data_9BJN # _entry.id 9BJN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.397 _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 9BJN pdb_00009bjn 10.2210/pdb9bjn/pdb WWPDB D_1000283473 ? ? EMDB EMD-44636 ? ? # 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 2024-09-18 2 'Structure model' 1 1 2024-10-02 # _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' # 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' citation 2 2 'Structure model' em_admin 3 2 'Structure model' struct_conn # 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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_em_admin.last_update' 5 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9BJN _pdbx_database_status.recvd_initial_deposition_date 2024-04-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible N # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM of Azo-ffspy fiber' _pdbx_database_related.db_id EMD-44636 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email fw2@uab.edu _pdbx_contact_author.name_first Fengbin _pdbx_contact_author.name_last Wang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-1008-663X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zia, A.' 1 ? 'Guo, J.' 2 ? 'Xu, B.' 3 ? 'Wang, F.' 4 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 146 _citation.language ? _citation.page_first 26102 _citation.page_last 26112 _citation.title 'Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.4c06775 _citation.pdbx_database_id_PubMed 39255453 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Guo, J.' 1 0000-0002-0254-0401 primary 'Zia, A.' 2 ? primary 'Qiu, Q.' 3 ? primary 'Norton, M.' 4 ? primary 'Qiu, K.' 5 ? primary 'Usuba, J.' 6 ? primary 'Liu, Z.' 7 ? primary 'Yi, M.' 8 0000-0002-1912-1043 primary 'Rich-New, S.T.' 9 ? primary 'Hagan, M.' 10 0000-0002-9211-2434 primary 'Fraden, S.' 11 ? primary 'Han, G.D.' 12 ? primary 'Diao, J.' 13 0000-0003-4288-3203 primary 'Wang, F.' 14 0000-0003-1008-663X primary 'Xu, B.' 15 0000-0002-4639-387X # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'D-peptide ffspy' _entity.formula_weight 850.809 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(D)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(A1APX)(DPN)(DPN)(DSN)(A1AP1)' _entity_poly.pdbx_seq_one_letter_code_can XFFSW _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A1APX n 1 2 DPN n 1 3 DPN n 1 4 DSN n 1 5 A1AP1 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 5 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A1AP1 'D-peptide linking' . O-phosphono-D-tyrosine ? 'C9 H12 N O6 P' 261.168 A1APX non-polymer . '4-[(E)-phenyldiazenyl]benzoic acid' ? 'C13 H10 N2 O2' 226.231 DPN 'D-peptide linking' . D-PHENYLALANINE ? 'C9 H11 N O2' 165.189 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 # 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 A1APX 1 1 1 A1APX AZO A . n A 1 2 DPN 2 2 2 DPN DPN A . n A 1 3 DPN 3 3 3 DPN DPN A . n A 1 4 DSN 4 4 4 DSN DSN A . n A 1 5 A1AP1 5 5 5 A1AP1 DP5 A . n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 A1APX ? ? A1APX ? ? 'SUBJECT OF INVESTIGATION' ? 2 A1AP1 ? ? A1AP1 ? ? 'SUBJECT OF INVESTIGATION' ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9BJN _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9BJN _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high . _refine.ls_d_res_low ? _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.009 ? 5040 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 2.634 ? 6640 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 18.983 ? 1040 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.041 ? 320 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.011 ? 