data_3FX8 # _entry.id 3FX8 # _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 3FX8 pdb_00003fx8 10.2210/pdb3fx8/pdb NDB BD0109 ? ? RCSB RCSB051153 ? ? WWPDB D_1000051153 ? ? # 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 2010-03-16 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3FX8 _pdbx_database_status.recvd_initial_deposition_date 2009-01-20 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2ET0 ;Recognition of three-way DNA junctions by a metallo-supramolecular cylinder ('helicate') at two distinct sites ; unspecified PDB 3FX9 ;Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate') ; unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Boer, D.R.' 1 'Uson, I.' 2 'Coll, M.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders. ; Angew.Chem.Int.Ed.Engl. 49 2336 2339 2010 ? GE 1433-7851 9999 ? 20191645 10.1002/anie.200906742 1 'Molecular recognition of a three-way DNA junction by a metallosupramolecular helicate.' Angew.Chem.Int.Ed.Engl. 45 1227 1231 2006 ? GE 1433-7851 9999 ? 16463312 10.1002/anie.200503822 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Boer, D.R.' 1 ? primary 'Kerckhoffs, J.M.' 2 ? primary 'Parajo, Y.' 3 ? primary 'Pascu, M.' 4 ? primary 'Uson, I.' 5 ? primary 'Lincoln, P.' 6 ? primary 'Hannon, M.J.' 7 ? primary 'Coll, M.' 8 ? 1 'Oleksy, A.' 9 ? 1 'Blanco, A.G.' 10 ? 1 'Boer, R.' 11 ? 1 'Uson, I.' 12 ? 1 'Aymami, J.' 13 ? 1 'Rodger, A.' 14 ? 1 'Hannon, M.J.' 15 ? 1 'Coll, M.' 16 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "(5'-D(*CP*GP*TP*AP*CP*G)-3'" 1809.217 1 ? ? ? 'Synthetic hexanucleotide' 2 non-polymer syn 'FE (II) ION' 55.845 4 ? ? ? ? 3 non-polymer syn "4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}" 394.492 2 ? ? ? ? # _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)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'FE (II) ION' FE2 3 "4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}" 5PM # 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 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 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 'Synthetic hexanucleotide. The sequence is palindromic' # 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 5PM non-polymer . "4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}" '1,1-Bis(N-(4-phenyl)-2-pyridylcarboxaldimine)thioether' 'C24 H18 N4 S' 394.492 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 FE2 non-polymer . 'FE (II) ION' ? 'Fe 2' 55.845 # 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 C . n A 1 2 DG 2 2 2 DG G C . n A 1 3 DT 3 3 3 DT T C . n A 1 4 DA 4 4 4 DA A C . n A 1 5 DC 5 5 5 DC C C . n A 1 6 DG 6 6 6 DG G C . 