_555 61.3 ? 8 "O4'" A B DG 3 ? B DG 13 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 238 ? 1_555 138.7 ? 9 O ? E HOH . ? B HOH 204 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 238 ? 1_555 99.9 ? 10 O ? E HOH . ? B HOH 208 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 238 ? 1_555 140.5 ? 11 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 240 ? 1_555 104.1 ? 12 "O4'" A B DG 3 ? B DG 13 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 240 ? 1_555 131.1 ? 13 O ? E HOH . ? B HOH 204 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 240 ? 1_555 53.2 ? 14 O ? E HOH . ? B HOH 208 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 240 ? 1_555 103.1 ? 15 O ? E HOH . ? B HOH 238 ? 1_555 NA ? C NA . ? B NA 101 ? 1_555 O ? E HOH . ? B HOH 240 ? 1_555 51.4 ? # 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 2012-08-15 2 'Structure model' 1 1 2023-09-13 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' pdbx_initial_refinement_model 5 2 'Structure model' pdbx_struct_conn_angle 6 2 'Structure model' struct_conn 7 2 '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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 6 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 13 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 2 'Structure model' '_pdbx_struct_conn_angle.value' 18 2 'Structure model' '_struct_conn.pdbx_dist_value' 19 2 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 20 2 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 2 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 2 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 2 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 2 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 2 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 2 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 2 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 32 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 33 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 EPMR phasing . ? 2 CNS refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 O2 B DC 12 ? B 1_555 O A HOH 117 ? ? 2_657 1.64 2 1 OP1 B DC 12 ? A 1_555 O A HOH 102 ? ? 2_657 1.65 3 1 O6 B DG 13 ? B 1_555 O B HOH 220 ? ? 1_556 1.81 4 1 OP2 A DA 4 ? A 1_555 O B HOH 273 ? ? 1_545 2.01 5 1 OP2 A DA 4 ? B 1_555 O B HOH 261 ? ? 2_658 2.05 6 1 O B HOH 244 ? ? 1_555 O B HOH 267 ? ? 1_565 2.07 7 1 OP2 B DG 14 ? B 1_555 O B HOH 233 ? ? 2_647 2.12 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 NA NA NA N N 147 # 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 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 3TOK _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 0.678 -0.492 0.373 -5.087 -12.849 -3.510 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.386 -0.114 0.160 -2.587 -6.145 0.931 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.844 -0.242 -0.071 -6.806 -8.039 5.973 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B DT 7 1_555 -0.123 0.074 0.235 -3.242 -27.318 1.540 4 A_DA4:DT17_B A 4 ? B 17 ? 20 1 1 A DT 5 1_555 B DA 6 1_555 -0.400 0.294 -0.163 -3.451 -15.684 -2.542 5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.009 -0.054 -0.079 0.728 -14.383 -1.942 6 A_DA6:DT15_B A 6 ? B 15 ? 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 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.650 2.162 3.535 10.238 3.820 40.864 2.555 0.292 3.763 5.357 -14.356 42.239 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 -0.168 2.649 3.410 2.516 3.027 33.619 4.025 0.724 3.607 5.212 -4.331 33.842 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 DA 4 1_555 B DT 7 1_555 -1.171 1.667 3.262 -10.094 1.041 42.029 2.158 0.556 3.478 1.426 13.833 43.183 3 AA_DG3DA4:DT17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B DT 7 1_555 A DT 5 1_555 B DA 6 1_555 -0.222 -0.385 3.269 1.983 0.754 30.944 -0.864 0.794 3.239 1.411 -3.710 31.015 4 AA_DA4DT5:DA16DT17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 0.904 0.947 3.229 2.551 4.467 40.178 0.862 -1.017 3.359 6.471 -3.695 40.492 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 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 2ORG _pdbx_initial_refinement_model.details ? #