640 ? f_plane_restr ? ? # _struct.entry_id 9BJN _struct.title 'Cryo-EM of Azo-ffspy fiber' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9BJN _struct_keywords.text 'D-peptide, peptide-fiber, helical, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9BJN _struct_ref.pdbx_db_accession 9BJN _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9BJN _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 5 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 9BJN _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 5 _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 5 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'representative helical assembly' ? 24-meric 24 2 'helical asymmetric unit' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-24)' A 2 13 A # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # 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 'helical symmetry operation' ? ? 0.15850300 -0.98735900 0.00000000 0.00000 0.98735900 0.15850300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -6.97200 2 'helical symmetry operation' ? ? -0.15850300 0.98735900 0.00000000 0.00000 -0.98735900 -0.15850300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -6.97200 3 'helical symmetry operation' ? ? -0.60737600 -0.79441500 0.00000000 0.00000 0.79441500 -0.60737600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -5.81000 4 'helical symmetry operation' ? ? 0.60737600 0.79441500 0.00000000 0.00000 -0.79441500 0.60737600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -5.81000 5 'helical symmetry operation' ? ? -0.99437500 -0.10591700 0.00000000 0.00000 0.10591700 -0.99437500 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -4.64800 6 'helical symmetry operation' ? ? 0.99437500 0.10591700 0.00000000 0.00000 -0.10591700 0.99437500 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -4.64800 7 'helical symmetry operation' ? ? -0.76108600 0.64865100 0.00000000 0.00000 -0.64865100 -0.76108600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -3.48600 8 'helical symmetry operation' ? ? 0.76108600 -0.64865100 0.00000000 0.00000 0.64865100 0.76108600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -3.48600 9 'helical symmetry operation' ? ? -0.05303300 0.99859300 0.00000000 0.00000 -0.99859300 -0.05303300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -2.32400 10 'helical symmetry operation' ? ? 0.05303300 -0.99859300 0.00000000 0.00000 0.99859300 0.05303300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -2.32400 11 'helical symmetry operation' ? ? 0.68810100 0.72561500 0.00000000 0.00000 -0.72561500 0.68810100 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -1.16200 12 'helical symmetry operation' ? ? -0.68810100 -0.72561500 0.00000000 0.00000 0.72561500 -0.68810100 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -1.16200 13 'identity operation' 1_555 x,y,z 1.00000000 -0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 14 'helical symmetry operation' ? ? -1.00000000 -0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 15 'helical symmetry operation' ? ? 0.68810100 -0.72561500 0.00000000 0.00000 0.72561500 0.68810100 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 1.16200 16 'helical symmetry operation' ? ? -0.68810100 0.72561500 0.00000000 0.00000 -0.72561500 -0.68810100 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 1.16200 17 'helical symmetry operation' ? ? -0.05303300 -0.99859300 0.00000000 0.00000 0.99859300 -0.05303300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 2.32400 18 'helical symmetry operation' ? ? 0.05303300 0.99859300 0.00000000 0.00000 -0.99859300 0.05303300 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 2.32400 19 'helical symmetry operation' ? ? -0.76108600 -0.64865100 0.00000000 0.00000 0.64865100 -0.76108600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 3.48600 20 'helical symmetry operation' ? ? 