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 FE2 1 101 1 FE2 5PM C . C 2 FE2 1 102 1 FE2 5PM C . D 2 FE2 1 201 1 FE2 5PM C . E 2 FE2 1 202 1 FE2 5PM C . F 3 5PM 1 111 1 5PM 5PM C . G 3 5PM 1 211 1 5PM 5PM C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ProDC 'data collection' . ? 1 SHELXDE phasing . ? 2 SHELXL-97 refinement . ? 3 MOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 3FX8 _cell.length_a 49.249 _cell.length_b 49.249 _cell.length_c 49.249 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3FX8 _symmetry.space_group_name_H-M 'P 21 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3FX8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 5.50 _exptl_crystal.density_percent_sol 77.64 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details ;1 microliter of 10 mM cylinder, 1 microliter of 3 mM DNA, 2 microliters of crystallization buffer (10 mM Magnesium chloride, 5% v/v Isopropanol, 50 mM Tris-HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'Magnesium chloride' ? ? ? 1 2 1 Isopropanol ? ? ? 1 3 1 Tris-HCl ? ? ? 1 4 2 'Magnesium chloride' ? ? ? 1 5 2 Isopropanol ? ? ? 1 6 2 Tris-HCl ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2006-02-23 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.7366 1.0 2 1.7410 1.0 3 1.7311 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.7366, 1.7410, 1.7311' # _reflns.entry_id 3FX8 _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 24.63 _reflns.d_resolution_high 2.44 _reflns.number_obs 1573 _reflns.number_all 1573 _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 36.1 _reflns.B_iso_Wilson_estimate 94 _reflns.pdbx_redundancy 8.4 _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 2.44 _reflns_shell.d_res_low 2.58 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.447 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.2 _reflns_shell.pdbx_redundancy 5.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 228 _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 3FX8 _refine.ls_number_reflns_obs 1540 _refine.ls_number_reflns_all 1573 _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 24.63 _refine.ls_d_res_high 2.44 _refine.ls_percent_reflns_obs 98 _refine.ls_R_factor_obs 0.187 _refine.ls_R_factor_all 0.187 _refine.ls_R_factor_R_work 0.187 _refine.ls_R_factor_R_free 0.212 _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 74 _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 79.4 _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 'BABINET (SHELXL SWAT)' _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 ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model isotropic _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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 ? _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 