data_7DOU # _entry.id 7DOU # _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 7DOU pdb_00007dou 10.2210/pdb7dou/pdb WWPDB D_1300019860 ? ? EMDB EMD-30800 ? ? # 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 2021-10-27 2 'Structure model' 1 1 2022-02-23 3 'Structure model' 1 2 2024-06-05 # _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' 'Database references' 2 3 'Structure model' 'Data collection' # 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 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.year' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7DOU _pdbx_database_status.recvd_initial_deposition_date 2020-12-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB 'Capsid structure of the closely related H. pylori phage KHP30' EMD-30778 'other EM volume' EMDB 'Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40' EMD-30800 'associated EM volume' # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kamiya, R.' 1 ? 'Uchiyama, J.' 2 ? 'Matsuzaki, S.' 3 ? 'Murata, K.' 4 ? 'Iwasaki, K.' 5 ? 'Miyazaki, N.' 6 0000-0002-4880-7300 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Structure _citation.journal_id_ASTM STRUE6 _citation.journal_id_CSD 2005 _citation.journal_id_ISSN 0969-2126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 30 _citation.language ? _citation.page_first 300 _citation.page_last ? _citation.title 'Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.str.2021.09.001 _citation.pdbx_database_id_PubMed 34597601 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kamiya, R.' 1 ? primary 'Uchiyama, J.' 2 ? primary 'Matsuzaki, S.' 3 ? primary 'Murata, K.' 4 ? primary 'Iwasaki, K.' 5 ? primary 'Miyazaki, N.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method nat _entity.pdbx_description 'Cement protein gp16' _entity.formula_weight 13469.469 _entity.pdbx_number_of_molecules 3 _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 ;MKQKVHSVSYLAKAEFEYKNGVYDLVALPTGAEVIKISLEVVGLPTAGHVSVGFKDESKKNYSSILTLPVNETSGVVTKD YTVKSDKIVAAEVKDALAEGSDGRPVKCVLRALYFLPSVIEVEY ; _entity_poly.pdbx_seq_one_letter_code_can ;MKQKVHSVSYLAKAEFEYKNGVYDLVALPTGAEVIKISLEVVGLPTAGHVSVGFKDESKKNYSSILTLPVNETSGVVTKD YTVKSDKIVAAEVKDALAEGSDGRPVKCVLRALYFLPSVIEVEY ; _entity_poly.pdbx_strand_id 4,5,6 _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 MET n 1 2 LYS n 1 3 GLN n 1 4 LYS n 1 5 VAL n 1 6 HIS n 1 7 SER n 1 8 VAL n 1 9 SER n 1 10 TYR n 1 11 LEU n 1 12 ALA n 1 13 LYS n 1 14 ALA n 1 15 GLU n 1 16 PHE n 1 17 GLU n 1 18 TYR n 1 19 LYS n 1 20 ASN n 1 21 GLY n 1 22 VAL n 1 23 TYR n 1 24 ASP n 1 25 LEU n 1 26 VAL n 1 27 ALA n 1 28 LEU n 1 29 PRO n 1 30 THR n 1 31 GLY n 1 32 ALA n 1 33 GLU n 1 34 VAL n 1 35 ILE n 1 36 LYS n 1 37 ILE n 1 38 SER n 1 39 LEU n 1 40 GLU n 1 41 VAL n 1 42 VAL n 1 43 GLY n 1 44 LEU n 1 45 PRO n 1 46 THR n 1 47 ALA n 1 48 GLY n 1 49 HIS n 1 50 VAL n 1 51 SER n 1 52 VAL n 1 53 GLY n 1 54 PHE n 1 55 LYS n 1 56 ASP n 1 57 GLU n 1 58 SER n 1 59 LYS n 1 60 LYS n 1 61 ASN n 1 62 TYR n 1 63 SER n 1 64 SER n 1 65 ILE n 1 66 LEU n 1 67 THR n 1 68 LEU n 1 69 PRO n 1 70 VAL n 1 71 ASN n 1 72 GLU n 1 73 THR n 1 74 SER n 1 75 GLY n 1 76 VAL n 1 77 VAL n 1 78 THR n 1 79 LYS n 1 80 ASP n 1 81 TYR n 1 82 THR n 1 83 VAL n 1 84 LYS n 1 85 SER n 1 86 ASP n 1 87 LYS n 1 88 ILE n 1 89 VAL n 1 90 ALA n 1 91 ALA n 1 92 GLU n 1 93 VAL n 1 94 LYS n 1 95 ASP n 1 96 ALA n 1 97 LEU n 1 98 ALA n 1 99 GLU n 1 100 GLY n 1 101 SER n 1 102 ASP n 1 103 GLY n 1 104 ARG n 1 105 PRO n 1 106 VAL n 1 107 LYS n 1 108 CYS n 1 109 VAL n 1 110 LEU n 1 111 ARG n 1 112 ALA n 1 113 LEU n 1 114 TYR n 1 115 PHE n 1 116 LEU n 1 117 PRO n 1 118 SER n 1 119 VAL n 1 120 ILE n 1 121 GLU n 1 122 VAL n 1 123 GLU n 1 124 TYR 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 124 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Helicobacter phage KHP40' _entity_src_nat.pdbx_ncbi_taxonomy_id 1204178 _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 ? # 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 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 MET 1 1 1 MET MET 4 . n A 1 2 LYS 2 2 2 LYS LYS 4 . n A 1 3 GLN 3 3 3 GLN GLN 4 . n A 1 4 LYS 4 4 4 LYS LYS 4 . n A 1 5 VAL 5 5 5 VAL VAL 4 . n A 1 6 HIS 6 6 6 HIS HIS 4 . n A 1 7 SER 7 7 7 SER SER 4 . n A 1 8 VAL 8 8 8 VAL VAL 4 . n