data_8A05 # _entry.id 8A05 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.362 _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 8A05 pdb_00008a05 10.2210/pdb8a05/pdb WWPDB D_1292123203 ? ? EMDB EMD-15048 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Bacteriophage phiCjT23 major capsid protein trimer type 1' _pdbx_database_related.db_id EMD-15048 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8A05 _pdbx_database_status.recvd_initial_deposition_date 2022-05-26 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Rissanen, I.' 1 ? 'Huiskonen, J.T.' 2 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 13 _citation.language ? _citation.page_first 7478 _citation.page_last 7478 _citation.title 'Cryo-EM structure of ssDNA bacteriophage Phi CjT23 provides insight into early virus evolution.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-022-35123-6 _citation.pdbx_database_id_PubMed 36463224 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kejzar, N.' 1 ? primary 'Laanto, E.' 2 0000-0003-4172-3128 primary 'Rissanen, I.' 3 0000-0003-4937-1825 primary 'Abrishami, V.' 4 0000-0002-3772-7663 primary 'Selvaraj, M.' 5 0000-0001-7793-6323 primary 'Moineau, S.' 6 0000-0002-2832-5101 primary 'Ravantti, J.' 7 ? primary 'Sundberg, L.R.' 8 0000-0003-3510-4398 primary 'Huiskonen, J.T.' 9 0000-0002-0348-7323 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8A05 _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8A05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # 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 nat 'Spike protein P13 N-terminal, capsid internal domain' 10438.764 1 ? ? ? ? 2 polymer nat 'Unknown vertex protein' 443.539 1 ? ? ? ? # 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 'polypeptide(L)' no no ;MNFIQYIDDSYAVKVKEINSSEGFYINGIQTPFFILSVFIGNKRVTGVEFNNYDSLPMLSVINDLGNIDLNVIPQNYFAT AFTEIYFNIPF ; ;MNFIQYIDDSYAVKVKEINSSEGFYINGIQTPFFILSVFIGNKRVTGVEFNNYDSLPMLSVINDLGNIDLNVIPQNYFAT AFTEIYFNIPF ; P ? 2 'polypeptide(L)' no no '(UNK)(UNK)(UNK)(UNK)(UNK)' XXXXX X ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ASN n 1 3 PHE n 1 4 ILE n 1 5 GLN n 1 6 TYR n 1 7 ILE n 1 8 ASP n 1 9 ASP n 1 10 SER n 1 11 TYR n 1 12 ALA n 1 13 VAL n 1 14 LYS n 1 15 VAL n 1 16 LYS n 1 17 GLU n 1 18 ILE n 1 19 ASN n 1 20 SER n 1 21 SER n 1 22 GLU n 1 23 GLY n 1 24 PHE n 1 25 TYR n 1 26 ILE n 1 27 ASN n 1 28 GLY n 1 29 ILE n 1 30 GLN n 1 31 THR n 1 32 PRO n 1 33 PHE n 1 34 PHE n 1 35 ILE n 1 36 LEU n 1 37 SER n 1 38 VAL n 1 39 PHE n 1 40 ILE n 1 41 GLY n 1 42 ASN n 1 43 LYS n 1 44 ARG n 1 45 VAL n 1 46 THR n 1 47 GLY n 1 48 VAL n 1 49 GLU n 1 50 PHE n 1 51 ASN n 1 52 ASN n 1 53 TYR n 1 54 ASP n 1 55 SER n 1 56 LEU n 1 57 PRO n 1 58 MET n 1 59 LEU n 1 60 SER n 1 61 VAL n 1 62 ILE n 1 63 ASN n 1 64 ASP n 1 65 LEU n 1 66 GLY n 1 67 ASN n 1 68 ILE n 1 69 ASP n 1 70 LEU n 1 71 ASN n 1 72 VAL n 1 73 ILE n 1 74 PRO n 1 75 GLN n 1 76 ASN n 1 77 TYR n 1 78 PHE n 1 79 ALA n 1 80 THR n 1 81 ALA n 1 82 PHE n 1 83 THR n 1 84 GLU n 1 85 ILE n 1 86 TYR n 1 87 PHE n 1 88 ASN n 1 89 ILE n 1 90 PRO n 1 91 PHE n 2 1 UNK n 2 2 UNK n 2 3 UNK n 2 4 UNK n 2 5 UNK n # loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_alt_source_flag _entity_src_nat.pdbx_beg_seq_num _entity_src_nat.pdbx_end_seq_num _entity_src_nat.common_name _entity_src_nat.pdbx_organism_scientific _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.strain _entity_src_nat.tissue _entity_src_nat.tissue_fraction _entity_src_nat.pdbx_secretion _entity_src_nat.pdbx_fragment _entity_src_nat.pdbx_variant _entity_src_nat.pdbx_cell_line _entity_src_nat.pdbx_atcc _entity_src_nat.pdbx_cellular_location _entity_src_nat.pdbx_organ _entity_src_nat.pdbx_organelle _entity_src_nat.pdbx_cell _entity_src_nat.pdbx_plasmid_name _entity_src_nat.pdbx_plasmid_details _entity_src_nat.details 1 1 sample 1 91 ? 'Flavobacterium phage' 908820 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 1 5 ? unidentified 32644 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 8A05 8A05 ? 1 ? 1 2 PDB 8A05 8A05 ? 2 ? 1 # 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 8A05 P 1 ? 91 ? 8A05 1 ? 91 ? 1 91 2 2 8A05 X 1 ? 5 ? 8A05 1 ? 5 ? 1 5 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 UNK 'L-peptide linking' . UNKNOWN ? 'C4 H9 N O2' 103.120 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _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 8A05 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 8A05 _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _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 ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _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 ? # 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' ? 0.002 ? 782 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.415 ? 1063 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 2.900 ? 101 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.047 ? 119 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.004 ? 138 ? f_plane_restr ? ? # _struct.entry_id 8A05 _struct.title 'Bacteriophage phiCjT23 spike protein penton domain' _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 8A05 _struct_keywords.text 'bacteriophage, phiCjT23, VIRUS' _struct_keywords.pdbx_keywords VIRUS # 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 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 SER A 55 ? ASP A 64 ? SER P 55 ASP P 64 1 ? 10 HELX_P HELX_P2 AA2 PRO A 74 ? PHE A 78 ? PRO P 74 PHE P 78 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 13 ? GLU A 17 ? VAL P 13 GLU P 17 AA1 2 PHE A 3 ? ILE A 7 ? PHE P 3 ILE P 7 AA1 3 PHE A 34 ? ILE A 40 ? PHE P 34 ILE P 40 AA1 4 LYS A 43 ? ARG A 44 ? LYS P 43 ARG P 44 AA2 1 PHE A 24 ? ILE A 26 ? PHE P 24 ILE P 26 AA2 2 ILE A 85 ? PHE A 87 ? ILE P 85 PHE P 87 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 O LYS A 16 ? O LYS P 16 N ILE A 4 ? N ILE P 4 AA1 2 3 N PHE A 3 ? N PHE P 3 O PHE A 39 ? O PHE P 39 AA1 3 4 N ILE A 40 ? N ILE P 40 O LYS A 43 ? O LYS P 43 AA2 1 2 N PHE A 24 ? N PHE P 24 O PHE A 87 ? O PHE P 87 # _atom_sites.entry_id 8A05 _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.