120 _refine_hist.pdbx_number_atoms_ligand 62 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 182 _refine_hist.d_res_high 2.44 _refine_hist.d_res_low 24.63 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_angle_d 0.021 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.005 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.031 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.44 _refine_ls_shell.d_res_low 2.55 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.358 _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.number_reflns_obs 165 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3FX8 _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 3FX8 _struct.title ;Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate') ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3FX8 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Self-assembly, DNA-based nanomaterial, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3FX8 _struct_ref.pdbx_db_accession 3FX8 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code CGTACG _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3FX8 _struct_ref_seq.pdbx_strand_id C _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3FX8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _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 6 # _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 # 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)' 4580 ? 1 MORE -68.9 ? 1 'SSA (A^2)' 2430 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # 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' 6_467 z-1/2,-x+3/2,-y+2 0.0000000000 0.0000000000 1.0000000000 -24.6245000000 -1.0000000000 0.0000000000 0.0000000000 73.8735000000 0.0000000000 -1.0000000000 0.0000000000 98.4980000000 3 'crystal symmetry operation' 12_675 -y+3/2,-z+2,x+1/2 0.0000000000 -1.0000000000 0.0000000000 73.8735000000 0.0000000000 0.0000000000 -1.0000000000 98.4980000000 1.0000000000 0.0000000000 0.0000000000 24.6245000000 # loop_ _struct_biol.id _struct_biol.details 1 ? 2 ;A THREE-WAY JUNCTION (CHAINS A AND C) WITH DISCONTINUOUS DNA STRANDS CAN BE GENERATED THROUGH THE FOLLOWING TRANSFORMATIONS ON CHAIN C: [Z+1/2,-X+1/2,-Y+(0 1 1)], [Y+1/2,-Z+1/2,-X+(-1 1 1)], [-X, Y+1/2,-Z+1/2+(0 1 0)], [-Z,X+1/2,-Y+1/2+(0 1 1)], [Y,Z,X+(0 2 1)] AND THE FOLLOWING TRANSFORMATIONS ON CHAIN A: [-Z,X+1/2,-Y+1/2 +(0 1 1)], [Y+1/2,-Z+1/2,-X +(-1 1 1)] ; # 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 FE2 . FE ? ? ? 1_555 F 5PM . N11 ? ? C FE2 101 C 5PM 111 1_555 ? ? ? ? ? ? ? 1.982 ? ? metalc2 metalc ? ? B FE2 . FE ? ? ? 1_555 F 5PM . N12 ? ? C FE2 101 C 5PM 111 1_555 ? ? ? ? ? ? ? 1.936 ? ? metalc3 metalc ? ? C FE2 . FE ? ? ? 