A 1 9 SER 9 9 9 SER SER 4 . n A 1 10 TYR 10 10 10 TYR TYR 4 . n A 1 11 LEU 11 11 11 LEU LEU 4 . n A 1 12 ALA 12 12 12 ALA ALA 4 . n A 1 13 LYS 13 13 13 LYS LYS 4 . n A 1 14 ALA 14 14 14 ALA ALA 4 . n A 1 15 GLU 15 15 15 GLU GLU 4 . n A 1 16 PHE 16 16 16 PHE PHE 4 . n A 1 17 GLU 17 17 17 GLU GLU 4 . n A 1 18 TYR 18 18 18 TYR TYR 4 . n A 1 19 LYS 19 19 19 LYS LYS 4 . n A 1 20 ASN 20 20 20 ASN ASN 4 . n A 1 21 GLY 21 21 21 GLY GLY 4 . n A 1 22 VAL 22 22 22 VAL VAL 4 . n A 1 23 TYR 23 23 23 TYR TYR 4 . n A 1 24 ASP 24 24 24 ASP ASP 4 . n A 1 25 LEU 25 25 25 LEU LEU 4 . n A 1 26 VAL 26 26 26 VAL VAL 4 . n A 1 27 ALA 27 27 27 ALA ALA 4 . n A 1 28 LEU 28 28 28 LEU LEU 4 . n A 1 29 PRO 29 29 29 PRO PRO 4 . n A 1 30 THR 30 30 30 THR THR 4 . n A 1 31 GLY 31 31 31 GLY GLY 4 . n A 1 32 ALA 32 32 32 ALA ALA 4 . n A 1 33 GLU 33 33 33 GLU GLU 4 . n A 1 34 VAL 34 34 34 VAL VAL 4 . n A 1 35 ILE 35 35 35 ILE ILE 4 . n A 1 36 LYS 36 36 36 LYS LYS 4 . n A 1 37 ILE 37 37 37 ILE ILE 4 . n A 1 38 SER 38 38 38 SER SER 4 . n A 1 39 LEU 39 39 39 LEU LEU 4 . n A 1 40 GLU 40 40 40 GLU GLU 4 . n A 1 41 VAL 41 41 41 VAL VAL 4 . n A 1 42 VAL 42 42 42 VAL VAL 4 . n A 1 43 GLY 43 43 43 GLY GLY 4 . n A 1 44 LEU 44 44 44 LEU LEU 4 . n A 1 45 PRO 45 45 45 PRO PRO 4 . n A 1 46 THR 46 46 46 THR THR 4 . n A 1 47 ALA 47 47 47 ALA ALA 4 . n A 1 48 GLY 48 48 48 GLY GLY 4 . n A 1 49 HIS 49 49 49 HIS HIS 4 . n A 1 50 VAL 50 50 50 VAL VAL 4 . n A 1 51 SER 51 51 51 SER SER 4 . n A 1 52 VAL 52 52 52 VAL VAL 4 . n A 1 53 GLY 53 53 53 GLY GLY 4 . n A 1 54 PHE 54 54 54 PHE PHE 4 . n A 1 55 LYS 55 55 55 LYS LYS 4 . n A 1 56 ASP 56 56 56 ASP ASP 4 . n A 1 57 GLU 57 57 57 GLU GLU 4 . n A 1 58 SER 58 58 58 SER SER 4 . n A 1 59 LYS 59 59 59 LYS LYS 4 . n A 1 60 LYS 60 60 60 LYS LYS 4 . n A 1 61 ASN 61 61 61 ASN ASN 4 . n A 1 62 TYR 62 62 62 TYR TYR 4 . n A 1 63 SER 63 63 63 SER SER 4 . n A 1 64 SER 64 64 64 SER SER 4 . n A 1 65 ILE 65 65 65 ILE ILE 4 . n A 1 66 LEU 66 66 66 LEU LEU 4 . n A 1 67 THR 67 67 67 THR THR 4 . n A 1 68 LEU 68 68 68 LEU LEU 4 . n A 1 69 PRO 69 69 69 PRO PRO 4 . n A 1 70 VAL 70 70 70 VAL VAL 4 . n A 1 71 ASN 71 71 71 ASN ASN 4 . n A 1 72 GLU 72 72 72 GLU GLU 4 . n A 1 73 THR 73 73 73 THR THR 4 . n A 1 74 SER 74 74 74 SER SER 4 . n A 1 75 GLY 75 75 75 GLY GLY 4 . n A 1 76 VAL 76 76 76 VAL VAL 4 . n A 1 77 VAL 77 77 77 VAL VAL 4 . n A 1 78 THR 78 78 78 THR THR 4 . n A 1 79 LYS 79 79 79 LYS LYS 4 . n A 1 80 ASP 80 80 80 ASP ASP 4 . n A 1 81 TYR 81 81 81 TYR TYR 4 . n A 1 82 THR 82 82 82 THR THR 4 . n A 1 83 VAL 83 83 83 VAL VAL 4 . n A 1 84 LYS 84 84 84 LYS LYS 4 . n A 1 85 SER 85 85 85 SER SER 4 . n A 1 86 ASP 86 86 86 ASP ASP 4 . n A 1 87 LYS 87 87 87 LYS LYS 4 . n A 1 88 ILE 88 88 88 ILE ILE 4 . n A 1 89 VAL 89 89 89 VAL VAL 4 . n A 1 90 ALA 90 90 90 ALA ALA 4 . n A 1 91 ALA 91 91 91 ALA ALA 4 . n A 1 92 GLU 92 92 92 GLU GLU 4 . n A 1 93 VAL 93 93 93 VAL VAL 4 . n A 1 94 LYS 94 94 94 LYS LYS 4 . n A 1 95 ASP 95 95 95 ASP ASP 4 . n A 1 96 ALA 96 96 96 ALA ALA 4 . n A 1 97 LEU 97 97 97 LEU LEU 4 . n A 1 98 ALA 98 98 98 ALA ALA 4 . n A 1 99 GLU 99 99 99 GLU GLU 4 . n A 1 100 GLY 100 100 100 GLY GLY 4 . n A 1 101 SER 101 101 101 SER SER 4 . n A 1 102 ASP 102 102 102 ASP ASP 4 . n A 1 103 GLY 103 103 103 GLY GLY 4 . n A 1 104 ARG 104 104 104 ARG ARG 4 . n A 1 105 PRO 105 105 105 PRO PRO 4 . n A 1 106 VAL 106 106 106 VAL VAL 4 . n A 1 107 LYS 107 107 107 LYS LYS 4 . n A 1 108 CYS 108 108 108 CYS CYS 4 . n A 1 109 VAL 109 109 109 VAL VAL 4 . n A 1 110 LEU 110 110 110 LEU LEU 4 . n A 1 111 ARG 111 111 111 ARG ARG 4 . n A 1 112 ALA 112 112 112 ALA ALA 4 . n A 1 113 LEU 113 113 113 LEU LEU 4 . n A 1 114 TYR 114 114 114 TYR TYR 4 . n A 1 115 PHE 115 115 115 PHE PHE 4 . n A 1 116 LEU 116 116 116 LEU LEU 4 . n A 1 117 PRO 117 117 117 PRO PRO 4 . n A 1 118 SER 118 118 118 SER SER 4 . n A 1 119 VAL 119 119 119 VAL VAL 4 . n A 1 120 ILE 120 120 120 ILE ILE 4 . n A 1 121 GLU 121 121 121 GLU GLU 4 . n A 1 122 VAL 122 122 122 VAL VAL 4 . n A 1 123 GLU 123 123 123 GLU GLU 4 . n A 1 124 TYR 124 124 124 TYR TYR 4 . n B 1 1 MET 1 1 1 MET MET 5 . n B 1 2 LYS 2 2 2 LYS LYS 5 . n B 1 3 GLN 3 3 3 GLN GLN 5 . n B 1 4 LYS 4 4 4 LYS LYS 5 . n B 1 5 VAL 5 5 5 VAL VAL 5 . n B 1 6 HIS 6 6 6 HIS HIS 5 . n B 1 7 SER 7 7 7 SER SER 5 . n B 1 8 VAL 8 8 8 VAL