data_8A06 # _entry.id 8A06 # _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 8A06 pdb_00008a06 10.2210/pdb8a06/pdb WWPDB D_1292123208 ? ? EMDB EMD-15051 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Flavobacterium infecting lipid-containing phage FLiP penton protein' _pdbx_database_related.db_id EMD-15051 _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 8A06 _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 ? # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_patent _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary 'Nat Commun' ? ? 2041-1723 ? ? 13 ? 7478 7478 'Cryo-EM structure of ssDNA bacteriophage Phi CjT23 provides insight into early virus evolution.' 2022 ? 10.1038/s41467-022-35123-6 36463224 ? ? ? ? ? ? ? ? ? US ? ? 1 'Proc Natl Acad Sci U S A' PNASA6 0040 1091-6490 ? ? 114 ? 8378 8383 'Virus found in a boreal lake links ssDNA and dsDNA viruses.' 2017 ? 10.1073/pnas.1703834114 ? ? ? # 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 1 'Laanto, E.' 10 0000-0003-4172-3128 1 'Mantynen, S.' 11 ? 1 'De Colibus, L.' 12 ? 1 'Marjakangas, J.' 13 ? 1 'Gillum, A.' 14 ? 1 'Stuart, D.I.' 15 ? 1 'Ravantti, J.J.' 16 ? 1 'Huiskonen, J.T.' 17 ? 1 'Sundberg, L.R.' 18 ? # _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 8A06 _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 8A06 _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 ? # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description 'Penton protein P12' _entity.formula_weight 16851.057 _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(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;DFSTIPIDYVKAKDPNTIDFCLSYLELYHTTKAVKACTPFSFILGSDAGMQRATETTESLYWGKVILDINPNLSPLVNTT IVLEIESMLSSNSINRSENKRITRYIEKENFVNESSERFEFFKSMELSHLSTAYDVYVTFIGFKIDL ; _entity_poly.pdbx_seq_one_letter_code_can ;DFSTIPIDYVKAKDPNTIDFCLSYLELYHTTKAVKACTPFSFILGSDAGMQRATETTESLYWGKVILDINPNLSPLVNTT IVLEIESMLSSNSINRSENKRITRYIEKENFVNESSERFEFFKSMELSHLSTAYDVYVTFIGFKIDL ; _entity_poly.pdbx_strand_id E _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 ASP n 1 2 PHE n 1 3 SER n 1 4 THR n 1 5 ILE n 1 6 PRO n 1 7 ILE n 1 8 ASP n 1 9 TYR n 1 10 VAL n 1 11 LYS n 1 12 ALA n 1 13 LYS n 1 14 ASP n 1 15 PRO n 1 16 ASN n 1 17 THR n 1 18 ILE n 1 19 ASP n 1 20 PHE n 1 21 CYS n 1 22 LEU n 1 23 SER n 1 24 TYR n 1 25 LEU n 1 26 GLU n 1 27 LEU n 1 28 TYR n 1 29 HIS n 1 30 THR n 1 31 THR n 1 32 LYS n 1 33 ALA n 1 34 VAL n 1 35 LYS n 1 36 ALA n 1 37 CYS n 1 38 THR n 1 39 PRO n 1 40 PHE n 1 41 SER n 1 42 PHE n 1 43 ILE n 1 44 LEU n 1 45 GLY n 1 46 SER n 1 47 ASP n 1 48 ALA n 1 49 GLY n 1 50 MET n 1 51 GLN n 1 52 ARG n 1 53 ALA n 1 54 THR n 1 55 GLU n 1 56 THR n 1 57 THR n 1 58 GLU n 1 59 SER n 1 60 LEU n 1 61 TYR n 1 62 TRP n 1 63 GLY n 1 64 LYS n 1 65 VAL n 1 66 ILE n 1 67 LEU n 1 68 ASP n 1 69 ILE n 1 70 ASN n 1 71 PRO n 1 72 ASN n 1 73 LEU n 1 74 SER n 1 75 PRO n 1 76 LEU n 1 77 VAL n 1 78 ASN n 1 79 THR n 1 80 THR n 1 81 ILE n 1 82 VAL n 1 83 LEU n 1 84 GLU n 1 85 ILE n 1 86 GLU n 1 87 SER n 1 88 MET n 1 89 LEU n 1 90 SER n 1 91 SER n 1 92 ASN n 1 93 SER n 1 94 ILE n 1 95 ASN n 1 96 ARG n 1 97 SER n 1 98 GLU n 1 99 ASN n 1 100 LYS n 1 101 ARG n 1 102 ILE n 1 103 THR n 1 104 ARG n 1 105 TYR n 1 106 ILE n 1 107 GLU n 1 108 LYS n 1 109 GLU n 1 110 ASN n 1 111 PHE n 1 112 VAL n 1 113 ASN n 1 114 GLU n 1 115 SER n 1 116 SER n 1 117 GLU n 1 118 ARG n 1 119 PHE n 1 120 GLU n 1 121 PHE n 1 122 PHE n 1 123 LYS n 1 124 SER