1_555 F 5PM . N13 ? ? C FE2 102 C 5PM 111 1_555 ? ? ? ? ? ? ? 1.982 ? ? metalc4 metalc ? ? C FE2 . FE ? ? ? 1_555 F 5PM . N14 ? ? C FE2 102 C 5PM 111 1_555 ? ? ? ? ? ? ? 1.977 ? ? metalc5 metalc ? ? D FE2 . FE ? ? ? 1_555 G 5PM . N11 ? ? C FE2 201 C 5PM 211 1_555 ? ? ? ? ? ? ? 1.989 ? ? metalc6 metalc ? ? D FE2 . FE ? ? ? 1_555 G 5PM . N12 ? ? C FE2 201 C 5PM 211 1_555 ? ? ? ? ? ? ? 1.957 ? ? metalc7 metalc ? ? E FE2 . FE ? ? ? 1_555 G 5PM . N13 ? ? C FE2 202 C 5PM 211 1_555 ? ? ? ? ? ? ? 1.990 ? ? metalc8 metalc ? ? E FE2 . FE ? ? ? 1_555 G 5PM . N14 ? ? C FE2 202 C 5PM 211 1_555 ? ? ? ? ? ? ? 1.969 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 6 N1 ? ? C DC 1 C DG 6 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 6 O6 ? ? C DC 1 C DG 6 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 6 N2 ? ? C DC 1 C DG 6 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 5 N3 ? ? C DG 2 C DC 5 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 5 O2 ? ? C DG 2 C DC 5 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 5 N4 ? ? C DG 2 C DC 5 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 4 N1 ? ? C DT 3 C DA 4 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 4 N6 ? ? C DT 3 C DA 4 6_467 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 N11 ? F 5PM . ? C 5PM 111 ? 1_555 FE ? B FE2 . ? C FE2 101 ? 1_555 N12 ? F 5PM . ? C 5PM 111 ? 1_555 81.7 ? 2 N13 ? F 5PM . ? C 5PM 111 ? 1_555 FE ? C FE2 . ? C FE2 102 ? 1_555 N14 ? F 5PM . ? C 5PM 111 ? 1_555 80.9 ? 3 N11 ? G 5PM . ? C 5PM 211 ? 1_555 FE ? D FE2 . ? C FE2 201 ? 1_555 N12 ? G 5PM . ? C 5PM 211 ? 1_555 81.1 ? 4 N13 ? G 5PM . ? C 5PM 211 ? 1_555 FE ? E FE2 . ? C FE2 202 ? 1_555 N14 ? G 5PM . ? C 5PM 211 ? 1_555 81.1 ? # 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 C FE2 101 ? 3 'BINDING SITE FOR RESIDUE FE2 C 101' AC2 Software C FE2 102 ? 3 'BINDING SITE FOR RESIDUE FE2 C 102' AC3 Software C FE2 201 ? 3 'BINDING SITE FOR RESIDUE FE2 C 201' AC4 Software C FE2 202 ? 3 'BINDING SITE FOR RESIDUE FE2 C 202' AC5 Software C 5PM 111 ? 8 'BINDING SITE FOR RESIDUE 5PM C 111' AC6 Software C 5PM 211 ? 10 'BINDING SITE FOR RESIDUE 5PM C 211' # 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 5PM F . ? 5PM C 111 . ? 8_667 ? 2 AC1 3 5PM F . ? 5PM C 111 . ? 11_376 ? 3 AC1 3 5PM F . ? 5PM C 111 . ? 1_555 ? 4 AC2 3 5PM F . ? 5PM C 111 . ? 1_555 ? 5 AC2 3 5PM F . ? 5PM C 111 . ? 8_667 ? 6 AC2 3 5PM F . ? 5PM C 111 . ? 11_376 ? 7 AC3 3 5PM G . ? 5PM C 211 . ? 1_555 ? 8 AC3 3 5PM G . ? 5PM C 211 . ? 6_467 ? 9 AC3 3 5PM G . ? 5PM C 211 . ? 12_675 ? 10 AC4 3 5PM G . ? 5PM C 211 . ? 12_675 ? 11 AC4 3 5PM G . ? 5PM C 211 . ? 1_555 ? 12 AC4 3 5PM G . ? 5PM C 211 . ? 6_467 ? 13 AC5 8 DC A 1 ? DC C 1 . ? 11_376 ? 14 AC5 8 DG A 6 ? DG C 6 . ? 