VAL 5 . n B 1 9 SER 9 9 9 SER SER 5 . n B 1 10 TYR 10 10 10 TYR TYR 5 . n B 1 11 LEU 11 11 11 LEU LEU 5 . n B 1 12 ALA 12 12 12 ALA ALA 5 . n B 1 13 LYS 13 13 13 LYS LYS 5 . n B 1 14 ALA 14 14 14 ALA ALA 5 . n B 1 15 GLU 15 15 15 GLU GLU 5 . n B 1 16 PHE 16 16 16 PHE PHE 5 . n B 1 17 GLU 17 17 17 GLU GLU 5 . n B 1 18 TYR 18 18 18 TYR TYR 5 . n B 1 19 LYS 19 19 19 LYS LYS 5 . n B 1 20 ASN 20 20 20 ASN ASN 5 . n B 1 21 GLY 21 21 21 GLY GLY 5 . n B 1 22 VAL 22 22 22 VAL VAL 5 . n B 1 23 TYR 23 23 23 TYR TYR 5 . n B 1 24 ASP 24 24 24 ASP ASP 5 . n B 1 25 LEU 25 25 25 LEU LEU 5 . n B 1 26 VAL 26 26 26 VAL VAL 5 . n B 1 27 ALA 27 27 27 ALA ALA 5 . n B 1 28 LEU 28 28 28 LEU LEU 5 . n B 1 29 PRO 29 29 29 PRO PRO 5 . n B 1 30 THR 30 30 30 THR THR 5 . n B 1 31 GLY 31 31 31 GLY GLY 5 . n B 1 32 ALA 32 32 32 ALA ALA 5 . n B 1 33 GLU 33 33 33 GLU GLU 5 . n B 1 34 VAL 34 34 34 VAL VAL 5 . n B 1 35 ILE 35 35 35 ILE ILE 5 . n B 1 36 LYS 36 36 36 LYS LYS 5 . n B 1 37 ILE 37 37 37 ILE ILE 5 . n B 1 38 SER 38 38 38 SER SER 5 . n B 1 39 LEU 39 39 39 LEU LEU 5 . n B 1 40 GLU 40 40 40 GLU GLU 5 . n B 1 41 VAL 41 41 41 VAL VAL 5 . n B 1 42 VAL 42 42 42 VAL VAL 5 . n B 1 43 GLY 43 43 43 GLY GLY 5 . n B 1 44 LEU 44 44 44 LEU LEU 5 . n B 1 45 PRO 45 45 45 PRO PRO 5 . n B 1 46 THR 46 46 46 THR THR 5 . n B 1 47 ALA 47 47 47 ALA ALA 5 . n B 1 48 GLY 48 48 48 GLY GLY 5 . n B 1 49 HIS 49 49 49 HIS HIS 5 . n B 1 50 VAL 50 50 50 VAL VAL 5 . n B 1 51 SER 51 51 51 SER SER 5 . n B 1 52 VAL 52 52 52 VAL VAL 5 . n B 1 53 GLY 53 53 53 GLY GLY 5 . n B 1 54 PHE 54 54 54 PHE PHE 5 . n B 1 55 LYS 55 55 55 LYS LYS 5 . n B 1 56 ASP 56 56 56 ASP ASP 5 . n B 1 57 GLU 57 57 57 GLU GLU 5 . n B 1 58 SER 58 58 58 SER SER 5 . n B 1 59 LYS 59 59 59 LYS LYS 5 . n B 1 60 LYS 60 60 60 LYS LYS 5 . n B 1 61 ASN 61 61 61 ASN ASN 5 . n B 1 62 TYR 62 62 62 TYR TYR 5 . n B 1 63 SER 63 63 63 SER SER 5 . n B 1 64 SER 64 64 64 SER SER 5 . n B 1 65 ILE 65 65 65 ILE ILE 5 . n B 1 66 LEU 66 66 66 LEU LEU 5 . n B 1 67 THR 67 67 67 THR THR 5 . n B 1 68 LEU 68 68 68 LEU LEU 5 . n B 1 69 PRO 69 69 69 PRO PRO 5 . n B 1 70 VAL 70 70 70 VAL VAL 5 . n B 1 71 ASN 71 71 71 ASN ASN 5 . n B 1 72 GLU 72 72 72 GLU GLU 5 . n B 1 73 THR 73 73 73 THR THR 5 . n B 1 74 SER 74 74 74 SER SER 5 . n B 1 75 GLY 75 75 75 GLY GLY 5 . n B 1 76 VAL 76 76 76 VAL VAL 5 . n B 1 77 VAL 77 77 77 VAL VAL 5 . n B 1 78 THR 78 78 78 THR THR 5 . n B 1 79 LYS 79 79 79 LYS LYS 5 . n B 1 80 ASP 80 80 80 ASP ASP 5 . n B 1 81 TYR 81 81 81 TYR TYR 5 . n B 1 82 THR 82 82 82 THR THR 5 . n B 1 83 VAL 83 83 83 VAL VAL 5 . n B 1 84 LYS 84 84 84 LYS LYS 5 . n B 1 85 SER 85 85 85 SER SER 5 . n B 1 86 ASP 86 86 86 ASP ASP 5 . n B 1 87 LYS 87 87 87 LYS LYS 5 . n B 1 88 ILE 88 88 88 ILE ILE 5 . n B 1 89 VAL 89 89 89 VAL VAL 5 . n B 1 90 ALA 90 90 90 ALA ALA 5 . n B 1 91 ALA 91 91 91 ALA ALA 5 . n B 1 92 GLU 92 92 92 GLU GLU 5 . n B 1 93 VAL 93 93 93 VAL VAL 5 . n B 1 94 LYS 94 94 94 LYS LYS 5 . n B 1 95 ASP 95 95 95 ASP ASP 5 . n B 1 96 ALA 96 96 96 ALA ALA 5 . n B 1 97 LEU 97 97 97 LEU LEU 5 . n B 1 98 ALA 98 98 98 ALA ALA 5 . n B 1 99 GLU 99 99 99 GLU GLU 5 . n B 1 100 GLY 100 100 100 GLY GLY 5 . n B 1 101 SER 101 101 101 SER SER 5 . n B 1 102 ASP 102 102 102 ASP ASP 5 . n B 1 103 GLY 103 103 103 GLY GLY 5 . n B 1 104 ARG 104 104 104 ARG ARG 5 . n B 1 105 PRO 105 105 105 PRO PRO 5 . n B 1 106 VAL 106 106 106 VAL VAL 5 . n B 1 107 LYS 107 107 107 LYS LYS 5 . n B 1 108 CYS 108 108 108 CYS CYS 5 . n B 1 109 VAL 109 109 109 VAL VAL 5 . n B 1 110 LEU 110 110 110 LEU LEU 5 . n B 1 111 ARG 111 111 111 ARG ARG 5 . n B 1 112 ALA 112 112 112 ALA ALA 5 . n B 1 113 LEU 113 113 113 LEU LEU 5 . n B 1 114 TYR 114 114 114 TYR TYR 5 . n B 1 115 PHE 115 115 115 PHE PHE 5 . n B 1 116 LEU 116 116 116 LEU LEU 5 . n B 1 117 PRO 117 117 117 PRO PRO 5 . n B 1 118 SER 118 118 118 SER SER 5 . n B 1 119 VAL 119 119 119 VAL VAL 5 . n B 1 120 ILE 120 120 120 ILE ILE 5 . n B 1 121 GLU 121 121 121 GLU GLU 5 . n B 1 122 VAL 122 122 122 VAL VAL 5 . n B 1 123 GLU 123 123 123 GLU GLU 5 . n B 1 124 TYR 124 124 124 TYR TYR 5 . n C 1 1 MET 1 1 1 MET MET 6 . n C 1 2 LYS 2 2 2 LYS LYS 6 . n C 1 3 GLN 3 3 3 GLN GLN 6 . n C 1 4 LYS 4 4 4 LYS LYS 6 . n C 1 5 VAL 5 5 5 VAL VAL 6 . n C 1 6 HIS 6 6 6 HIS HIS 6 . n C 1 7 SER 7 7 7 SER SER 6 . n C 1 8 VAL 