n 1 125 MET n 1 126 GLU n 1 127 LEU n 1 128 SER n 1 129 HIS n 1 130 LEU n 1 131 SER n 1 132 THR n 1 133 ALA n 1 134 TYR n 1 135 ASP n 1 136 VAL n 1 137 TYR n 1 138 VAL n 1 139 THR n 1 140 PHE n 1 141 ILE n 1 142 GLY n 1 143 PHE n 1 144 LYS n 1 145 ILE n 1 146 ASP n 1 147 LEU n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 147 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Flavobacterium phage FLiP' _entity_src_nat.pdbx_ncbi_taxonomy_id 2023716 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A0A222NP85_9VIRU _struct_ref.pdbx_db_accession A0A222NP85 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DFSTIPIDYVKAKDPNTIDFCLSYLELYHTTKAVKACTPFSFILGSDAGMQRATETTESLYWGKVILDINPNLSPLVNTT IVLEIESMLSSNSINRSENKRITRYIEKENFVNESSERFEFFKSMELSHLSTAYDVYVTFIGFKIDL ; _struct_ref.pdbx_align_begin 2 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8A06 _struct_ref_seq.pdbx_strand_id E _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 147 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A0A222NP85 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 148 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg -2 _struct_ref_seq.pdbx_auth_seq_align_end 144 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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 8A06 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 8A06 _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' ? 0.003 ? 1210 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.551 ? 1640 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 4.278 ? 158 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.045 ? 190 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.004 ? 206 ? f_plane_restr ? ? # _struct.entry_id 8A06 _struct.title 'Flavobacterium infecting lipid-containing phage FLiP penton protein' _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 8A06 _struct_keywords.text 'bacteriophage, Flavobacterium, lipid-containing, phage, FLiP, penton protein, VIRUS' _struct_keywords.pdbx_keywords VIRUS # _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 ? # 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 THR A 17 ? HIS A 29 ? THR E 14 HIS E 26 1 ? 13 HELX_P HELX_P2 AA2 SER A 90 ? ASN A 95 ? SER E 87 ASN E 92 1 ? 6 # _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 ? 3 ? # 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 AA2 2 3 ? 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 CYS A 37 ? GLY A 45 ? CYS E 34 GLY E 42 AA1 2 TYR A 134 ? ASP A 146 ? TYR E 131 ASP E 143 AA1 3 SER A 59 ? PRO A 71 ? SER E 56 PRO E 68 AA1 4 GLU A 114 ? PHE A 122 ? GLU E 111 PHE E 119 AA2 1 GLU A 98 ? TYR A 105 ? GLU E 95 TYR E 102 AA2 2 THR A 80 ? SER A 87 ? THR E 77 SER E 84 AA2 3 MET A 125 ? HIS A 129 ? MET E 122 HIS E 126 # 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 N THR A 38 ? N THR E 35 O LYS A 144 ? O LYS E 141 AA1 2 3 O PHE A 143 ? O PHE E 140 N TRP A 62 ? N TRP E 59 AA1 3 4 N TYR A 61 ? N TYR E 58 O PHE A 122 ? O PHE E 119 AA2 1 2 O LYS A 100 ? O LYS E 97 N ILE A 85 ? N ILE E 82 AA2 2 3 N GLU A 84 ? N GLU E 81 O GLU A 126 ? O GLU E 123 # _atom_sites.entry_id 8A06 _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 ASP 1 -2 -2 ASP ASP E . n A 1 2 PHE 2 -1 -1 PHE PHE E . n A 1 3 SER 3 0 0 SER SER E . n A 1 4 THR 4 1 1 THR THR E . n A 1 5 ILE 5 2 2 ILE ILE E . n A 1 6 PRO 6 3 3 PRO PRO E . n A 1 7 ILE 7 4 4 ILE ILE E . n A 1 8 ASP 8 5 5 ASP ASP E . n A 1 9 TYR 9 6 6 TYR