6_467 ? 15 AC5 8 FE2 B . ? FE2 C 101 . ? 11_376 ? 16 AC5 8 FE2 B . ? FE2 C 101 . ? 8_667 ? 17 AC5 8 FE2 B . ? FE2 C 101 . ? 1_555 ? 18 AC5 8 FE2 C . ? FE2 C 102 . ? 11_376 ? 19 AC5 8 FE2 C . ? FE2 C 102 . ? 8_667 ? 20 AC5 8 FE2 C . ? FE2 C 102 . ? 1_555 ? 21 AC6 10 DT A 3 ? DT C 3 . ? 1_555 ? 22 AC6 10 DA A 4 ? DA C 4 . ? 1_555 ? 23 AC6 10 DA A 4 ? DA C 4 . ? 12_675 ? 24 AC6 10 DC A 5 ? DC C 5 . ? 1_555 ? 25 AC6 10 FE2 D . ? FE2 C 201 . ? 1_555 ? 26 AC6 10 FE2 D . ? FE2 C 201 . ? 12_675 ? 27 AC6 10 FE2 D . ? FE2 C 201 . ? 6_467 ? 28 AC6 10 FE2 E . ? FE2 C 202 . ? 12_675 ? 29 AC6 10 FE2 E . ? FE2 C 202 . ? 6_467 ? 30 AC6 10 FE2 E . ? FE2 C 202 . ? 1_555 ? # 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'" C DG 2 ? ? "C4'" C DG 2 ? ? "C3'" C DG 2 ? ? 99.41 104.50 -5.09 0.40 N 2 1 "O4'" C DG 2 ? ? "C1'" C DG 2 ? ? N9 C DG 2 ? ? 112.61 108.30 4.31 0.30 N 3 1 "O4'" C DC 5 ? ? "C4'" C DC 5 ? ? "C3'" C DC 5 ? ? 102.03 104.50 -2.47 0.40 N 4 1 "C3'" C DC 5 ? ? "O3'" C DC 5 ? ? P C DG 6 ? ? 128.58 119.70 8.88 1.20 Y 5 1 "C3'" C DG 6 ? ? "C2'" C DG 6 ? ? "C1'" C DG 6 ? ? 97.04 102.40 -5.36 0.80 N 6 1 "O4'" C DG 6 ? ? "C1'" C DG 6 ? ? N9 C DG 6 ? ? 110.25 108.30 1.95 0.30 N # 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 C FE2 101 ? B FE2 . 2 1 C FE2 102 ? C FE2 . 3 1 C FE2 201 ? D FE2 . 4 1 C FE2 202 ? E FE2 . # _pdbx_entry_details.entry_id 3FX8 _pdbx_entry_details.nonpolymer_details ;LIGAND 5PM C 111 WITH TWO IRON ATOMS FE2 C 101 AND C 102 IS THE M HELICAL ENANTIOMER OF [FE2L3], WHERE L IS 4,4'-SULFANEDIYLBIS{N-[(1E)-PYRIDIN-2-YLMETHYLIDENE]ANILINE} ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 5PM N11 N Y N 1 5PM N12 N N N 2 5PM N13 N N N 3 5PM N14 N Y N 4 5PM C1A C Y N 5 5PM C1B C Y N 6 5PM C1C C Y N 7 5PM C1D C Y N 8 5PM C1E C Y N 9 5PM C1F C N N 10 5PM C1G C Y N 11 5PM C1H C Y N 12 5PM C1I C Y N 13 5PM C1J C Y N 14 5PM C1K C Y N 15 5PM C1L C Y N 16 5PM S1M S N N 17 5PM C1N C Y N 18 5PM C1O C Y N 19 5PM C1P C Y N 20 5PM C1Q C Y N 21 5PM C1R C Y N 22 5PM C1S C Y N 23 5PM C1T C N N 24 5PM C1U C Y N 25 5PM C1V C Y N 26 5PM C1W C Y N 27 5PM C1X C Y N 28 5PM C1Y C Y N 29 5PM H1A H N N 30 5PM H1B H N N 31 5PM H1C H N N 32 5PM H1D H N N 33 5PM H1F H N N 34 5PM H1H H N N 35 5PM H1I H N N 36 5PM H1K H N N 37 5PM H1L H N N 38 5PM H1O H N N 39 5PM H1P H N N 40 5PM H1R H N N 41 5PM H1S H N N 42 5PM H1T H N N 43 5PM H1V H N N 44 5PM H1W H N N 45 5PM H1X H N N 46 5PM H1Y H N N 47 DA OP3 O N N 48 DA P P N N 49 DA OP1 O N N 50 DA OP2 O N N 51 DA "O5'" O N N 52 DA "C5'" C N N 53 DA "C4'" C N R 54 DA "O4'" O N N 55 DA "C3'" C N S 56 DA "O3'" O N N 57 DA "C2'" C N N 58 DA "C1'" C N R 59 DA N9 N Y N 60 DA C8 C Y N 61 DA N7 N Y N 62 DA C5 C Y N 63 DA C6 C Y N 64 DA N6 N N N 65 DA N1 N Y N 66 DA C2 C Y N 67 DA N3 N Y N 68 DA C4 C Y N 69 DA HOP3 H N N 70 DA HOP2 H N N 71 DA "H5'" H N N 72 DA "H5''" H N N 73 DA "H4'" H N N 74 DA "H3'" H N N 75 DA "HO3'" H N N 76 DA "H2'" H N N 77 DA "H2''" H N N 78 DA "H1'" H N N 79 DA H8 H N N 80 DA H61 H N N 81 DA H62 H N N 82 DA H2 H N N 83 DC OP3 O N N 84 DC P P N N 85 DC OP1 O N N 86 DC OP2 O N N 87 DC "O5'" O N N 88 DC "C5'" C N N 89 DC "C4'" C N R 90 DC "O4'" O N N 91 DC "C3'" C N S 92 DC "O3'" O N N 93 DC "C2'" C N N 94 DC "C1'" C N R 95 DC N1 N N N 96 DC C2 C N N 97 DC O2 O N N 98 DC N3 N N N 99 DC C4 C N N 100 DC N4 N N N 101 DC C5 C N N 102 DC C6 C N N 103 DC HOP3 H N N 104 DC HOP2 H N N 105 DC "H5'" H N N 106 DC "H5''" H N N 107 DC "H4'" H N N 108 DC "H3'" H N N 109 DC "HO3'" H N N 110 DC "H2'" H N N 111 DC "H2''" H N N 112 DC "H1'" H N N 113 DC H41 H N N 114 DC H42 H N N 115 DC H5 H N N 116 DC H6 H N N 117 DG OP3 O N N 118 DG P P N N 119 DG OP1 O N N 120 DG OP2 O N N 121 DG "O5'" O N N 122 DG "C5'" C N N 123 DG "C4'" C N R 124 DG "O4'" O N N 125 DG "C3'" C N S 126 DG "O3'" O N N 127 DG "C2'" C N N 128 DG "C1'" C N R 129 DG N9 N Y N 130 DG C8 C Y N 131 DG N7 N Y N 132 DG C5 C Y N 133 DG C6 C N N 134 DG O6 O N N 135 DG N1 N N N 136 DG C2 C N N 137 DG N2 N N N 138 DG N3 N N N 139 DG C4 C Y N 140 DG HOP3 H N N 141 DG HOP2 H N N 142 DG "H5'" H N N 143 DG "H5''" H N N 144 DG "H4'" H N N 145 DG "H3'" H N N 146 DG "HO3'" H N N 147 DG "H2'" H N N 148 DG "H2''" H N N 149 DG "H1'" H N N 150 DG H8 H N N 151 DG H1 H N N 152 DG H21 H N N 153 DG H22 H N N 154 DT OP3 O N N 155 DT P P N N 156 DT OP1 O N N 157 DT OP2 O N N 158 DT "O5'" O N N 159 DT "C5'" C N N 160 DT "C4'" C N R 161 DT "O4'" O N N 162 DT "C3'" C N S 163 DT "O3'" O N N 164 DT "C2'" C N N 165 DT "C1'" C N R 166 DT N1 N N N 167 DT C2 C N N 168 DT O2 O N N 169 DT N3 N N N 170 DT C4 C N N 171 DT O4 O N N 172 DT C5 C N N 173 DT C7 C N N 174 DT C6 C N N 175 DT HOP3 H N N 176 DT HOP2 H N N 177 DT "H5'" H N N 178 DT "H5''" H N N 179 DT "H4'" H N N 180 DT "H3'" H N N 181 DT "HO3'" H N N 182 DT "H2'" H N N 183 DT "H2''" H N N 184 DT "H1'" H N N 185 DT H3 H N N 186 DT H71 H N N 187 DT H72 H N N 188 DT H73 H N N 189 DT H6 H N N 190 FE2 FE FE N N 191 # 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 5PM C1A N11 doub Y N 1 5PM N11 C1E sing Y N 2 5PM C1F N12 doub N N 3 5PM N12 C1G sing N N 4 5PM C1Q N13 sing N N 5 5PM N13 C1T doub N N 6 5PM N14 C1Y doub Y N 7 5PM N14 C1U sing Y N 8 5PM C1B C1A sing Y N 9 5PM C1A H1A sing N N 10 5PM C1B C1C doub Y N 11 5PM C1B H1B sing N N 12 5PM C1C C1D sing Y N 13 5PM C1C H1C sing N N 14 5PM C1D C1E doub Y N 15 5PM C1D H1D sing N N 16 5PM C1E C1F sing N N 17 5PM C1F H1F sing N N 18 5PM C1G C1L doub Y N 19 5PM C1G C1H