8 8 8 VAL VAL 6 . n C 1 9 SER 9 9 9 SER SER 6 . n C 1 10 TYR 10 10 10 TYR TYR 6 . n C 1 11 LEU 11 11 11 LEU LEU 6 . n C 1 12 ALA 12 12 12 ALA ALA 6 . n C 1 13 LYS 13 13 13 LYS LYS 6 . n C 1 14 ALA 14 14 14 ALA ALA 6 . n C 1 15 GLU 15 15 15 GLU GLU 6 . n C 1 16 PHE 16 16 16 PHE PHE 6 . n C 1 17 GLU 17 17 17 GLU GLU 6 . n C 1 18 TYR 18 18 18 TYR TYR 6 . n C 1 19 LYS 19 19 19 LYS LYS 6 . n C 1 20 ASN 20 20 20 ASN ASN 6 . n C 1 21 GLY 21 21 21 GLY GLY 6 . n C 1 22 VAL 22 22 22 VAL VAL 6 . n C 1 23 TYR 23 23 23 TYR TYR 6 . n C 1 24 ASP 24 24 24 ASP ASP 6 . n C 1 25 LEU 25 25 25 LEU LEU 6 . n C 1 26 VAL 26 26 26 VAL VAL 6 . n C 1 27 ALA 27 27 27 ALA ALA 6 . n C 1 28 LEU 28 28 28 LEU LEU 6 . n C 1 29 PRO 29 29 29 PRO PRO 6 . n C 1 30 THR 30 30 30 THR THR 6 . n C 1 31 GLY 31 31 31 GLY GLY 6 . n C 1 32 ALA 32 32 32 ALA ALA 6 . n C 1 33 GLU 33 33 33 GLU GLU 6 . n C 1 34 VAL 34 34 34 VAL VAL 6 . n C 1 35 ILE 35 35 35 ILE ILE 6 . n C 1 36 LYS 36 36 36 LYS LYS 6 . n C 1 37 ILE 37 37 37 ILE ILE 6 . n C 1 38 SER 38 38 38 SER SER 6 . n C 1 39 LEU 39 39 39 LEU LEU 6 . n C 1 40 GLU 40 40 40 GLU GLU 6 . n C 1 41 VAL 41 41 41 VAL VAL 6 . n C 1 42 VAL 42 42 42 VAL VAL 6 . n C 1 43 GLY 43 43 43 GLY GLY 6 . n C 1 44 LEU 44 44 44 LEU LEU 6 . n C 1 45 PRO 45 45 45 PRO PRO 6 . n C 1 46 THR 46 46 46 THR THR 6 . n C 1 47 ALA 47 47 47 ALA ALA 6 . n C 1 48 GLY 48 48 48 GLY GLY 6 . n C 1 49 HIS 49 49 49 HIS HIS 6 . n C 1 50 VAL 50 50 50 VAL VAL 6 . n C 1 51 SER 51 51 51 SER SER 6 . n C 1 52 VAL 52 52 52 VAL VAL 6 . n C 1 53 GLY 53 53 53 GLY GLY 6 . n C 1 54 PHE 54 54 54 PHE PHE 6 . n C 1 55 LYS 55 55 55 LYS LYS 6 . n C 1 56 ASP 56 56 56 ASP ASP 6 . n C 1 57 GLU 57 57 57 GLU GLU 6 . n C 1 58 SER 58 58 58 SER SER 6 . n C 1 59 LYS 59 59 59 LYS LYS 6 . n C 1 60 LYS 60 60 60 LYS LYS 6 . n C 1 61 ASN 61 61 61 ASN ASN 6 . n C 1 62 TYR 62 62 62 TYR TYR 6 . n C 1 63 SER 63 63 63 SER SER 6 . n C 1 64 SER 64 64 64 SER SER 6 . n C 1 65 ILE 65 65 65 ILE ILE 6 . n C 1 66 LEU 66 66 66 LEU LEU 6 . n C 1 67 THR 67 67 67 THR THR 6 . n C 1 68 LEU 68 68 68 LEU LEU 6 . n C 1 69 PRO 69 69 69 PRO PRO 6 . n C 1 70 VAL 70 70 70 VAL VAL 6 . n C 1 71 ASN 71 71 71 ASN ASN 6 . n C 1 72 GLU 72 72 72 GLU GLU 6 . n C 1 73 THR 73 73 73 THR THR 6 . n C 1 74 SER 74 74 74 SER SER 6 . n C 1 75 GLY 75 75 75 GLY GLY 6 . n C 1 76 VAL 76 76 76 VAL VAL 6 . n C 1 77 VAL 77 77 77 VAL VAL 6 . n C 1 78 THR 78 78 78 THR THR 6 . n C 1 79 LYS 79 79 79 LYS LYS 6 . n C 1 80 ASP 80 80 80 ASP ASP 6 . n C 1 81 TYR 81 81 81 TYR TYR 6 . n C 1 82 THR 82 82 82 THR THR 6 . n C 1 83 VAL 83 83 83 VAL VAL 6 . n C 1 84 LYS 84 84 84 LYS LYS 6 . n C 1 85 SER 85 85 85 SER SER 6 . n C 1 86 ASP 86 86 86 ASP ASP 6 . n C 1 87 LYS 87 87 87 LYS LYS 6 . n C 1 88 ILE 88 88 88 ILE ILE 6 . n C 1 89 VAL 89 89 89 VAL VAL 6 . n C 1 90 ALA 90 90 90 ALA ALA 6 . n C 1 91 ALA 91 91 91 ALA ALA 6 . n C 1 92 GLU 92 92 92 GLU GLU 6 . n C 1 93 VAL 93 93 93 VAL VAL 6 . n C 1 94 LYS 94 94 94 LYS LYS 6 . n C 1 95 ASP 95 95 95 ASP ASP 6 . n C 1 96 ALA 96 96 96 ALA ALA 6 . n C 1 97 LEU 97 97 97 LEU LEU 6 . n C 1 98 ALA 98 98 98 ALA ALA 6 . n C 1 99 GLU 99 99 99 GLU GLU 6 . n C 1 100 GLY 100 100 100 GLY GLY 6 . n C 1 101 SER 101 101 101 SER SER 6 . n C 1 102 ASP 102 102 102 ASP ASP 6 . n C 1 103 GLY 103 103 103 GLY GLY 6 . n C 1 104 ARG 104 104 104 ARG ARG 6 . n C 1 105 PRO 105 105 105 PRO PRO 6 . n C 1 106 VAL 106 106 106 VAL VAL 6 . n C 1 107 LYS 107 107 107 LYS LYS 6 . n C 1 108 CYS 108 108 108 CYS CYS 6 . n C 1 109 VAL 109 109 109 VAL VAL 6 . n C 1 110 LEU 110 110 110 LEU LEU 6 . n C 1 111 ARG 111 111 111 ARG ARG 6 . n C 1 112 ALA 112 112 112 ALA ALA 6 . n C 1 113 LEU 113 113 113 LEU LEU 6 . n C 1 114 TYR 114 114 114 TYR TYR 6 . n C 1 115 PHE 115 115 115 PHE PHE 6 . n C 1 116 LEU 116 116 116 LEU LEU 6 . n C 1 117 PRO 117 117 117 PRO PRO 6 . n C 1 118 SER 118 118 118 SER SER 6 . n C 1 119 VAL 119 119 119 VAL VAL 6 . n C 1 120 ILE 120 120 120 ILE ILE 6 . n C 1 121 GLU 121 121 121 GLU GLU 6 . n C 1 122 VAL 122 122 122 VAL VAL 6 . n C 1 123 GLU 123 123 123 GLU GLU 6 . n C 1 124 TYR 124 124 124 TYR TYR 6 . n # _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 1.18.2_3874: _software.pdbx_ordinal 1 # _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 7DOU _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 7DOU _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 7DOU _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7DOU _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 ? 