TYR E . n A 1 10 VAL 10 7 7 VAL VAL E . n A 1 11 LYS 11 8 8 LYS LYS E . n A 1 12 ALA 12 9 9 ALA ALA E . n A 1 13 LYS 13 10 10 LYS LYS E . n A 1 14 ASP 14 11 11 ASP ASP E . n A 1 15 PRO 15 12 12 PRO PRO E . n A 1 16 ASN 16 13 13 ASN ASN E . n A 1 17 THR 17 14 14 THR THR E . n A 1 18 ILE 18 15 15 ILE ILE E . n A 1 19 ASP 19 16 16 ASP ASP E . n A 1 20 PHE 20 17 17 PHE PHE E . n A 1 21 CYS 21 18 18 CYS CYS E . n A 1 22 LEU 22 19 19 LEU LEU E . n A 1 23 SER 23 20 20 SER SER E . n A 1 24 TYR 24 21 21 TYR TYR E . n A 1 25 LEU 25 22 22 LEU LEU E . n A 1 26 GLU 26 23 23 GLU GLU E . n A 1 27 LEU 27 24 24 LEU LEU E . n A 1 28 TYR 28 25 25 TYR TYR E . n A 1 29 HIS 29 26 26 HIS HIS E . n A 1 30 THR 30 27 27 THR THR E . n A 1 31 THR 31 28 28 THR THR E . n A 1 32 LYS 32 29 29 LYS LYS E . n A 1 33 ALA 33 30 30 ALA ALA E . n A 1 34 VAL 34 31 31 VAL VAL E . n A 1 35 LYS 35 32 32 LYS LYS E . n A 1 36 ALA 36 33 33 ALA ALA E . n A 1 37 CYS 37 34 34 CYS CYS E . n A 1 38 THR 38 35 35 THR THR E . n A 1 39 PRO 39 36 36 PRO PRO E . n A 1 40 PHE 40 37 37 PHE PHE E . n A 1 41 SER 41 38 38 SER SER E . n A 1 42 PHE 42 39 39 PHE PHE E . n A 1 43 ILE 43 40 40 ILE ILE E . n A 1 44 LEU 44 41 41 LEU LEU E . n A 1 45 GLY 45 42 42 GLY GLY E . n A 1 46 SER 46 43 43 SER SER E . n A 1 47 ASP 47 44 44 ASP ASP E . n A 1 48 ALA 48 45 45 ALA ALA E . n A 1 49 GLY 49 46 46 GLY GLY E . n A 1 50 MET 50 47 47 MET MET E . n A 1 51 GLN 51 48 48 GLN GLN E . n A 1 52 ARG 52 49 49 ARG ARG E . n A 1 53 ALA 53 50 50 ALA ALA E . n A 1 54 THR 54 51 51 THR THR E . n A 1 55 GLU 55 52 52 GLU GLU E . n A 1 56 THR 56 53 53 THR THR E . n A 1 57 THR 57 54 54 THR THR E . n A 1 58 GLU 58 55 55 GLU GLU E . n A 1 59 SER 59 56 56 SER SER E . n A 1 60 LEU 60 57 57 LEU LEU E . n A 1 61 TYR 61 58 58 TYR TYR E . n A 1 62 TRP 62 59 59 TRP TRP E . n A 1 63 GLY 63 60 60 GLY GLY E . n A 1 64 LYS 64 61 61 LYS LYS E . n A 1 65 VAL 65 62 62 VAL VAL E . n A 1 66 ILE 66 63 63 ILE ILE E . n A 1 67 LEU 67 64 64 LEU LEU E . n A 1 68 ASP 68 65 65 ASP ASP E . n A 1 69 ILE 69 66 66 ILE ILE E . n A 1 70 ASN 70 67 67 ASN ASN E . n A 1 71 PRO 71 68 68 PRO PRO E . n A 1 72 ASN 72 69 69 ASN ASN E . n A 1 73 LEU 73 70 70 LEU LEU E . n A 1 74 SER 74 71 71 SER SER E . n A 1 75 PRO 75 72 72 PRO PRO E . n A 1 76 LEU 76 73 73 LEU LEU E . n A 1 77 VAL 77 74 74 VAL VAL E . n A 1 78 ASN 78 75 75 ASN ASN E . n A 1 79 THR 79 76 76 THR THR E . n A 1 80 THR 80 77 77 THR THR E . n A 1 81 ILE 81 78 78 ILE ILE E . n A 1 82 VAL 82 79 79 VAL VAL E . n A 1 83 LEU 83 80 80 LEU LEU E . n A 1 84 GLU 84 81 81 GLU GLU E . n A 1 85 ILE 85 82 82 ILE ILE E . n A 1 86 GLU 86 83 83 GLU GLU E . n A 1 87 SER 87 84 84 SER SER E . n A 1 88 MET 88 85 85 MET MET E . n A 1 89 LEU 89 86 86 LEU LEU E . n A 1 90 SER 90 87 87 SER SER E . n A 1 91 SER 91 88 88 SER SER E . n A 1 92 ASN 92 89 89 ASN ASN E . n A 1 93 SER 93 90 90 SER SER E . n A 1 94 ILE 94 91 91 ILE ILE E . n A 1 95 ASN 95 92 92 ASN ASN E . n A 1 96 ARG 96 93 93 ARG ARG E . n A 1 97 SER 97 94 94 SER SER E . n A 1 98 GLU 98 95 95 GLU GLU E . n A 1 99 ASN 99 96 96 ASN ASN E . n A 1 100 LYS 100 97 97 LYS LYS E . n A 1 101 ARG 101 98 98 ARG ARG E . n A 1 102 ILE 102 99 99 ILE ILE E . n A 1 103 THR 103 100 100 THR THR E . n A 1 104 ARG 104 101 101 ARG ARG E . n A 1 105 TYR 105 102 102 TYR TYR E . n A 1 106 ILE 106 103 103 ILE ILE E . n A 1 107 GLU 107 104 104 GLU GLU E . n A 1 108 LYS 108 105 105 LYS LYS E . n A 1 109 GLU 109 106 106 GLU GLU