data_6TUP # _entry.id 6TUP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.322 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6TUP WWPDB D_1292106091 EMDB EMD-10593 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of Pf4 bacteriophage coat protein with single-stranded DNA' _pdbx_database_related.db_id EMD-10593 _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 6TUP _pdbx_database_status.recvd_initial_deposition_date 2020-01-08 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Tarafder, A.K.' 1 0000-0002-0368-6111 'von Kugelgen, A.' 2 0000-0002-0017-2414 'Bharat, T.A.M.' 3 0000-0002-0168-0277 # _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 Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 117 _citation.language ? _citation.page_first 4724 _citation.page_last 4731 _citation.title 'Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.1917726117 _citation.pdbx_database_id_PubMed 32071243 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tarafder, A.K.' 1 ? primary 'von Kugelgen, A.' 2 ? primary 'Mellul, A.J.' 3 ? primary 'Schulze, U.' 4 ? primary 'Aarts, D.G.A.L.' 5 ? primary 'Bharat, T.A.M.' 6 ? # _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 6TUP _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 ? # _symmetry.entry_id 6TUP _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 'Coat protein B of bacteriophage Pf1' 4612.393 1 ? ? ? ? 2 polymer nat ;DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3') ; 1834.283 1 ? ? ? 'Model of pf4 single-stranded DNA genome' # _entity_name_com.entity_id 1 _entity_name_com.name 'Phage coat protein B' # 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 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA A ? 2 polydeoxyribonucleotide no no '(DA)(DA)(DA)(DA)(DA)(DA)' AAAAAA z ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 VAL n 1 3 ILE n 1 4 ASP n 1 5 THR n 1 6 SER n 1 7 ALA n 1 8 VAL n 1 9 GLU n 1 10 SER n 1 11 ALA n 1 12 ILE n 1 13 THR n 1 14 ASP n 1 15 GLY n 1 16 GLN n 1 17 GLY n 1 18 ASP n 1 19 MET n 1 20 LYS n 1 21 ALA n 1 22 ILE n 1 23 GLY n 1 24 GLY n 1 25 TYR n 1 26 ILE n 1 27 VAL n 1 28 GLY n 1 29 ALA n 1 30 LEU n 1 31 VAL n 1 32 ILE n 1 33 LEU n 1 34 ALA n 1 35 VAL n 1 36 ALA n 1 37 GLY n 1 38 LEU n 1 39 ILE n 1 40 TYR n 1 41 SER n 1 42 MET n 1 43 LEU n 1 44 ARG n 1 45 LYS n 1 46 ALA n 2 1 DA n 2 2 DA n 2 3 DA n 2 4 DA n 2 5 DA n 2 6 DA 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 46 ? 'Pseudomonas virus Pf1' 2011081 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 1 6 ? 'Pseudomonas aeruginosa PAO1' 208964 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # 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 UNP Q9I5K5_PSEAE Q9I5K5 ? 1 GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA 37 2 PDB 6TUP 6TUP ? 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 6TUP A 1 ? 46 ? Q9I5K5 37 ? 82 ? 1 46 2 2 6TUP z 1 ? 6 ? 6TUP 1 ? 6 ? 1 6 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 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 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 6TUP _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 6TUP _struct.title 'Cryo-EM structure of Pf4 bacteriophage coat protein with single-stranded DNA' _struct.pdbx_descriptor 'Coat protein B of bacteriophage Pf1/DNA Complex' _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 6TUP _struct_keywords.text 'Bacteriophage, helical, filamentous, 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 THR A 5 ? LYS A 20 ? THR A 5 LYS A 20 1 ? 16 HELX_P HELX_P2 AA2 LYS A 20 ? VAL A 31 ? LYS A 20 VAL A 31 1 ? 12 HELX_P HELX_P3 AA3 VAL A 31 ? ILE A 39 ? VAL A 31 ILE A 39 1 ? 9 HELX_P HELX_P4 AA4 ILE A 39 ? ALA A 46 ? ILE A 39 ALA A 46 1 ? 8 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 6TUP _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 P 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 GLY 1 1 1 GLY GLY A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 ASP 4 4 4 ASP ASP A . n A 1 5 THR 5 5 5 THR THR A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 ALA 7 7 7 ALA ALA A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 GLU 9 9 9 GLU GLU A . n A 1 10 SER 10 10 10 SER SER A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 THR 13 13 13 THR THR A . n A 1 14 ASP 14 14 14 ASP ASP A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 GLN 16 16 16 GLN GLN A . n A 1 17 GLY 17 17 17 GLY GLY A . n A 1 18 ASP 18 18 18 ASP ASP A . n A 1 19 MET 19 19 19 MET MET A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 ILE 22 22 22 ILE ILE A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 TYR 25 25 25 TYR TYR A . n A 1 26 ILE 26 26 26 ILE ILE A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 LEU 30 30 30 LEU LEU A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 ILE 32 32 32 ILE ILE A . n A 1 33 LEU 33 33 33 LEU LEU A . n A 1 34 ALA 34 34 34 ALA ALA A . n A 1 35 VAL 35 35 35 VAL VAL A . n A 1 36 ALA 36 36 36 ALA ALA A . n A 1 37 GLY 37 37 37 GLY GLY A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 ILE 39 39 39 ILE ILE A . n A 1 40 TYR 40 40 40 TYR TYR A . n A 1 41 SER 41 41 41 SER SER A . n A 1 42 MET 42 42 42 MET MET A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ARG 44 44 44 ARG ARG A . n A 1 45 LYS 45 45 45 LYS LYS A . n A 1 46 ALA 46 46 46 ALA ALA A . n B 2 1 DA 1 1 1 DA DA z . n B 2 2 DA 2 2 2 DA DA z . n B 2 3 DA 3 3 3 DA DA z . n B 2 4 DA 4 4 4 DA DA z . n B 2 5 DA 5 5 5 DA DA z . n B 2 6 DA 6 6 6 DA DA z . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ;The helical filament symmetry is only applied to the Pf4 coat protein and not the DNA. The reason for this is that the DNA bases are not resolved clearly due to averaging along the ssDNA genome of the phage, meaning that refinement of the protein into the map is of a higher quality than the ssDNA, where a poly-adenine model has been built. ; _pdbx_struct_assembly.oligomeric_details 51-meric _pdbx_struct_assembly.oligomeric_count 51 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 ;1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50 ; A 1 1 B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' ? ? 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'point symmetry operation' ? ? 0.9938755800 -0.1102803900 -0.0070398800 34.2630249200 0.1103345500 0.9938636400 0.0078328600 -30.5907581700 0.0061328700 -0.0085616300 0.9999445400 35.1966237000 3 'point symmetry operation' ? ? 0.8732190700 0.4873276600 -0.0004505400 -98.9604415600 -0.4873059000 0.8731881100 0.0086886800 167.2535471300 0.0046276400 -0.0073675700 0.9999621500 16.4676487000 4 'point symmetry operation' ? ? 0.9146099500 0.4043319500 -0.0020761300 -86.9748701200 -0.4042945500 0.9145759000 0.0098406800 132.7428230000 0.0058776800 -0.0081610200 0.9999494200 50.6723126500 5 'point symmetry operation' ? ? 0.4782343200 0.8782230000 -0.0040360200 -97.3894758100 -0.8782293300 0.4782395700 0.0003930700 386.3494303900 0.0022753900 0.0033565700 0.9999917800 29.5980241000 6 'point symmetry operation' ? ? -0.1430410300 0.9896821400 -0.0082777000 44.2349028100 -0.9897167500 -0.1430352000 0.0012957600 588.6958374500 0.0000983900 0.0083779200 0.9999649000 10.0444526900 7 'point symmetry operation' ? ? 0.0115847400 0.9998889900 0.0093707800 -5.1891029500 -0.9999181800 0.0115332200 0.0055330500 546.8938445600 0.0054243700 -0.0094341100 0.9999407900 48.0703977500 8 'point symmetry operation' ? ? -0.6219432800 0.7830534400 -0.0037229800 232.4596367600 -0.7830602800 -0.6219238800 0.0052232000 662.8505592000 0.0017746400 0.0061638500 0.9999794300 25.7872141200 9 'point symmetry operation' ? ? -0.9622757500 0.2720582800 -0.0031100400 467.5650778500 -0.2720753400 -0.9622365100 0.0087129200 614.9028838800 -0.0006221700 0.0092304000 0.9999572100 6.8667260600 10 'point symmetry operation' ? ? -0.9237501400 0.3829911600 0.0018569000 424.7454349600 -0.3829942400 -0.9237490500 -0.0017605100 637.2759982600 0.0010410500 -0.0023374500 0.9999967300 44.0104574900 11 'point symmetry operation' ? ? -0.9633972300 -0.2680668900 0.0024328800 615.9400204800 0.2680754800 -0.9633099200 0.0130203800 464.8168193400 -0.0011467100 0.0131959900 0.9999122700 21.3055132500 12 'point symmetry operation' ? ? -0.6287231500 -0.7775559500 0.0106748100 662.0211088700 0.7776265900 -0.6286261000 0.0112296700 231.9074609000 -0.0020212300 0.0153613700 0.9998799600 2.2483583100 13 'point symmetry operation' ? ? -0.7562321400 -0.6543029500 -0.0007793700 664.7188068700 0.6542334400 -0.7561333000 -0.0155253900 308.3756085700 0.0095690000 -0.0122506800 0.9998791700 41.6011187700 14 'point symmetry operation' ? ? -0.2567359300 -0.9663895000 -0.0133418700 616.2531654100 0.9664707400 -0.2566431600 -0.0082826700 82.9004986900 0.0045801800 -0.0150209800 0.9998766900 24.9911576200 15 'point symmetry operation' ? ? 0.4110889500 -0.9115891000 -0.0033435600 415.1560740000 0.9115689500 0.4111021900 -0.0060857400 -87.4537495000 0.0069222400 -0.0005461000 0.9999758900 1.4462464900 16 'point symmetry operation' ? ? 0.2162685200 -0.9757829600 -0.0327955800 493.5035828000 0.9762998000 0.2164197500 -0.0010915200 -51.2017778500 0.0081627000 -0.0317822600 0.9994614800 44.5855902000 17 'point symmetry operation' ? ? 0.8019097500 -0.5973584700 -0.0101791400 222.4647269000 0.5973979100 0.8019442400 0.0010834700 -110.1131794400 0.0075158800 -0.0069498400 0.9999476000 18.7684217400 18 'point symmetry operation' ? ? 0.7566741200 -0.6537556100 -0.0069190500 249.5449150600 0.6537561300 0.7567011800 -0.0025006500 -112.4072886700 0.0068704700 -0.0026311900 0.9999729400 52.0005362100 19 'point symmetry operation' ? ? -0.9426714700 -0.3336994000 0.0038996000 627.6714618500 0.3337161900 -0.9426602300 0.0050190300 443.1529681500 0.0020011500 0.0060326500 0.9999798000 -11.5919663400 20 'point symmetry operation' ? ? -0.5815787300 -0.8134719100 0.0054436500 659.8507604200 0.8134894100 -0.5815740500 0.0025691200 211.2918963700 0.0010759800 0.0059225000 0.9999818800 -30.0888142100 21 'point symmetry operation' ? ? -0.0522305500 -0.9986228800 -0.0049298800 566.9678807200 0.9986236900 -0.0522057700 -0.0050278400 16.4528530900 0.0047635500 -0.0051857000 0.9999752100 -46.6078432700 22 'point symmetry operation' ? ? 0.4568512200 -0.8894324400 -0.0140323600 398.9914120300 0.8895272300 0.4568805200 0.0012290000 -95.3808705800 0.0053180000 -0.0130436300 0.9999007900 -28.7935485300 23 'point symmetry operation' ? ? 0.8943780500 -0.4472800700 -0.0053338000 154.2429239400 0.4472853400 0.8943912900 -0.0002268900 -93.7193563900 0.0048719900 -0.0021828100 0.9999857500 -50.4576040100 24 'point symmetry operation' ? ? 0.8482196600 -0.5295639800 -0.0092409500 190.6975624200 0.5296214100 0.8482166800 0.0054424900 -105.2110811200 0.0049561800 -0.0095106300 0.9999424900 -14.0164163200 25 'point symmetry operation' ? ? 0.9986233300 0.0522487400 -0.0046373600 -12.3327849500 -0.0521944000 0.9985746700 0.0111525300 12.1534102300 0.0052134600 -0.0108951300 0.9999270600 -32.4961554500 26 'point symmetry operation' ? ? 0.8212889600 0.5705030700 -0.0032687600 -106.8989702700 -0.5704911700 0.8212943400 0.0039281900 205.6268226200 0.0049256600 -0.0013613800 0.9999869400 -19.6187978300 27 'point symmetry operation' ? ? 0.3068617900 0.9517349500 -0.0060349300 -70.0237748000 -0.9517535000 0.3068624900 -0.0008321600 454.3361187800 0.0010599000 0.0059991300 0.9999814400 -39.4576299500 28 'point symmetry operation' ? ? 0.3965395900 0.9179860100 -0.0076179500 -84.8577060500 -0.9180142700 0.3965469200 -0.0005874700 420.1606288900 0.0024815900 0.0072263400 0.9999708100 -5.8765424100 29 'point symmetry operation' ? ? -0.2268399300 0.9738993900 -0.0079767900 71.6693278100 -0.9739319600 -0.2268358000 0.0014315100 607.4197340900 -0.0004152700 0.0080935700 0.9999671600 -24.0333051300 30 'point symmetry operation' ? ? -0.7548738300 0.6558117400 -0.0087445400 305.5875157500 -0.6558635800 -0.7548584500 0.0056281500 664.5652906200 -0.0029098800 0.0099837700 0.9999459300 -42.6313105700 31 'point symmetry operation' ? ? -0.6507524900 0.7592661500 0.0060092800 244.5182163300 -0.7592722600 -0.6507709600 0.0016704900 664.2695405100 0.0051790100 -0.0034756100 0.9999805500 -6.6023640500 32 'point symmetry operation' ? ? -0.9819737500 0.1889912900 -0.0031376400 495.9697857200 -0.1890113700 -0.9819393200 0.0083593300 597.4694494700 -0.0015011400 0.0088016900 0.9999601400 -27.0513911000 33 'point symmetry operation' ? ? -0.9160616200 -0.4010198300 0.0037699300 638.7499691100 0.4010273800 -0.9160648600 0.0014886800 417.8994238500 0.0028565100 0.0028755700 0.9999917900 -45.2092409600 34 'point symmetry operation' ? ? 0.7774112700 0.6289892700 -0.0020519500 -111.0024364600 -0.6289584500 0.7773989100 0.0078866600 232.9830559400 0.0065558100 -0.0048405900 0.9999667900 -53.2921613700 35 'point symmetry operation' ? ? -0.5127745900 -0.8584899400 0.0075661200 652.6326657900 0.8585197200 -0.5127779200 0.0016407600 180.1314191100 0.0024711600 0.0073370000 0.9999700300 -65.0996244700 36 'point symmetry operation' ? ? -0.0011074400 -0.9998385300 -0.0179355000 556.2477735500 0.9999578700 -0.0009437800 -0.0091306100 3.5691535200 0.0091122100 -0.0179448500 0.9997974500 -78.1107851900 37 'point symmetry operation' ? ? 0.6336294200 -0.7736309000 -0.0029984600 315.6018308300 0.7736198400 0.6336364400 -0.0041474700 -111.2615277900 0.0051085400 0.0003082900 0.9999869000 -101.0838674800 38 'point symmetry operation' ? ? 0.5428743300 -0.8398007700 -0.0047038600 359.1407134500 0.8398102100 0.5428801000 0.0000598600 -105.1231079700 0.0025033600 -0.0039828500 0.9999889300 -64.8475307100 39 'point symmetry operation' ? ? 0.9313467100 -0.3641105900 -0.0040965200 120.8164465500 0.3641239100 0.9313451200 0.0031702700 -82.1511636700 0.0026609400 -0.0044442600 0.9999865800 -83.7106047300 40 'point symmetry operation' ? ? 0.9665184900 0.2565246300 -0.0060934300 -59.8052799000 -0.2565187000 0.9665376900 0.0017492700 79.5029904400 0.0063382600 -0.0001276200 0.9999799000 -104.5896066600 41 'point symmetry operation' ? ? 0.9854932500 0.1696670200 -0.0040201700 -41.6141284400 -0.1696683100 0.9855012300 0.0000217700 50.9749144400 0.0039655700 0.0006606400 0.9999919200 -69.8041694600 42 'point symmetry operation' ? ? 0.7170456900 0.6970259200 -0.0005932800 -113.6132834800 -0.6970105900 0.7170350900 0.0060755700 268.7224513000 0.0046602300 -0.0039429300 0.9999813700 -87.3039029400 43 'point symmetry operation' ? ? 0.2362037400 0.9717022200 -0.0016109100 -57.0001577800 -0.9717032600 0.2362046400 0.0003850200 478.9580249400 0.0007546200 0.0014743800 0.9999986300 -72.3054206400 44 'point symmetry operation' ? ? -0.4059304900 0.9138370700 -0.0110568000 138.5522480000 -0.9139039600 -0.4059005000 0.0049339800 639.5751841700 0.0000208900 0.0121077000 0.9999267000 -94.0117785400 45 'point symmetry operation' ? ? -0.3087712200 0.9510902200 -0.0093662100 100.8933212400 -0.9511363200 -0.3087582200 0.0028397000 623.3183110800 -0.0001910800 0.0097853600 0.9999521000 -58.8711827500 46 'point symmetry operation' ? ? -0.7925426200 0.6098138000 0.0018230300 325.7440290300 -0.6098091800 -0.7925442100 0.0025366600 662.5201348600 0.0029917200 0.0008987100 0.9999951200 -75.8128076500 47 'point symmetry operation' ? ? -0.9997345800 0.0229523400 0.0019892300 545.1655054700 -0.0229412200 -0.9997219900 0.0054437300 557.1316466900 0.0021136200 0.0053966500 0.9999832000 -95.6194676000 48 'point symmetry operation' ? ? -0.9967528200 0.0804828600 -0.0025158000 530.0558351100 -0.0805049700 -0.9966991400 0.0104771400 571.2390037000 -0.0016642700 0.0106456600 0.9999419500 -62.0133868200 49 'point symmetry operation' ? ? -0.8734914600 -0.4868216500 0.0041660200 650.5497774100 0.4868394700 -0.8734602400 0.0073854000 380.9495171800 0.0000434800 0.0084792700 0.9999640500 -80.3487467700 50 'point symmetry operation' ? ? -0.4440500800 -0.8959872300 0.0051393500 644.4904398600 0.8960009900 -0.4440507800 0.0010675200 150.8721155400 0.0013256500 0.0050789000 0.9999862200 -98.3775127600 # 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 2020-02-26 2 'Structure model' 1 1 2020-03-04 3 'Structure model' 1 2 2020-03-11 # _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' 'Source and taxonomy' 4 3 'Structure model' 'Database references' # 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' citation_author 3 2 'Structure model' em_imaging_optics 4 2 'Structure model' entity_src_nat 5 3 'Structure model' citation # 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.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 2 'Structure model' '_citation_author.identifier_ORCID' 11 2 'Structure model' '_citation_author.name' 12 2 'Structure model' '_em_imaging_optics.chr_aberration_corrector' 13 2 'Structure model' '_em_imaging_optics.phase_plate' 14 2 'Structure model' '_em_imaging_optics.sph_aberration_corrector' 15 2 'Structure model' '_entity_src_nat.pdbx_organism_scientific' 16 3 'Structure model' '_citation.journal_volume' 17 3 'Structure model' '_citation.page_first' 18 3 'Structure model' '_citation.page_last' # _em_3d_fitting.entry_id 6TUP _em_3d_fitting.id 1 _em_3d_fitting.details ;The helical filament symmetry is only applied to the Pf4 coat protein and not the DNA. The reason for this is that the DNA bases are not resolved clearly due to averaging along the ssDNA genome of the phage, meaning that refinement of the protein into the map is of a higher quality than the ssDNA, where a poly-adenine model has been built. ; _em_3d_fitting.overall_b_value 93.74 _em_3d_fitting.ref_protocol 'BACKBONE TRACE' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria 'Correlation coefficient' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 6TUP _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm 'FOURIER SPACE' _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages 1 _em_3d_reconstruction.num_particles 185002 _em_3d_reconstruction.resolution 3.2 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type HELICAL _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 '1x Phosphate buffered saline' _em_buffer.pH 7.4 _em_buffer.specimen_id 1 _em_buffer.name ? # loop_ _em_entity_assembly.id _em_entity_assembly.parent_id _em_entity_assembly.details _em_entity_assembly.name _em_entity_assembly.source _em_entity_assembly.type _em_entity_assembly.entity_id_list _em_entity_assembly.synonym _em_entity_assembly.oligomeric_details 1 0 ? 'Pseudomonas virus Pf1' 'MULTIPLE SOURCES' VIRUS '1, 2' ? ? 2 1 ? 'Pseudomonas virus Pf1' NATURAL COMPLEX 1 ? ? 3 1 ? DNA NATURAL COMPLEX 2 ? ? # _em_image_scans.entry_id 6TUP _em_image_scans.id 1 _em_image_scans.dimension_height ? _em_image_scans.dimension_width ? _em_image_scans.frames_per_image 40 _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image 1-40 _em_image_scans.citation_id ? _em_image_scans.number_digital_images ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.details ? # _em_imaging.id 1 _em_imaging.entry_id 6TUP _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure 'ZEMLIN TABLEAU' _em_imaging.c2_aperture_diameter 50.0 _em_imaging.calibrated_defocus_max -3000 _em_imaging.calibrated_defocus_min -1000 _em_imaging.calibrated_magnification 105000 _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max -3000 _em_imaging.nominal_defocus_min -1000 _em_imaging.nominal_magnification 105000 _em_imaging.recording_temperature_maximum 80 _em_imaging.recording_temperature_minimum 80 _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _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_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details '20 second glow discharge at 15 mA in a LeicaEM ACE200' _em_sample_support.grid_material COPPER/RHODIUM _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type 'Quantifoil R2/2' _em_sample_support.method ? _em_sample_support.film_material ? # _em_virus_entity.entity_assembly_id 1 _em_virus_entity.empty NO _em_virus_entity.enveloped NO _em_virus_entity.virus_isolate STRAIN _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 283 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ;Samples for cryo-EM were prepared by pipetting 2.5 ul of the sample onto freshly glow-discharged Quantifoil grids (Cu/Rh R2/2, 200 mesh). Grids were blotted for 2.5 seconds with a blot force of -15, 0.5 second drain and 0 second wait times. ; _em_vitrification.humidity 100 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 6TUP _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 6TUP _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method HELICAL _em_experiment.entity_assembly_id 1 # loop_ _em_buffer_component.buffer_id _em_buffer_component.id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.name 1 1 8 g/l NaCl 'sodium chloride' 1 2 0.2 g/l KCl 'potassium chloride' 1 3 1.15 g/l Na2HPO4 'sodium phosphate dibasic' 1 4 0.2 g/l KH2PO4 'potassium phosphate monobasic' # _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 'Wiener filter implemented in the RELION refinement algorithm' # _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 ? # loop_ _em_entity_assembly_naturalsource.id _em_entity_assembly_naturalsource.entity_assembly_id _em_entity_assembly_naturalsource.cell _em_entity_assembly_naturalsource.cellular_location _em_entity_assembly_naturalsource.ncbi_tax_id _em_entity_assembly_naturalsource.organ _em_entity_assembly_naturalsource.organelle _em_entity_assembly_naturalsource.organism _em_entity_assembly_naturalsource.strain _em_entity_assembly_naturalsource.tissue 1 2 ? ? 2011081 ? ? 'Pseudomonas virus Pf1' ? ? 2 3 ? ? 208964 ? ? 'Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)' ? ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.angular_rotation_per_subunit 65.9 _em_helical_entity.axial_rise_per_subunit 3.14 _em_helical_entity.axial_symmetry C1 _em_helical_entity.details ? # _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 43 _em_image_recording.average_exposure_time 10 _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _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 2 _em_image_recording.num_real_images 4110 # _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_name 'GIF Bioquantum' _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.energyfilter_slit_width 20 _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? # _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.details ? _em_particle_selection.method ? _em_particle_selection.num_particles_selected 351381 _em_particle_selection.reference_model ? # 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' ? RELION 2.0 1 ? ? 2 'IMAGE ACQUISITION' ? EPU ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? RELION 2.0 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? Coot ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'MODEL REFINEMENT' ? PHENIX ? ? 1 ? 10 'INITIAL EULER ASSIGNMENT' ? RELION 2.0 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? RELION 2.0 1 ? ? 12 CLASSIFICATION ? RELION 3.0 1 ? ? 13 RECONSTRUCTION ? RELION 3.0 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 5 _em_specimen.details 'Filamentous phage purified from source' _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 208964 _em_virus_natural_host.organism 'Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)' _em_virus_natural_host.strain ? # _em_virus_shell.id 1 _em_virus_shell.entity_assembly_id 1 _em_virus_shell.diameter 62 _em_virus_shell.name 'Coat protein B (CoaB)' _em_virus_shell.triangulation ? # _pdbx_audit_support.funding_organization 'Wellcome Trust' _pdbx_audit_support.country 'United Kingdom' _pdbx_audit_support.grant_number 202231/Z/16/Z _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 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? #