2889 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.644 ? 3915 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 5.899 ? 396 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.046 ? 471 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.005 ? 486 ? f_plane_restr ? ? # _struct.entry_id 7DOU _struct.title 'Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40' _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 7DOU _struct_keywords.text 'CAPSID, PHAGE, PHAGE HEAD, CRYOEM, 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 1 ? C N N 1 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code I7GUT5_9CAUD _struct_ref.pdbx_db_accession I7GUT5 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKQKVHSVSYLAKAEFEYKNGVYDLVALPTGAEVIKISLEVVGLPTAGHVSVGFKDESKKNYSSILTLPVNETSGVVTKD YTVKSDKIVAAEVKDALAEGSDGRPVKCVLRALYFLPSVIEVEY ; _struct_ref.pdbx_align_begin 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 7DOU 4 1 ? 124 ? I7GUT5 1 ? 124 ? 1 124 2 1 7DOU 5 1 ? 124 ? I7GUT5 1 ? 124 ? 1 124 3 1 7DOU 6 1 ? 124 ? I7GUT5 1 ? 124 ? 1 124 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 ? # _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 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 6 ? AA2 ? 6 ? AA3 ? 4 ? AA4 ? 4 ? AA5 ? 4 ? AA6 ? 2 ? AA7 ? 4 ? AA8 ? 4 ? AA9 ? 4 ? AB1 ? 2 ? AB2 ? 4 ? # 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 AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA2 5 6 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA5 3 4 ? anti-parallel AA6 1 2 ? anti-parallel AA7 1 2 ? anti-parallel AA7 2 3 ? anti-parallel AA7 3 4 ? anti-parallel AA8 1 2 ? anti-parallel AA8 2 3 ? anti-parallel AA8 3 4 ? anti-parallel AA9 1 2 ? anti-parallel AA9 2 3 ? anti-parallel AA9 3 4 ? anti-parallel AB1 1 2 ? anti-parallel AB2 1 2 ? anti-parallel AB2 2 3 ? anti-parallel AB2 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 119 ? GLU A 123 ? VAL 4 119 GLU 4 123 AA1 2 LYS A 2 ? HIS A 6 ? LYS 4 2 HIS 4 6 AA1 3 SER C 9 ? PHE C 16 ? SER 6 9 PHE 6 16 AA1 4 LYS C 107 ? PHE C 115 ? LYS 6 107 PHE 6 115 AA1 5 GLU C 33 ? VAL C 42 ? GLU 6 33 VAL 6 42 AA1 6 SER C 74 ? VAL C 76 ? SER 6 74 VAL 6 76 AA2 1 VAL A 119 ? GLU A 123 ? VAL 4 119 GLU 4 123 AA2 2 LYS A 2 ? HIS A 6 ? LYS 4 2 HIS 4 6 AA2 3 SER C 9 ? PHE C 16 ? SER 6 9 PHE 6 16 AA2 4 LYS C 107 ? PHE C 115 ? LYS 6 107 PHE 6 115 AA2 5 GLU C 33 ? VAL C 42 ? GLU 6 33 VAL 6 42 AA2 6 TYR C 81 ? THR C 82 ? TYR 6 81 THR 6 82 AA3 1 SER A 9 ? PHE A 16 ? SER 4 9 PHE 4 16 AA3 2 LYS A 107 ? PHE A 115 ? LYS 4 107 PHE 4 115 AA3 3 GLU A 33 ? VAL A 42 ? GLU 4 33 VAL 4 42 AA3 4 SER A 74 ? VAL A 76 ? SER 4 74 VAL 4 76 AA4 1 SER A 9 ? PHE A 16 ? SER 4 9 PHE 4 16 AA4 2 LYS A 107 ? PHE A 115 ? LYS 4 107 PHE 4 115 AA4 3 GLU A 33 ? VAL A 42 ? GLU 4 33 VAL 4 42 AA4 4 TYR A 81 ? THR A 82 ? TYR 4 81 THR 4 82 AA5 1 GLY A 21 ? ALA A 27 ? GLY 4 21 ALA 4 27 AA5 2 ILE A 88 ? ALA A 96 ? ILE 4 88 ALA 4 96 AA5 3 GLY A 48 ? LYS A 55 ? GLY 4 48 LYS 4 55 AA5 4 SER A 63 ? PRO A 69 ? SER 4 63 PRO 4 69 AA6 1 LYS B 2 ? HIS B 6 ? LYS 5 2 HIS 5 6 AA6 2 VAL B 119 ? GLU B 123 ? VAL 5 119 GLU 5 123 AA7 1 SER B 9 ? PHE B 16 ? SER 5 9 PHE 5 16 AA7 2 LYS B 107 ? PHE B 115 ? LYS 5 107 PHE 5 115 AA7 3 GLU B 33 ? VAL B 42 ? GLU 5 33 VAL 5 42 AA7 4 SER B 74 ? VAL B 76 ? SER 5 74 VAL 5 76 AA8 1 SER B 9 ? PHE B 16 ? SER 5 9 PHE 5 16 AA8 2 LYS B 107 ? PHE B 115 ? LYS 5 107 PHE 5 115 AA8 3 GLU B 33 ? VAL B 42 ? GLU 5 33 VAL 5 42 AA8 4 TYR B 81 ? THR B 82 ? TYR 5 81 THR 5 82 AA9 1 GLY B 21 ? ALA B 27 ? GLY 5 21 ALA 5 27 AA9 2 ILE B 88 ? ALA B 96 ? ILE 5 88 ALA 5 96 AA9 3 GLY B 48 ? LYS B 55 ? GLY 5 48 LYS 5 55 AA9 4 SER B 63 ? PRO B 69 ? SER 5 63 PRO 5 69 AB1 1 LYS C 2 ? HIS C 6 ? LYS 6 2 HIS 6 6 AB1 2 VAL C 119 ? GLU C 123 ? VAL 6 119 GLU 6 123 AB2 1 GLY C 21 ? ALA C 27 ? GLY 6 21 ALA 6 27 AB2 2 ILE C 88 ? ALA C 96 ? ILE 6 88 ALA 6 96 AB2 3 GLY C 48 ? LYS C 55 ? GLY 6 48 LYS 6 55 AB2 4 SER C 63 ? PRO C 69 ? SER 6 63 PRO 6 69 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 O ILE A 120 ? O ILE 4 120 N VAL A 5 ? N VAL 4 5 AA1 2 3 N HIS A 6 ? N HIS 4 6 O LEU C 11 ? O LEU 6 11 AA1 3 4 N TYR