E . n A 1 110 ASN 110 107 107 ASN ASN E . n A 1 111 PHE 111 108 108 PHE PHE E . n A 1 112 VAL 112 109 109 VAL VAL E . n A 1 113 ASN 113 110 110 ASN ASN E . n A 1 114 GLU 114 111 111 GLU GLU E . n A 1 115 SER 115 112 112 SER SER E . n A 1 116 SER 116 113 113 SER SER E . n A 1 117 GLU 117 114 114 GLU GLU E . n A 1 118 ARG 118 115 115 ARG ARG E . n A 1 119 PHE 119 116 116 PHE PHE E . n A 1 120 GLU 120 117 117 GLU GLU E . n A 1 121 PHE 121 118 118 PHE PHE E . n A 1 122 PHE 122 119 119 PHE PHE E . n A 1 123 LYS 123 120 120 LYS LYS E . n A 1 124 SER 124 121 121 SER SER E . n A 1 125 MET 125 122 122 MET MET E . n A 1 126 GLU 126 123 123 GLU GLU E . n A 1 127 LEU 127 124 124 LEU LEU E . n A 1 128 SER 128 125 125 SER SER E . n A 1 129 HIS 129 126 126 HIS HIS E . n A 1 130 LEU 130 127 127 LEU LEU E . n A 1 131 SER 131 128 128 SER SER E . n A 1 132 THR 132 129 129 THR THR E . n A 1 133 ALA 133 130 130 ALA ALA E . n A 1 134 TYR 134 131 131 TYR TYR E . n A 1 135 ASP 135 132 132 ASP ASP E . n A 1 136 VAL 136 133 133 VAL VAL E . n A 1 137 TYR 137 134 134 TYR TYR E . n A 1 138 VAL 138 135 135 VAL VAL E . n A 1 139 THR 139 136 136 THR THR E . n A 1 140 PHE 140 137 137 PHE PHE E . n A 1 141 ILE 141 138 138 ILE ILE E . n A 1 142 GLY 142 139 139 GLY GLY E . n A 1 143 PHE 143 140 140 PHE PHE E . n A 1 144 LYS 144 141 141 LYS LYS E . n A 1 145 ILE 145 142 142 ILE ILE E . n A 1 146 ASP 146 143 143 ASP ASP E . n A 1 147 LEU 147 144 144 LEU LEU E . 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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # 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)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 9190 ? # _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 8A06 _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 ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 8A06 _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 28212 _em_3d_reconstruction.resolution 4.0 _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 'Flavobacterium phage FLiP' _em_entity_assembly.source NATURAL _em_entity_assembly.type VIRUS _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 8A06 _em_imaging.accelerating_voltage 300 _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 POLARA 300' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 2500 _em_imaging.nominal_defocus_min 700 _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 8A06 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8A06 _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 8A06 _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C5 # _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_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 2023716 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Flavobacterium phage FLiP' _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 22 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (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 'PARTICLE SELECTION' ? ? ? 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 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 10 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 CLASSIFICATION ? ? ? 1 ? ? 12 RECONSTRUCTION ? ? ? 1 ? ? 13 'MODEL REFINEMENT' ? PHENIX ? ? 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 237 _em_virus_natural_host.organism Flavobacterium _em_virus_natural_host.strain ? # _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 ? #