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 S # 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 MET 1 1 1 MET MET P . n A 1 2 ASN 2 2 2 ASN ASN P . n A 1 3 PHE 3 3 3 PHE PHE P . n A 1 4 ILE 4 4 4 ILE ILE P . n A 1 5 GLN 5 5 5 GLN GLN P . n A 1 6 TYR 6 6 6 TYR TYR P . n A 1 7 ILE 7 7 7 ILE ILE P . n A 1 8 ASP 8 8 8 ASP ASP P . n A 1 9 ASP 9 9 9 ASP ASP P . n A 1 10 SER 10 10 10 SER SER P . n A 1 11 TYR 11 11 11 TYR TYR P . n A 1 12 ALA 12 12 12 ALA ALA P . n A 1 13 VAL 13 13 13 VAL VAL P . n A 1 14 LYS 14 14 14 LYS LYS P . n A 1 15 VAL 15 15 15 VAL VAL P . n A 1 16 LYS 16 16 16 LYS LYS P . n A 1 17 GLU 17 17 17 GLU GLU P . n A 1 18 ILE 18 18 18 ILE ILE P . n A 1 19 ASN 19 19 19 ASN ASN P . n A 1 20 SER 20 20 20 SER SER P . n A 1 21 SER 21 21 21 SER SER P . n A 1 22 GLU 22 22 22 GLU GLU P . n A 1 23 GLY 23 23 23 GLY GLY P . n A 1 24 PHE 24 24 24 PHE PHE P . n A 1 25 TYR 25 25 25 TYR TYR P . n A 1 26 ILE 26 26 26 ILE ILE P . n A 1 27 ASN 27 27 27 ASN ASN P . n A 1 28 GLY 28 28 28 GLY GLY P . n A 1 29 ILE 29 29 29 ILE ILE P . n A 1 30 GLN 30 30 30 GLN GLN P . n A 1 31 THR 31 31 31 THR THR P . n A 1 32 PRO 32 32 32 PRO PRO P . n A 1 33 PHE 33 33 33 PHE PHE P . n A 1 34 PHE 34 34 34 PHE PHE P . n A 1 35 ILE 35 35 35 ILE ILE P . n A 1 36 LEU 36 36 36 LEU LEU P . n A 1 37 SER 37 37 37 SER SER P . n A 1 38 VAL 38 38 38 VAL VAL P . n A 1 39 PHE 39 39 39 PHE PHE P . n A 1 40 ILE 40 40 40 ILE ILE P . n A 1 41 GLY 41 41 41 GLY GLY P . n A 1 42 ASN 42 42 42 ASN ASN P . n A 1 43 LYS 43 43 43 LYS LYS P . n A 1 44 ARG 44 44 44 ARG ARG P . n A 1 45 VAL 45 45 45 VAL VAL P . n A 1 46 THR 46 46 46 THR THR P . n A 1 47 GLY 47 47 47 GLY GLY P . n A 1 48 VAL 48 48 48 VAL VAL P . n A 1 49 GLU 49 49 49 GLU GLU P . n A 1 50 PHE 50 50 50 PHE PHE P . n A 1 51 ASN 51 51 51 ASN ASN P . n A 1 52 ASN 52 52 52 ASN ASN P . n A 1 53 TYR 53 53 53 TYR TYR P . n A 1 54 ASP 54 54 54 ASP ASP P . n A 1 55 SER 55 55 55 SER SER P . n A 1 56 LEU 56 56 56 LEU LEU P . n A 1 57 PRO 57 57 57 PRO PRO P . n A 1 58 MET 58 58 58 MET MET P . n A 1 59 LEU 59 59 59 LEU LEU P . n A 1 60 SER 60 60 60 SER SER P . n A 1 61 VAL 61 61 61 VAL VAL P . n A 1 62 ILE 62 62 62 ILE ILE P . n A 1 63 ASN 63 63 63 ASN ASN P . n A 1 64 ASP 64 64 64 ASP ASP P . n A 1 65 LEU 65 65 65 LEU LEU P . n A 1 66 GLY 66 66 66 GLY GLY P . n A 1 67 ASN 67 67 67 ASN ASN P . n A 1 68 ILE 68 68 68 ILE ILE P . n A 1 69 ASP 69 69 69 ASP ASP P . n A 1 70 LEU 70 70 70 LEU LEU P . n A 1 71 ASN 71 71 71 ASN ASN P . n A 1 72 VAL 72 72 72 VAL VAL P . n A 1 73 ILE 73 73 73 ILE ILE P . n A 1 74 PRO 74 74 74 PRO PRO P . n A 1 75 GLN 75 75 75 GLN GLN P . n A 1 76 ASN 76 76 76 ASN ASN P . n A 1 77 TYR 77 77 77 TYR TYR P . n A 1 78 PHE 78 78 78 PHE PHE P . n A 1 79 ALA 79 79 79 ALA ALA P . n A 1 80 THR 80 80 80 THR THR P . n A 1 81 ALA 81 81 81 ALA ALA P . n A 1 82 PHE 82 82 82 PHE PHE P . n A 1 83 THR 83 83 83 THR THR P . n A 1 84 GLU 84 84 84 GLU GLU P . n A 1 85 ILE 85 85 85 ILE ILE P . n A 1 86 TYR 86 86 86 TYR TYR P . n A 1 87 PHE 87 87 87 PHE PHE P . n A 1 88 ASN 88 88 88 ASN ASN P . n A 1 89 ILE 89 89 89 ILE ILE P . n A 1 90 PRO 90 90 90 PRO PRO P . n A 1 91 PHE 91 91 91 PHE PHE P . n B 2 1 UNK 1 1 1 UNK UNK X . n B 2 2 UNK 2 2 2 UNK UNK X . n B 2 3 UNK 3 3 3 UNK UNK X . n B 2 4 UNK 4 4 4 UNK UNK X . n B 2 5 UNK 5 5 5 UNK UNK X . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email juha.huiskonen@helsinki.fi _pdbx_contact_author.name_first Juha _pdbx_contact_author.name_last Huiskonen _pdbx_contact_author.name_mi T. _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0348-7323 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 420 ? 1 MORE -3 ? 1 'SSA (A^2)' 5780 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2022-12-14 # _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 ? # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name PHENIX _software.os ? _software.os_version ? _software.type ? _software.version . _software.pdbx_ordinal 1 # _em_3d_fitting.entry_id 8A05 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'AB INITIO MODEL' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 8A05 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 18122 _em_3d_reconstruction.resolution 3.4 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7.2 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name unidentified _em_entity_assembly.source NATURAL _em_entity_assembly.type VIRUS _em_entity_assembly.entity_id_list '1, 2' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 8A05 _em_imaging.accelerating_voltage 200 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TECNAI ARCTICA' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 2200 _em_imaging.nominal_defocus_min 300 _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_virus_entity.entity_assembly_id 1 _em_virus_entity.empty NO _em_virus_entity.enveloped YES _em_virus_entity.virus_isolate SPECIES _em_virus_entity.virus_type VIRION _em_virus_entity.id 1 _em_virus_entity.virus_host_category ? _em_virus_entity.details ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 8A05 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8A05 _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 8A05 _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C5 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id GLN _pdbx_validate_torsion.auth_asym_id P _pdbx_validate_torsion.auth_seq_id 30 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 75.17 _pdbx_validate_torsion.psi -6.44 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 32644 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism unidentified _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 15 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'FEI FALCON III (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 2 'IMAGE ACQUISITION' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? Coot ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'MODEL REFINEMENT' ? PHENIX ? ? 1 ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? ? ? 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _em_virus_natural_host.id 1 _em_virus_natural_host.entity_assembly_id 1 _em_virus_natural_host.ncbi_tax_id 376686 _em_virus_natural_host.organism 'Flavobacterium johnsoniae UW101' _em_virus_natural_host.strain ? # _em_virus_shell.id 1 _em_virus_shell.entity_assembly_id 1 _em_virus_shell.diameter 600 _em_virus_shell.name Capsid _em_virus_shell.triangulation 21 # _pdbx_audit_support.funding_organization 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #