data_6TUP # _entry.id 6TUP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 6TUP pdb_00006tup 10.2210/pdb6tup/pdb WWPDB D_1292106091 ? ? EMDB EMD-10593 ? ? # 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 4 'Structure model' 1 3 2024-05-22 # _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' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 2 'Structure model' em_imaging_optics 4 2 'Structure model' entity_src_nat 5 3 'Structure model' citation 6 4 'Structure model' chem_comp_atom 7 4 'Structure model' chem_comp_bond 8 4 'Structure model' database_2 9 4 'Structure model' pdbx_struct_oper_list # 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' 19 4 'Structure model' '_database_2.pdbx_DOI' 20 4 'Structure model' '_database_2.pdbx_database_accession' 21 4 'Structure model' '_pdbx_struct_oper_list.name' 22 4 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _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' # 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 ? # 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_ _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 # 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 # _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 ? # _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_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_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 # _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 # _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 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 '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_ _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 ? # _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_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASP N N N N 41 ASP CA C N S 42 ASP C C N N 43 ASP O O N N 44 ASP CB C N N 45 ASP CG C N N 46 ASP OD1 O N N 47 ASP OD2 O N N 48 ASP OXT O N N 49 ASP H H N N 50 ASP H2 H N N 51 ASP HA H N N 52 ASP HB2 H N N 53 ASP HB3 H N N 54 ASP HD2 H N N 55 ASP HXT H N N 56 DA OP3 O N N 57 DA P P N N 58 DA OP1 O N N 59 DA OP2 O N N 60 DA "O5'" O N N 61 DA "C5'" C N N 62 DA "C4'" C N R 63 DA "O4'" O N N 64 DA "C3'" C N S 65 DA "O3'" O N N 66 DA "C2'" C N N 67 DA "C1'" C N R 68 DA N9 N Y N 69 DA C8 C Y N 70 DA N7 N Y N 71 DA C5 C Y N 72 DA C6 C Y N 73 DA N6 N N N 74 DA N1 N Y N 75 DA C2 C Y N 76 DA N3 N Y N 77 DA C4 C Y N 78 DA HOP3 H N N 79 DA HOP2 H N N 80 DA "H5'" H N N 81 DA "H5''" H N N 82 DA "H4'" H N N 83 DA "H3'" H N N 84 DA "HO3'" H N N 85 DA "H2'" H N N 86 DA "H2''" H N N 87 DA "H1'" H N N 88 DA H8 H N N 89 DA H61 H N N 90 DA H62 H N N 91 DA H2 H N N 92 GLN N N N N 93 GLN CA C N S 94 GLN C C N N 95 GLN O O N N 96 GLN CB C N N 97 GLN CG C N N 98 GLN CD C N N 99 GLN OE1 O N N 100 GLN NE2 N N N 101 GLN OXT O N N 102 GLN H H N N 103 GLN H2 H N N 104 GLN HA H N N 105 GLN HB2 H N N 106 GLN HB3 H N N 107 GLN HG2 H N N 108 GLN HG3 H N N 109 GLN HE21 H N N 110 GLN HE22 H N N 111 GLN HXT H N N 112 GLU N N N N 113 GLU CA C N S 114 GLU C C N N 115 GLU O O N N 116 GLU CB C N N 117 GLU CG C N N 118 GLU CD C N N 119 GLU OE1 O N N 120 GLU OE2 O N N 121 GLU OXT O N N 122 GLU H H N N 123 GLU H2 H N N 124 GLU HA H N N 125 GLU HB2 H N N 126 GLU HB3 H N N 127 GLU HG2 H N N 128 GLU HG3 H N N 129 GLU HE2 H N N 130 GLU HXT H N N 131 GLY N N N N 132 GLY CA C N N 133 GLY C C N N 134 GLY O O N N 135 GLY OXT O N N 136 GLY H H N N 137 GLY H2 H N N 138 GLY HA2 H N N 139 GLY HA3 H N N 140 GLY HXT H N N 141 ILE N N N N 142 ILE CA C N S 143 ILE C C N N 144 ILE O O N N 145 ILE CB C N S 146 ILE CG1 C N N 147 ILE CG2 C N N 148 ILE CD1 C N N 149 ILE OXT O N N 150 ILE H H N N 151 ILE H2 H N N 152 ILE HA H N N 153 ILE HB H N N 154 ILE HG12 H N N 155 ILE HG13 H N N 156 ILE HG21 H N N 157 ILE HG22 H N N 158 ILE HG23 H N N 159 ILE HD11 H N N 160 ILE HD12 H N N 161 ILE HD13 H N N 162 ILE HXT H N N 163 LEU N N N N 164 LEU CA C N S 165 LEU C C N N 166 LEU O O N N 167 LEU CB C N N 168 LEU CG C N N 169 LEU CD1 C N N 170 LEU CD2 C N N 171 LEU OXT O N N 172 LEU H H N N 173 LEU H2 H N N 174 LEU HA H N N 175 LEU HB2 H N N 176 LEU HB3 H N N 177 LEU HG H N N 178 LEU HD11 H N N 179 LEU HD12 H N N 180 LEU HD13 H N N 181 LEU HD21 H N N 182 LEU HD22 H N N 183 LEU HD23 H N N 184 LEU HXT H N N 185 LYS N N N N 186 LYS CA C N S 187 LYS C C N N 188 LYS O O N N 189 LYS CB C N N 190 LYS CG C N N 191 LYS CD C N N 192 LYS CE C N N 193 LYS NZ N N N 194 LYS OXT O N N 195 LYS H H N N 196 LYS H2 H N N 197 LYS HA H N N 198 LYS HB2 H N N 199 LYS HB3 H N N 200 LYS HG2 H N N 201 LYS HG3 H N N 202 LYS HD2 H N N 203 LYS HD3 H N N 204 LYS HE2 H N N 205 LYS HE3 H N N 206 LYS HZ1 H N N 207 LYS HZ2 H N N 208 LYS HZ3 H N N 209 LYS HXT H N N 210 MET N N N N 211 MET CA C N S 212 MET C C N N 213 MET O O N N 214 MET CB C N N 215 MET CG C N N 216 MET SD S N N 217 MET CE C N N 218 MET OXT O N N 219 MET H H N N 220 MET H2 H N N 221 MET HA H N N 222 MET HB2 H N N 223 MET HB3 H N N 224 MET HG2 H N N 225 MET HG3 H N N 226 MET HE1 H N N 227 MET HE2 H N N 228 MET HE3 H N N 229 MET HXT H N N 230 SER N N N N 231 SER CA C N S 232 SER C C N N 233 SER O O N N 234 SER CB C N N 235 SER OG O N N 236 SER OXT O N N 237 SER H H N N 238 SER H2 H N N 239 SER HA H N N 240 SER HB2 H N N 241 SER HB3 H N N 242 SER HG H N N 243 SER HXT H N N 244 THR N N N N 245 THR CA C N S 246 THR C C N N 247 THR O O N N 248 THR CB C N R 249 THR OG1 O N N 250 THR CG2 C N N 251 THR OXT O N N 252 THR H H N N 253 THR H2 H N N 254 THR HA H N N 255 THR HB H N N 256 THR HG1 H N N 257 THR HG21 H N N 258 THR HG22 H N N 259 THR HG23 H N N 260 THR HXT H N N 261 TYR N N N N 262 TYR CA C N S 263 TYR C C N N 264 TYR O O N N 265 TYR CB C N N 266 TYR CG C Y N 267 TYR CD1 C Y N 268 TYR CD2 C Y N 269 TYR CE1 C Y N 270 TYR CE2 C Y N 271 TYR CZ C Y N 272 TYR OH O N N 273 TYR OXT O N N 274 TYR H H N N 275 TYR H2 H N N 276 TYR HA H N N 277 TYR HB2 H N N 278 TYR HB3 H N N 279 TYR HD1 H N N 280 TYR HD2 H N N 281 TYR HE1 H N N 282 TYR HE2 H N N 283 TYR HH H N N 284 TYR HXT H N N 285 VAL N N N N 286 VAL CA C N S 287 VAL C C N N 288 VAL O O N N 289 VAL CB C N N 290 VAL CG1 C N N 291 VAL CG2 C N N 292 VAL OXT O N N 293 VAL H H N N 294 VAL H2 H N N 295 VAL HA H N N 296 VAL HB H N N 297 VAL HG11 H N N 298 VAL HG12 H N