0.76108600 0.64865100 0.00000000 0.00000 -0.64865100 0.76108600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 3.48600 21 'helical symmetry operation' ? ? -0.99437500 0.10591700 0.00000000 0.00000 -0.10591700 -0.99437500 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 4.64800 22 'helical symmetry operation' ? ? 0.99437500 -0.10591700 0.00000000 0.00000 0.10591700 0.99437500 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 4.64800 23 'helical symmetry operation' ? ? -0.60737600 0.79441500 0.00000000 0.00000 -0.79441500 -0.60737600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 5.81000 24 'helical symmetry operation' ? ? 0.60737600 -0.79441500 0.00000000 0.00000 0.79441500 0.60737600 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 5.81000 # 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 covale1 covale both ? A A1APX 1 C ? ? ? 1_555 A DPN 2 N ? ? A A1APX 1 A DPN 2 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale2 covale one ? A A1APX 1 O ? ? ? 1_555 A DPN 2 N ? ? A A1APX 1 A DPN 2 1_555 ? ? ? ? ? ? ? 1.282 ? ? covale3 covale both ? A DPN 2 C ? ? ? 1_555 A DPN 3 N ? ? A DPN 2 A DPN 3 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale4 covale both ? A DPN 3 C ? ? ? 1_555 A DSN 4 N ? ? A DPN 3 A DSN 4 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale5 covale both ? A DSN 4 C ? ? ? 1_555 A A1AP1 5 N ? ? A DSN 4 A A1AP1 5 1_555 ? ? ? ? ? ? ? 1.327 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 9BJN _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification ? # 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 O A A1APX 1 ? ? C A A1APX 1 ? ? N A DPN 2 ? ? 56.67 122.70 -66.03 1.60 Y 2 1 C A A1APX 1 ? ? N A DPN 2 ? ? CA A DPN 2 ? ? 136.93 121.70 15.23 2.50 Y # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id DPN _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 2 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 38.50 _pdbx_validate_torsion.psi -53.49 # _pdbx_helical_symmetry.entry_id 9BJN _pdbx_helical_symmetry.number_of_operations 24 _pdbx_helical_symmetry.rotation_per_n_subunits 46.520 _pdbx_helical_symmetry.rise_per_n_subunits 1.162 _pdbx_helical_symmetry.n_subunits_divisor 1 _pdbx_helical_symmetry.dyad_axis no _pdbx_helical_symmetry.circular_symmetry 2 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9BJN _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 9BJN _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 3.0 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 887952 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type HELICAL # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'ffspy fiber' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9BJN _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 9BJN _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9BJN _em_experiment.id 1 _em_experiment.reconstruction_method HELICAL _em_experiment.aggregation_state FILAMENT _em_experiment.entity_assembly_id 1 # 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 A1AP1 N N N N 1 A1AP1 CA C N R 2 A1AP1 C C N N 3 A1AP1 O O N N 4 A1AP1 CB C N N 5 A1AP1 CG C Y N 6 A1AP1 CD1 C Y N 7 A1AP1 CE1 C Y N 8 A1AP1 CZ C Y N 9 A1AP1 CE2 C Y N 10 A1AP1 CD2 C Y N 11 A1AP1 OH O N N 12 A1AP1 OP3 O N N 13 A1AP1 OP1 O N N 14 A1AP1 OP2 O N N 15 A1AP1 P P N N 16 A1AP1 H1 H N N 17 A1AP1 H2 H N N 18 A1AP1 HA H N N 19 A1AP1 HB2 H N N 20 A1AP1 HB3 H N N 21 A1AP1 HD1 H N N 22 A1AP1 HE1 H N N 23 A1AP1 HE2 H N N 24 A1AP1 HD2 H N N 25 A1AP1 H12 H N N 26 A1AP1 H13 H N N 27 A1AP1 OXT O N N 28 A1AP1 H3 H N N 29 A1APX C12 C Y N 30 A1APX C13 C Y N 31 A1APX C14 C Y N 32 A1APX C15 C Y N 33 A1APX C16 C Y N 34 A1APX C17 C Y N 35 A1APX C C N N 36 A1APX O O N N 37 A1APX C04 C Y N 38 A1APX C05 C Y N 39 A1APX C06 C Y N 40 A1APX C07 C Y N 41 A1APX C08 C Y N 42 A1APX C09 C Y N 43 A1APX N10 N N N 44 A1APX N11 N N N 45 A1APX O1 O N N 46 A1APX H1 H N N 47 A1APX H2 H N N 48 A1APX H3 H N N 49 A1APX H4 H N N 50 A1APX H5 H N N 