C 10 ? N TYR 6 10 O TYR C 114 ? O TYR 6 114 AA1 4 5 O PHE C 115 ? O PHE 6 115 N GLU C 33 ? N GLU 6 33 AA1 5 6 N LEU C 39 ? N LEU 6 39 O GLY C 75 ? O GLY 6 75 AA2 1 2 O ILE A 120 ? O ILE 4 120 N VAL A 5 ? N VAL 4 5 AA2 2 3 N HIS A 6 ? N HIS 4 6 O LEU C 11 ? O LEU 6 11 AA2 3 4 N TYR C 10 ? N TYR 6 10 O TYR C 114 ? O TYR 6 114 AA2 4 5 O PHE C 115 ? O PHE 6 115 N GLU C 33 ? N GLU 6 33 AA2 5 6 N VAL C 34 ? N VAL 6 34 O TYR C 81 ? O TYR 6 81 AA3 1 2 N TYR A 10 ? N TYR 4 10 O TYR A 114 ? O TYR 4 114 AA3 2 3 O PHE A 115 ? O PHE 4 115 N GLU A 33 ? N GLU 4 33 AA3 3 4 N LEU A 39 ? N LEU 4 39 O GLY A 75 ? O GLY 4 75 AA4 1 2 N TYR A 10 ? N TYR 4 10 O TYR A 114 ? O TYR 4 114 AA4 2 3 O PHE A 115 ? O PHE 4 115 N GLU A 33 ? N GLU 4 33 AA4 3 4 N VAL A 34 ? N VAL 4 34 O TYR A 81 ? O TYR 4 81 AA5 1 2 N GLY A 21 ? N GLY 4 21 O VAL A 93 ? O VAL 4 93 AA5 2 3 O ILE A 88 ? O ILE 4 88 N LYS A 55 ? N LYS 4 55 AA5 3 4 N VAL A 52 ? N VAL 4 52 O ILE A 65 ? O ILE 4 65 AA6 1 2 N VAL B 5 ? N VAL 5 5 O ILE B 120 ? O ILE 5 120 AA7 1 2 N TYR B 10 ? N TYR 5 10 O TYR B 114 ? O TYR 5 114 AA7 2 3 O PHE B 115 ? O PHE 5 115 N GLU B 33 ? N GLU 5 33 AA7 3 4 N LEU B 39 ? N LEU 5 39 O GLY B 75 ? O GLY 5 75 AA8 1 2 N TYR B 10 ? N TYR 5 10 O TYR B 114 ? O TYR 5 114 AA8 2 3 O PHE B 115 ? O PHE 5 115 N GLU B 33 ? N GLU 5 33 AA8 3 4 N VAL B 34 ? N VAL 5 34 O TYR B 81 ? O TYR 5 81 AA9 1 2 N GLY B 21 ? N GLY 5 21 O VAL B 93 ? O VAL 5 93 AA9 2 3 O ILE B 88 ? O ILE 5 88 N LYS B 55 ? N LYS 5 55 AA9 3 4 N VAL B 52 ? N VAL 5 52 O ILE B 65 ? O ILE 5 65 AB1 1 2 N VAL C 5 ? N VAL 6 5 O ILE C 120 ? O ILE 6 120 AB2 1 2 N GLY C 21 ? N GLY 6 21 O VAL C 93 ? O VAL 6 93 AB2 2 3 O ILE C 88 ? O ILE 6 88 N LYS C 55 ? N LYS 6 55 AB2 3 4 N VAL C 52 ? N VAL 6 52 O ILE C 65 ? O ILE 6 65 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OE2 _pdbx_validate_close_contact.auth_asym_id_1 5 _pdbx_validate_close_contact.auth_comp_id_1 GLU _pdbx_validate_close_contact.auth_seq_id_1 40 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 NZ _pdbx_validate_close_contact.auth_asym_id_2 6 _pdbx_validate_close_contact.auth_comp_id_2 LYS _pdbx_validate_close_contact.auth_seq_id_2 79 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.16 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 THR 4 73 ? ? 67.09 -0.69 2 1 SER 4 85 ? ? 68.40 -5.15 3 1 ALA 4 98 ? ? -66.05 -175.45 4 1 SER 4 101 ? ? 66.62 -4.85 5 1 THR 5 73 ? ? 67.10 -0.66 6 1 SER 5 85 ? ? 68.42 -5.11 7 1 ALA 5 98 ? ? -66.01 -175.51 8 1 SER 5 101 ? ? 66.62 -4.83 9 1 THR 6 73 ? ? 67.08 -0.65 10 1 SER 6 85 ? ? 68.40 -5.09 11 1 ALA 6 98 ? ? -66.04 -175.49 12 1 SER 6 101 ? ? 66.63 -4.89 # _em_3d_fitting.entry_id 7DOU _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7DOU _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 6772 _em_3d_reconstruction.resolution 3.0 _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 'Helicobacter phage KHP' _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 7DOU _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 TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _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 NO _em_virus_entity.virus_isolate OTHER _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 277 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 100 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 7DOU _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7DOU _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 7DOU _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry I # 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 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 ILE N N N N 158 ILE CA C N S 159 ILE C C N N 160 ILE O O N N 161 ILE CB C N S 162 ILE CG1 C N N 163 ILE CG2 C N N 164 ILE CD1 C N N 165 ILE OXT O N N 166 ILE H H N N 167 ILE H2 H N N 168 ILE HA H N N 169 ILE HB H N N 170 ILE HG12 H N N 171 ILE HG13 H N N 172 ILE HG21 H N N 173 ILE HG22 H N N 174 ILE HG23 H N N 175 ILE HD11 H N N 176 ILE HD12 H N N 177 ILE HD13 H N N 178 ILE HXT H N N 179 LEU N N N N 180 LEU CA C N S 181 LEU C C N N 182 LEU O O N N 183 LEU CB C N N 184 LEU CG C N N 185 LEU CD1 C N N 186 LEU CD2 C N N 187 LEU OXT O N N 188 LEU H H N N 189 LEU H2 H N N 190 LEU HA H N N 191 LEU HB2 H N N 192 LEU HB3 H N N 193 LEU HG H N N 194 LEU HD11 H N N 195 