sing Y N 20 5PM C1H C1I doub Y N 21 5PM C1H H1H sing N N 22 5PM C1I C1J sing Y N 23 5PM C1I H1I sing N N 24 5PM C1K C1J doub Y N 25 5PM C1J S1M sing N N 26 5PM C1L C1K sing Y N 27 5PM C1K H1K sing N N 28 5PM C1L H1L sing N N 29 5PM S1M C1N sing N N 30 5PM C1S C1N doub Y N 31 5PM C1N C1O sing Y N 32 5PM C1O C1P doub Y N 33 5PM C1O H1O sing N N 34 5PM C1Q C1P sing Y N 35 5PM C1P H1P sing N N 36 5PM C1R C1Q doub Y N 37 5PM C1S C1R sing Y N 38 5PM C1R H1R sing N N 39 5PM C1S H1S sing N N 40 5PM C1T C1U sing N N 41 5PM C1T H1T sing N N 42 5PM C1U C1V doub Y N 43 5PM C1V C1W sing Y N 44 5PM C1V H1V sing N N 45 5PM C1X C1W doub Y N 46 5PM C1W H1W sing N N 47 5PM C1Y C1X sing Y N 48 5PM C1X H1X sing N N 49 5PM C1Y H1Y sing N N 50 DA OP3 P sing N N 51 DA OP3 HOP3 sing N N 52 DA P OP1 doub N N 53 DA P OP2 sing N N 54 DA P "O5'" sing N N 55 DA OP2 HOP2 sing N N 56 DA "O5'" "C5'" sing N N 57 DA "C5'" "C4'" sing N N 58 DA "C5'" "H5'" sing N N 59 DA "C5'" "H5''" sing N N 60 DA "C4'" "O4'" sing N N 61 DA "C4'" "C3'" sing N N 62 DA "C4'" "H4'" sing N N 63 DA "O4'" "C1'" sing N N 64 DA "C3'" "O3'" sing N N 65 DA "C3'" "C2'" sing N N 66 DA "C3'" "H3'" sing N N 67 DA "O3'" "HO3'" sing N N 68 DA "C2'" "C1'" sing N N 69 DA "C2'" "H2'" sing N N 70 DA "C2'" "H2''" sing N N 71 DA "C1'" N9 sing N N 72 DA "C1'" "H1'" sing N N 73 DA N9 C8 sing Y N 74 DA N9 C4 sing Y N 75 DA C8 N7 doub Y N 76 DA C8 H8 sing N N 77 DA N7 C5 sing Y N 78 DA C5 C6 sing Y N 79 DA C5 C4 doub Y N 80 DA C6 N6 sing N N 81 DA C6 N1 doub Y N 82 DA N6 H61 sing N N 83 DA N6 H62 sing N N 84 DA N1 C2 sing Y N 85 DA C2 N3 doub Y N 86 DA C2 H2 sing N N 87 DA N3 C4 sing Y N 88 DC OP3 P sing N N 89 DC OP3 HOP3 sing N N 90 DC P OP1 doub N N 91 DC P OP2 sing N N 92 DC P "O5'" sing N N 93 DC OP2 HOP2 sing N N 94 DC "O5'" "C5'" sing N N 95 DC "C5'" "C4'" sing N N 96 DC "C5'" "H5'" sing N N 97 DC "C5'" "H5''" sing N N 98 DC "C4'" "O4'" sing N N 99 DC "C4'" "C3'" sing N N 100 DC "C4'" "H4'" sing N N 101 DC "O4'" "C1'" sing N N 102 DC "C3'" "O3'" sing N N 103 DC "C3'" "C2'" sing N N 104 DC "C3'" "H3'" sing N N 105 DC "O3'" "HO3'" sing N N 106 DC "C2'" "C1'" sing N N 107 DC "C2'" "H2'" sing N N 108 DC "C2'" "H2''" sing N N 109 DC "C1'" N1 sing N N 110 DC "C1'" "H1'" sing N N 111 DC N1 C2 sing N N 112 DC N1 C6 sing N N 113 DC C2 O2 doub N N 114 DC C2 N3 sing N N 115 DC N3 C4 doub N N 116 DC C4 N4 sing N N 117 DC C4 C5 sing N N 118 DC N4 H41 sing N N 119 DC N4 H42 sing N N 120 DC C5 C6 doub N N 121 DC C5 H5 sing N N 122 DC C6 H6 sing N N 123 DG OP3 P sing N N 124 DG OP3 HOP3 sing N N 125 DG P OP1 doub N N 126 DG P OP2 sing N N 127 DG P "O5'" sing N N 128 DG OP2 HOP2 sing N N 129 DG "O5'" "C5'" sing N N 130 DG "C5'" "C4'" sing N N 131 DG "C5'" "H5'" sing