51 A1APX H6 H N N 52 A1APX H7 H N N 53 A1APX H8 H N N 54 A1APX H9 H N N 55 A1APX H10 H N N 56 DPN N N N N 57 DPN CA C N R 58 DPN C C N N 59 DPN O O N N 60 DPN OXT O N N 61 DPN CB C N N 62 DPN CG C Y N 63 DPN CD1 C Y N 64 DPN CD2 C Y N 65 DPN CE1 C Y N 66 DPN CE2 C Y N 67 DPN CZ C Y N 68 DPN H H N N 69 DPN H2 H N N 70 DPN HA H N N 71 DPN HXT H N N 72 DPN HB2 H N N 73 DPN HB3 H N N 74 DPN HD1 H N N 75 DPN HD2 H N N 76 DPN HE1 H N N 77 DPN HE2 H N N 78 DPN HZ H N N 79 DSN N N N N 80 DSN CA C N R 81 DSN C C N N 82 DSN O O N N 83 DSN OXT O N N 84 DSN CB C N N 85 DSN OG O N N 86 DSN H H N N 87 DSN H2 H N N 88 DSN HA H N N 89 DSN HXT H N N 90 DSN HB2 H N N 91 DSN HB3 H N N 92 DSN HG H N N 93 # 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 A1AP1 O C doub N N 1 A1AP1 C CA sing N N 2 A1AP1 N CA sing N N 3 A1AP1 CA CB sing N N 4 A1AP1 CD2 CE2 doub Y N 5 A1AP1 CD2 CG sing Y N 6 A1AP1 CE2 CZ sing Y N 7 A1AP1 CB CG sing N N 8 A1AP1 CG CD1 doub Y N 9 A1AP1 OP1 P doub N N 10 A1AP1 OP3 P sing N N 11 A1AP1 CZ OH sing N N 12 A1AP1 CZ CE1 doub Y N 13 A1AP1 OH P sing N N 14 A1AP1 CD1 CE1 sing Y N 15 A1AP1 P OP2 sing N N 16 A1AP1 N H1 sing N N 17 A1AP1 N H2 sing N N 18 A1AP1 CA HA sing N N 19 A1AP1 CB HB2 sing N N 20 A1AP1 CB HB3 sing N N 21 A1AP1 CD1 HD1 sing N N 22 A1AP1 CE1 HE1 sing N N 23 A1AP1 CE2 HE2 sing N N 24 A1AP1 CD2 HD2 sing N N 25 A1AP1 OP3 H12 sing N N 26 A1AP1 OP2 H13 sing N N 27 A1AP1 C OXT sing N N 28 A1AP1 OXT H3 sing N N 29 A1APX C14 C13 doub Y N 30 A1APX C14 C15 sing Y N 31 A1APX C13 C12 sing Y N 32 A1APX C15 C16 doub Y N 33 A1APX C12 N11 sing N N 34 A1APX C12 C17 doub Y N 35 A1APX C16 C17 sing Y N 36 A1APX N11 N10 doub N N 37 A1APX C06 C05 doub Y N 38 A1APX C06 C09 sing Y N 39 A1APX C05 C04 sing Y N 40 A1APX N10 C09 sing N N 41 A1APX C09 C08 doub Y N 42 A1APX O C doub N N 43 A1APX C04 C sing N N 44 A1APX C04 C07 doub Y N 45 A1APX C08 C07 sing Y N 46 A1APX C O1 sing N N 47 A1APX C13 H1 sing N N 48 A1APX C14 H2 sing N N 49 A1APX C15 H3 sing N N 50 A1APX C16 H4 sing N N 51 A1APX C17 H5 sing N N 52 A1APX C05 H6 sing N N 53 A1APX C06 H7 sing N N 54 A1APX C07 H8 sing N N 55 A1APX C08 H9 sing N N 56 A1APX O1 H10 sing N N 57 DPN N CA sing N N 58 DPN N H sing N N 59 DPN N H2 sing N N 60 DPN CA C sing N N 61 DPN CA CB sing N N 62 DPN CA HA sing N N 63 DPN C O doub N N 64 DPN C OXT sing N N 65 DPN OXT HXT sing N N 66 DPN CB CG sing N N 67 DPN CB HB2 sing N N 68 DPN CB HB3 sing N N 69 DPN CG CD1 doub Y N 70 DPN CG CD2 sing Y N 71 DPN CD1 CE1 sing Y N 72 DPN CD1 HD1 sing N N 73 DPN CD2 CE2 doub Y N 74 DPN CD2 HD2 sing N N 75 DPN CE1 CZ doub Y N 76 DPN CE1 HE1 sing N N 77 DPN CE2 CZ sing Y N 78 DPN CE2 HE2 sing N N 79 DPN CZ HZ sing N N 80 DSN N CA sing N N 81 DSN N H sing N N 82 DSN N H2 sing N N 83 DSN CA C sing N N 84 DSN CA CB sing N N 85 DSN CA HA sing N N 86 DSN C O doub N N 87 DSN C OXT sing N N 88 DSN OXT HXT sing N N 89 DSN CB OG sing N N 90 DSN CB HB2 sing N N 91 DSN CB HB3 sing N N 92 DSN OG HG sing N N 93 # _em_admin.current_status REL _em_admin.deposition_date 2024-04-25 _em_admin.deposition_site RCSB _em_admin.entry_id 9BJN _em_admin.last_update 2024-10-02 _em_admin.map_release_date 2024-09-18 _em_admin.title 'Cryo-EM of Azo-ffspy fiber' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 32630 _em_entity_assembly_naturalsource.organism 'synthetic construct' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.details ? _em_helical_entity.axial_symmetry C2 _em_helical_entity.angular_rotation_per_subunit 46.520 _em_helical_entity.axial_rise_per_subunit 1.162 # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 50 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM138756 1 'National Institutes of Health/National Cancer Institute (NIH/NCI)' 'United States' CA142746 2 # _atom_sites.entry_id 9BJN _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O P # loop_