LEU HD12 H N N 196 LEU HD13 H N N 197 LEU HD21 H N N 198 LEU HD22 H N N 199 LEU HD23 H N N 200 LEU HXT H N N 201 LYS N N N N 202 LYS CA C N S 203 LYS C C N N 204 LYS O O N N 205 LYS CB C N N 206 LYS CG C N N 207 LYS CD C N N 208 LYS CE C N N 209 LYS NZ N N N 210 LYS OXT O N N 211 LYS H H N N 212 LYS H2 H N N 213 LYS HA H N N 214 LYS HB2 H N N 215 LYS HB3 H N N 216 LYS HG2 H N N 217 LYS HG3 H N N 218 LYS HD2 H N N 219 LYS HD3 H N N 220 LYS HE2 H N N 221 LYS HE3 H N N 222 LYS HZ1 H N N 223 LYS HZ2 H N N 224 LYS HZ3 H N N 225 LYS HXT H N N 226 MET N N N N 227 MET CA C N S 228 MET C C N N 229 MET O O N N 230 MET CB C N N 231 MET CG C N N 232 MET SD S N N 233 MET CE C N N 234 MET OXT O N N 235 MET H H N N 236 MET H2 H N N 237 MET HA H N N 238 MET HB2 H N N 239 MET HB3 H N N 240 MET HG2 H N N 241 MET HG3 H N N 242 MET HE1 H N N 243 MET HE2 H N N 244 MET HE3 H N N 245 MET HXT H N N 246 PHE N N N N 247 PHE CA C N S 248 PHE C C N N 249 PHE O O N N 250 PHE CB C N N 251 PHE CG C Y N 252 PHE CD1 C Y N 253 PHE CD2 C Y N 254 PHE CE1 C Y N 255 PHE CE2 C Y N 256 PHE CZ C Y N 257 PHE OXT O N N 258 PHE H H N N 259 PHE H2 H N N 260 PHE HA H N N 261 PHE HB2 H N N 262 PHE HB3 H N N 263 PHE HD1 H N N 264 PHE HD2 H N N 265 PHE HE1 H N N 266 PHE HE2 H N N 267 PHE HZ H N N 268 PHE HXT H N N 269 PRO N N N N 270 PRO CA C N S 271 PRO C C N N 272 PRO O O N N 273 PRO CB C N N 274 PRO CG C N N 275 PRO CD C N N 276 PRO OXT O N N 277 PRO H H N N 278 PRO HA H N N 279 PRO HB2 H N N 280 PRO HB3 H N N 281 PRO HG2 H N N 282 PRO HG3 H N N 283 PRO HD2 H N N 284 PRO HD3 H N N 285 PRO HXT H N N 286 SER N N N N 287 SER CA C N S 288 SER C C N N 289 SER O O N N 290 SER CB C N N 291 SER OG O N N 292 SER OXT O N N 293 SER H H N N 294 SER H2 H N N 295 SER HA H N N 296 SER HB2 H N N 297 SER HB3 H N N 298 SER HG H N N 299 SER HXT H N N 300 THR N N N N 301 THR CA C N S 302 THR C C N N 303 THR O O N N 304 THR CB C N R 305 THR OG1 O N N 306 THR CG2 C N N 307 THR OXT O N N 308 THR H H N N 309 THR H2 H N N 310 THR HA H N N 311 THR HB H N N 312 THR HG1 H N N 313 THR HG21 H N N 314 THR HG22 H N N 315 THR HG23 H N N 316 THR HXT H N N 317 TYR N N N N 318 TYR CA C N S 319 TYR C C N N 320 TYR O O N N 321 TYR CB C N N 322 TYR CG C Y N 323 TYR CD1 C Y N 324 TYR CD2 C Y N 325 TYR CE1 C Y N 326 TYR CE2 C Y N 327 TYR CZ C Y N 328 TYR OH O N N 329 TYR OXT O N N 330 TYR H H N N 331 TYR H2 H N N 332 TYR HA H N N 333 TYR HB2 H N N 334 TYR HB3 H N N 335 TYR HD1 H N N 336 TYR HD2 H N N 337 TYR HE1 H N N 338 TYR HE2 H N N 339 TYR HH H N N 340 TYR HXT H N N 341 VAL N N N N 342 VAL CA C N S 343 VAL C C N N 344 VAL O O N N 345 VAL CB C N N 346 VAL CG1 C N N 347 VAL CG2 C N N 348 VAL OXT O N N 349 VAL H H N N 350 VAL H2 H N N 351 VAL HA H N N 352 VAL HB H N N 353 VAL HG11 H N N 354 VAL HG12 H N N 355 VAL HG13 H N N 356 VAL HG21 H N N 357 VAL HG22 H N N 358 VAL HG23 H N N 359 VAL HXT H N N 360 # 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 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 ILE N CA sing N N 150 ILE N H sing N N 151 ILE N H2 sing N N 152 ILE CA C sing N N 153 ILE CA CB sing N N 154 ILE CA HA sing N N 155 ILE C O doub N N 156 ILE C OXT sing N N 157 ILE CB CG1 sing N N 158 ILE CB CG2 sing N N 159 ILE CB HB sing N N 160 ILE CG1 CD1 sing N N 161 ILE CG1 HG12 sing N N 162 ILE CG1 HG13 sing N N 163 ILE CG2 HG21 sing N N 164 ILE CG2 HG22 sing N N 165 ILE CG2 HG23 sing N N 166 ILE CD1 HD11 sing N N 167 ILE CD1 HD12 sing N N 168 ILE CD1 HD13 sing N N 169 ILE OXT HXT sing N N 170 LEU N CA sing N N 171 LEU N H sing N N 172 LEU N H2 sing N N 173 LEU CA C sing N N 174 LEU CA CB sing N N 175 LEU CA HA sing N N 176 LEU C O doub N N 177 LEU C OXT sing N N 178 LEU CB CG sing N N 179 LEU CB HB2 sing N N 180 LEU CB HB3 sing N N 181 LEU CG CD1 sing N N 182 LEU CG CD2 sing N N 183 LEU CG HG sing N N 184 LEU CD1 HD11 sing N N 185 LEU CD1 HD12 sing N N 186 LEU CD1 HD13 sing N N 187 LEU CD2 HD21 sing N N 188 LEU CD2 HD22 sing N N 189 LEU CD2 HD23 sing N N 190 LEU OXT HXT sing N N 191 LYS N CA sing N N 192 LYS N H sing N N 193 LYS N H2 sing N N 194 LYS CA C sing N N 195 LYS CA CB sing N N 196 LYS CA HA sing N N 197 LYS C O doub N N 198 LYS C OXT sing N N 199 LYS CB CG sing N N 200 LYS CB HB2 sing N N 201 LYS CB HB3 sing N N 202 LYS CG CD sing N N 203 LYS CG HG2 sing N N 204 LYS CG HG3 sing N N 205 LYS CD CE sing N N 206 LYS CD HD2 sing N N 207 LYS CD HD3 sing N N 208 LYS CE NZ sing N N 209 LYS CE HE2 sing N N 210 LYS CE HE3 sing N N 211 LYS NZ HZ1 sing N N 212 LYS NZ HZ2 sing N N 213 LYS NZ HZ3 sing N N 214 LYS OXT HXT sing N N 215 MET N CA sing N N 216 MET N H sing N N 217 MET N H2 sing N N 218 MET CA C sing N N 219 MET CA CB sing N N 220 MET CA HA sing N N 221 MET C O doub N N 222 MET C OXT sing N N 223 MET CB CG sing N N 224 MET CB HB2 sing N N 225 MET CB HB3 sing N N 226 MET CG SD sing N N 227 MET CG HG2 sing N N 228 MET CG HG3 sing N N 229 MET SD CE sing N N 230 MET CE HE1 sing N N 231 MET CE HE2 sing N N 232 MET CE HE3 sing N N 233 MET OXT HXT sing N N 234 PHE N CA sing N N 235 PHE N H sing N N 236 PHE N H2 sing N N 237 PHE CA C sing N N 238 PHE CA CB sing N N 239 PHE CA HA sing N N 240 PHE C O doub N N 241 PHE C OXT sing N N 242 PHE CB CG sing N N 243 PHE CB HB2 sing N N 244 PHE CB HB3 sing N N 245 PHE CG CD1 doub Y N 246 PHE CG CD2 sing Y N 247 PHE CD1 CE1 sing Y N 248 PHE CD1 HD1 sing N N 249 PHE CD2 CE2 doub Y N 250 PHE CD2 HD2 sing N N 251 PHE CE1 CZ doub Y N 252 PHE CE1 HE1 sing N N 253 PHE CE2 CZ sing Y N 254 PHE CE2 HE2 sing N N 255 PHE CZ HZ sing N N 256 PHE OXT HXT sing N N 257 PRO N CA sing N N 258 PRO N CD sing N N 259 PRO N H sing N N 260 PRO CA C sing N N 261 PRO CA CB sing N N 262 PRO CA HA sing N N 263 PRO C O doub N N 264 PRO C OXT sing N N 265 PRO CB CG sing N N 266 PRO CB HB2 sing N N 267 PRO CB HB3 sing N N 268 PRO CG CD sing N N 269 PRO CG HG2 sing N N 270 PRO CG HG3 sing N N 271 PRO CD HD2 sing N N 272 PRO CD HD3 sing N N 273 PRO OXT HXT sing N N 274 SER N CA sing N N 275 SER N H sing N N 276 SER N H2 sing N N 277 SER CA C sing N N 278 SER CA CB sing N N 279 SER CA HA sing N N 280 SER C O doub N N 281 SER C OXT sing N N 282 SER CB OG sing N N 283 SER CB HB2 sing N N 284 SER CB HB3 sing N N 285 SER OG HG sing N N 286 SER OXT HXT sing N N 287 THR N CA sing N N 288 THR N H sing N N 289 THR N H2 sing N N 290 THR CA C sing N N 291 THR CA CB sing N N 292 THR CA HA sing N N 293 THR C O doub N N 294 THR C OXT sing N N 295 THR CB OG1 sing N N 296 THR CB CG2 sing N N 297 THR CB HB sing N N 298 THR OG1 HG1 sing N N 299 THR CG2 HG21 sing N N 300 THR CG2 HG22 sing N N 301 THR CG2 HG23 sing N N 302 THR OXT HXT sing N N 303 TYR N CA sing N N 304 TYR N H sing N N 305 TYR N H2 sing N N 306 TYR CA C sing N N 307 TYR CA CB sing N N 308 TYR CA HA sing N N 309 TYR C O doub N N 310 TYR C OXT sing N N 311 TYR CB CG sing N N 312 TYR CB HB2 sing N N 313 TYR CB HB3 sing N N 314 TYR CG CD1 doub Y N 315 TYR CG CD2 sing Y N 316 TYR CD1 CE1 sing Y N 317 TYR CD1 HD1 sing N N 318 TYR CD2 CE2 doub Y N 319 TYR CD2 HD2 sing N N 320 TYR CE1 CZ doub Y N 321 TYR CE1 HE1 sing N N 322 TYR CE2 CZ sing Y N 323 TYR CE2 HE2 sing N N 324 TYR CZ OH sing N N 325 TYR OH HH sing N N 326 TYR OXT HXT sing N N 327 VAL N CA sing N N 328 VAL N H sing N N 329 VAL N H2 sing N N 330 VAL CA C sing N N 331 VAL CA CB sing N N 332 VAL CA HA sing N N 333 VAL C O doub N N 334 VAL C OXT sing N N 335 VAL CB CG1 sing N N 336 VAL CB CG2 sing N N 337 VAL CB HB sing N N 338 VAL CG1 HG11 sing N N 339 VAL CG1 HG12 sing N N 340 VAL CG1 HG13 sing N N 341 VAL CG2 HG21 sing N N 342 VAL CG2 HG22 sing N N 343 VAL CG2 HG23 sing N N 344 VAL OXT HXT sing N N 345 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 1208236 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Helicobacter phage KHP' _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 20.0 _em_image_recording.average_exposure_time 1.0 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'FEI FALCON II (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # 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' ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? ? ? ? ? ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? RELION ? 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_shell.id 1 _em_virus_shell.entity_assembly_id 1 _em_virus_shell.diameter 700 _em_virus_shell.name Head _em_virus_shell.triangulation 9 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan 15K18521 1 'Japan Society for the Promotion of Science (JSPS)' Japan 18K06154 2 # _atom_sites.entry_id 7DOU _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_