N N 132 DG "C5'" "H5''" sing N N 133 DG "C4'" "O4'" sing N N 134 DG "C4'" "C3'" sing N N 135 DG "C4'" "H4'" sing N N 136 DG "O4'" "C1'" sing N N 137 DG "C3'" "O3'" sing N N 138 DG "C3'" "C2'" sing N N 139 DG "C3'" "H3'" sing N N 140 DG "O3'" "HO3'" sing N N 141 DG "C2'" "C1'" sing N N 142 DG "C2'" "H2'" sing N N 143 DG "C2'" "H2''" sing N N 144 DG "C1'" N9 sing N N 145 DG "C1'" "H1'" sing N N 146 DG N9 C8 sing Y N 147 DG N9 C4 sing Y N 148 DG C8 N7 doub Y N 149 DG C8 H8 sing N N 150 DG N7 C5 sing Y N 151 DG C5 C6 sing N N 152 DG C5 C4 doub Y N 153 DG C6 O6 doub N N 154 DG C6 N1 sing N N 155 DG N1 C2 sing N N 156 DG N1 H1 sing N N 157 DG C2 N2 sing N N 158 DG C2 N3 doub N N 159 DG N2 H21 sing N N 160 DG N2 H22 sing N N 161 DG N3 C4 sing N N 162 DT OP3 P sing N N 163 DT OP3 HOP3 sing N N 164 DT P OP1 doub N N 165 DT P OP2 sing N N 166 DT P "O5'" sing N N 167 DT OP2 HOP2 sing N N 168 DT "O5'" "C5'" sing N N 169 DT "C5'" "C4'" sing N N 170 DT "C5'" "H5'" sing N N 171 DT "C5'" "H5''" sing N N 172 DT "C4'" "O4'" sing N N 173 DT "C4'" "C3'" sing N N 174 DT "C4'" "H4'" sing N N 175 DT "O4'" "C1'" sing N N 176 DT "C3'" "O3'" sing N N 177 DT "C3'" "C2'" sing N N 178 DT "C3'" "H3'" sing N N 179 DT "O3'" "HO3'" sing N N 180 DT "C2'" "C1'" sing N N 181 DT "C2'" "H2'" sing N N 182 DT "C2'" "H2''" sing N N 183 DT "C1'" N1 sing N N 184 DT "C1'" "H1'" sing N N 185 DT N1 C2 sing N N 186 DT N1 C6 sing N N 187 DT C2 O2 doub N N 188 DT C2 N3 sing N N 189 DT N3 C4 sing N N 190 DT N3 H3 sing N N 191 DT C4 O4 doub N N 192 DT C4 C5 sing N N 193 DT C5 C7 sing N N 194 DT C5 C6 doub N N 195 DT C7 H71 sing N N 196 DT C7 H72 sing N N 197 DT C7 H73 sing N N 198 DT C6 H6 sing N N 199 # _ndb_struct_conf_na.entry_id 3FX8 _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 A DG 6 6_467 0.155 -0.201 0.598 -6.488 -0.020 -8.368 1 C_DC1:DG6_C C 1 ? C 6 ? 19 1 1 A DG 2 1_555 A DC 5 6_467 -0.098 -0.134 0.724 6.535 -18.819 2.276 2 C_DG2:DC5_C C 2 ? C 5 ? 19 1 1 A DT 3 1_555 A DA 4 6_467 -0.011 0.030 0.080 4.765 -16.856 -4.041 3 C_DT3:DA4_C C 3 ? C 4 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 A DG 6 6_467 A DG 2 1_555 A DC 5 6_467 -0.063 0.591 2.982 2.352 2.499 32.098 0.657 0.496 3.006 4.504 -4.239 32.277 1 CC_DC1DG2:DC5DG6_CC C 1 ? C 6 ? C 2 ? C 5 ? 1 A DG 2 1_555 A DC 5 6_467 A DT 3 1_555 A DA 4 6_467 0.372 -0.587 3.333 3.459 -1.315 32.690 -0.806 -0.050 3.374 -2.327 -6.121 32.893 2 CC_DG2DT3:DA4DC5_CC C 2 ? C 5 ? C 3 ? C 4 ? # _atom_sites.entry_id 3FX8 _atom_sites.fract_transf_matrix[1][1] 0.020305 _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] 0.020305 _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] 0.020305 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C FE N O P S # loop_