N 299 VAL HG13 H N N 300 VAL HG21 H N N 301 VAL HG22 H N N 302 VAL HG23 H N N 303 VAL HXT H N N 304 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASP N CA sing N N 39 ASP N H sing N N 40 ASP N H2 sing N N 41 ASP CA C sing N N 42 ASP CA CB sing N N 43 ASP CA HA sing N N 44 ASP C O doub N N 45 ASP C OXT sing N N 46 ASP CB CG sing N N 47 ASP CB HB2 sing N N 48 ASP CB HB3 sing N N 49 ASP CG OD1 doub N N 50 ASP CG OD2 sing N N 51 ASP OD2 HD2 sing N N 52 ASP OXT HXT sing N N 53 DA OP3 P sing N N 54 DA OP3 HOP3 sing N N 55 DA P OP1 doub N N 56 DA P OP2 sing N N 57 DA P "O5'" sing N N 58 DA OP2 HOP2 sing N N 59 DA "O5'" "C5'" sing N N 60 DA "C5'" "C4'" sing N N 61 DA "C5'" "H5'" sing N N 62 DA "C5'" "H5''" sing N N 63 DA "C4'" "O4'" sing N N 64 DA "C4'" "C3'" sing N N 65 DA "C4'" "H4'" sing N N 66 DA "O4'" "C1'" sing N N 67 DA "C3'" "O3'" sing N N 68 DA "C3'" "C2'" sing N N 69 DA "C3'" "H3'" sing N N 70 DA "O3'" "HO3'" sing N N 71 DA "C2'" "C1'" sing N N 72 DA "C2'" "H2'" sing N N 73 DA "C2'" "H2''" sing N N 74 DA "C1'" N9 sing N N 75 DA "C1'" "H1'" sing N N 76 DA N9 C8 sing Y N 77 DA N9 C4 sing Y N 78 DA C8 N7 doub Y N 79 DA C8 H8 sing N N 80 DA N7 C5 sing Y N 81 DA C5 C6 sing Y N 82 DA C5 C4 doub Y N 83 DA C6 N6 sing N N 84 DA C6 N1 doub Y N 85 DA N6 H61 sing N N 86 DA N6 H62 sing N N 87 DA N1 C2 sing Y N 88 DA C2 N3 doub Y N 89 DA C2 H2 sing N N 90 DA N3 C4 sing Y N 91 GLN N CA sing N N 92 GLN N H sing N N 93 GLN N H2 sing N N 94 GLN CA C sing N N 95 GLN CA CB sing N N 96 GLN CA HA sing N N 97 GLN C O doub N N 98 GLN C OXT sing N N 99 GLN CB CG sing N N 100 GLN CB HB2 sing N N 101 GLN CB HB3 sing N N 102 GLN CG CD sing N N 103 GLN CG HG2 sing N N 104 GLN CG HG3 sing N N 105 GLN CD OE1 doub N N 106 GLN CD NE2 sing N N 107 GLN NE2 HE21 sing N N 108 GLN NE2 HE22 sing N N 109 GLN OXT HXT sing N N 110 GLU N CA sing N N 111 GLU N H sing N N 112 GLU N H2 sing N N 113 GLU CA C sing N N 114 GLU CA CB sing N N 115 GLU CA HA sing N N 116 GLU C O doub N N 117 GLU C OXT sing N N 118 GLU CB CG sing N N 119 GLU CB HB2 sing N N 120 GLU CB HB3 sing N N 121 GLU CG CD sing N N 122 GLU CG HG2 sing N N 123 GLU CG HG3 sing N N 124 GLU CD OE1 doub N N 125 GLU CD OE2 sing N N 126 GLU OE2 HE2 sing N N 127 GLU OXT HXT sing N N 128 GLY N CA sing N N 129 GLY N H sing N N 130 GLY N H2 sing N N 131 GLY CA C sing N N 132 GLY CA HA2 sing N N 133 GLY CA HA3 sing N N 134 GLY C O doub N N 135 GLY C OXT sing N N 136 GLY OXT HXT sing N N 137 ILE N CA sing N N 138 ILE N H sing N N 139 ILE N H2 sing N N 140 ILE CA C sing N N 141 ILE CA CB sing N N 142 ILE CA HA sing N N 143 ILE C O doub N N 144 ILE C OXT sing N N 145 ILE CB CG1 sing N N 146 ILE CB CG2 sing N N 147 ILE CB HB sing N N 148 ILE CG1 CD1 sing N N 149 ILE CG1 HG12 sing N N 150 ILE CG1 HG13 sing N N 151 ILE CG2 HG21 sing N N 152 ILE CG2 HG22 sing N N 153 ILE CG2 HG23 sing N N 154 ILE CD1 HD11 sing N N 155 ILE CD1 HD12 sing N N 156 ILE CD1 HD13 sing N N 157 ILE OXT HXT sing N N 158 LEU N CA sing N N 159 LEU N H sing N N 160 LEU N H2 sing N N 161 LEU CA C sing N N 162 LEU CA CB sing N N 163 LEU CA HA sing N N 164 LEU C O doub N N 165 LEU C OXT sing N N 166 LEU CB CG sing N N 167 LEU CB HB2 sing N N 168 LEU CB HB3 sing N N 169 LEU CG CD1 sing N N 170 LEU CG CD2 sing N N 171 LEU CG HG sing N N 172 LEU CD1 HD11 sing N N 173 LEU CD1 HD12 sing N N 174 LEU CD1 HD13 sing N N 175 LEU CD2 HD21 sing N N 176 LEU CD2 HD22 sing N N 177 LEU CD2 HD23 sing N N 178 LEU OXT HXT sing N N 179 LYS N CA sing N N 180 LYS N H sing N N 181 LYS N H2 sing N N 182 LYS CA C sing N N 183 LYS CA CB sing N N 184 LYS CA HA sing N N 185 LYS C O doub N N 186 LYS C OXT sing N N 187 LYS CB CG sing N N 188 LYS CB HB2 sing N N 189 LYS CB HB3 sing N N 190 LYS CG CD sing N N 191 LYS CG HG2 sing N N 192 LYS CG HG3 sing N N 193 LYS CD CE sing N N 194 LYS CD HD2 sing N N 195 LYS CD HD3 sing N N 196 LYS CE NZ sing N N 197 LYS CE HE2 sing N N 198 LYS CE HE3 sing N N 199 LYS NZ HZ1 sing N N 200 LYS NZ HZ2 sing N N 201 LYS NZ HZ3 sing N N 202 LYS OXT HXT sing N N 203 MET N CA sing N N 204 MET N H sing N N 205 MET N H2 sing N N 206 MET CA C sing N N 207 MET CA CB sing N N 208 MET CA HA sing N N 209 MET C O doub N N 210 MET C OXT sing N N 211 MET CB CG sing N N 212 MET CB HB2 sing N N 213 MET CB HB3 sing N N 214 MET CG SD sing N N 215 MET CG HG2 sing N N 216 MET CG HG3 sing N N 217 MET SD CE sing N N 218 MET CE HE1 sing N N 219 MET CE HE2 sing N N 220 MET CE HE3 sing N N 221 MET OXT HXT sing N N 222 SER N CA sing N N 223 SER N H sing N N 224 SER N H2 sing N N 225 SER CA C sing N N 226 SER CA CB sing N N 227 SER CA HA sing N N 228 SER C O doub N N 229 SER C OXT sing N N 230 SER CB OG sing N N 231 SER CB HB2 sing N N 232 SER CB HB3 sing N N 233 SER OG HG sing N N 234 SER OXT HXT sing N N 235 THR N CA sing N N 236 THR N H sing N N 237 THR N H2 sing N N 238 THR CA C sing N N 239 THR CA CB sing N N 240 THR CA HA sing N N 241 THR C O doub N N 242 THR C OXT sing N N 243 THR CB OG1 sing N N 244 THR CB CG2 sing N N 245 THR CB HB sing N N 246 THR OG1 HG1 sing N N 247 THR CG2 HG21 sing N N 248 THR CG2 HG22 sing N N 249 THR CG2 HG23 sing N N 250 THR OXT HXT sing N N 251 TYR N CA sing N N 252 TYR N H sing N N 253 TYR N H2 sing N N 254 TYR CA C sing N N 255 TYR CA CB sing N N 256 TYR CA HA sing N N 257 TYR C O doub N N 258 TYR C OXT sing N N 259 TYR CB CG sing N N 260 TYR CB HB2 sing N N 261 TYR CB HB3 sing N N 262 TYR CG CD1 doub Y N 263 TYR CG CD2 sing Y N 264 TYR CD1 CE1 sing Y N 265 TYR CD1 HD1 sing N N 266 TYR CD2 CE2 doub Y N 267 TYR CD2 HD2 sing N N 268 TYR CE1 CZ doub Y N 269 TYR CE1 HE1 sing N N 270 TYR CE2 CZ sing Y N 271 TYR CE2 HE2 sing N N 272 TYR CZ OH sing N N 273 TYR OH HH sing N N 274 TYR OXT HXT sing N N 275 VAL N CA sing N N 276 VAL N H sing N N 277 VAL N H2 sing N N 278 VAL CA C sing N N 279 VAL CA CB sing N N 280 VAL CA HA sing N N 281 VAL C O doub N N 282 VAL C OXT sing N N 283 VAL CB CG1 sing N N 284 VAL CB CG2 sing N N 285 VAL CB HB sing N N 286 VAL CG1 HG11 sing N N 287 VAL CG1 HG12 sing N N 288 VAL CG1 HG13 sing N N 289 VAL CG2 HG21 sing N N 290 VAL CG2 HG22 sing N N 291 VAL CG2 HG23 sing N N 292 VAL OXT HXT sing N N 293 # 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 # _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_