data_4D3E # _entry.id 4D3E # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 4D3E pdb_00004d3e 10.2210/pdb4d3e/pdb PDBE EBI-62074 ? ? WWPDB D_1290062074 ? ? # 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 2014-12-10 2 'Structure model' 1 1 2015-01-14 3 'Structure model' 1 2 2017-08-30 4 'Structure model' 1 3 2018-01-31 5 'Structure model' 1 4 2020-04-29 6 'Structure model' 1 5 2024-05-08 # _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' 3 4 'Structure model' 'Data processing' 4 5 'Structure model' 'Data processing' 5 6 'Structure model' 'Data collection' 6 6 'Structure model' 'Database references' 7 6 'Structure model' 'Refinement description' # 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 3 'Structure model' em_software 2 4 'Structure model' em_software 3 5 'Structure model' em_3d_reconstruction 4 6 'Structure model' chem_comp_atom 5 6 'Structure model' chem_comp_bond 6 6 'Structure model' database_2 7 6 'Structure model' em_3d_fitting_list 8 6 'Structure model' pdbx_initial_refinement_model 9 6 'Structure model' refine # 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 3 'Structure model' '_em_software.fitting_id' 2 3 'Structure model' '_em_software.image_processing_id' 3 4 'Structure model' '_em_software.details' 4 4 'Structure model' '_em_software.name' 5 5 'Structure model' '_em_3d_reconstruction.resolution' 6 6 'Structure model' '_database_2.pdbx_DOI' 7 6 'Structure model' '_database_2.pdbx_database_accession' 8 6 'Structure model' '_em_3d_fitting_list.accession_code' 9 6 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id' 10 6 'Structure model' '_em_3d_fitting_list.source_name' 11 6 'Structure model' '_em_3d_fitting_list.type' 12 6 'Structure model' '_refine.ls_d_res_high' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4D3E _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-10-21 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.db_id EMD-2801 _pdbx_database_related.content_type 'associated EM volume' _pdbx_database_related.details . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cheung, M.' 1 'Shen, D.-K.' 2 'Makino, F.' 3 'Kato, T.' 4 'Roehrich, D.' 5 'Martinez-Argudo, I.' 6 'Walker, M.L.' 7 'Murillo, I.' 8 'Liu, X.' 9 'Pain, M.' 10 'Brown, J.' 11 'Frazer, G.' 12 'Mantell, J.' 13 'Mina, P.' 14 'Todd, T.' 15 'Sessions, R.B.' 16 'Namba, K.' 17 'Blocker, A.J.' 18 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Three-Dimensional Electron Microscopy Reconstruction and Cysteine-Mediated Crosslinking Provide a Model of the T3Ss Needle Tip Complex. ; Mol.Microbiol. 95 31 ? 2015 MOMIEE UK 0950-382X 2007 ? 25353930 10.1111/MMI.12843 1 'Self-Chaperoning of the Type III Secretion System Needle Tip Proteins Ipad and Bipd' J.Biol.Chem. 282 4035 ? 2007 JBCHA3 US 0021-9258 0071 ? 17077085 10.1074/JBC.M607945200 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cheung, M.' 1 ? primary 'Shen, D.' 2 ? primary 'Makino, F.' 3 ? primary 'Kato, T.' 4 ? primary 'Roehrich, A.D.' 5 ? primary 'Martinez-Argudo, I.' 6 ? primary 'Walker, M.L.' 7 ? primary 'Murillo, I.' 8 ? primary 'Liu, X.' 9 ? primary 'Pain, M.' 10 ? primary 'Brown, J.' 11 ? primary 'Frazer, G.' 12 ? primary 'Mantell, J.' 13 ? primary 'Mina, P.' 14 ? primary 'Todd, T.' 15 ? primary 'Sessions, R.B.' 16 ? primary 'Namba, K.' 17 ? primary 'Blocker, A.J.' 18 ? 1 'Johnson, S.' 19 ? 1 'Roversi, P.' 20 ? 1 'Espina, M.' 21 ? 1 'Olive, A.' 22 ? 1 'Deane, J.E.' 23 ? 1 'Birket, S.' 24 ? 1 'Field, T.' 25 ? 1 'Picking, W.D.' 26 ? 1 'Blocker, A.J.' 27 ? 1 'Galyov, E.E.' 28 ? 1 'Picking, W.L.' 29 ? 1 'Lea, S.M.' 30 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'INVASIN IPAD' _entity.formula_weight 23076.775 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'COILDED-COIL AND GLOBULAR DOMAIN, UNP RESIDUES 125-332' _entity.details 'YES [LACKING FIRST 124 AA AND WITH LAST 10 AA MODELLED INTO HELIX]' # _entity_name_com.entity_id 1 _entity_name_com.name '36 KDA MEMBRANE ANTIGEN' # _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 ;GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKE KYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFS AEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSCTDTDKLFLHF ; _entity_poly.pdbx_seq_one_letter_code_can ;GDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKE KYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFS AEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSCTDTDKLFLHF ; _entity_poly.pdbx_strand_id D _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 GLY n 1 2 ASP n 1 3 GLN n 1 4 MET n 1 5 ILE n 1 6 SER n 1 7 HIS n 1 8 ARG n 1 9 GLU n 1 10 LEU n 1 11 TRP n 1 12 ALA n 1 13 LYS n 1 14 ILE n 1 15 ALA n 1 16 ASN n 1 17 SER n 1 18 ILE n 1 19 ASN n 1 20 ASP n 1 21 ILE n 1 22 ASN n 1 23 GLU n 1 24 GLN n 1 25 TYR n 1 26 LEU n 1 27 LYS n 1 28 VAL n 1 29 TYR n 1 30 GLU n 1 31 HIS n 1 32 ALA n 1 33 VAL n 1 34 SER n 1 35 SER n 1 36 TYR n 1 37 THR n 1 38 GLN n 1 39 MET n 1 40 TYR n 1 41 GLN n 1 42 ASP n 1 43 PHE n 1 44 SER n 1 45 ALA n 1 46 VAL n 1 47 LEU n 1 48 SER n 1 49 SER n 1 50 LEU n 1 51 ALA n 1 52 GLY n 1 53 TRP n 1 54 ILE n 1 55 SER n 1 56 PRO n 1 57 GLY n 1 58 GLY n 1 59 ASN n 1 60 ASP n 1 61 GLY n 1 62 ASN n 1 63 SER n 1 64 VAL n 1 65 LYS n 1 66 LEU n 1 67 GLN n 1 68 VAL n 1 69 ASN n 1 70 SER n 1 71 LEU n 1 72 LYS n 1 73 LYS n 1 74 ALA n 1 75 LEU n 1 76 GLU n 1 77 GLU n 1 78 LEU n 1 79 LYS n 1 80 GLU n 1 81 LYS n 1 82 TYR n 1 83 LYS n 1 84 ASP n 1 85 LYS n 1 86 PRO n 1 87 LEU n 1 88 TYR n 1 89 PRO n 1 90 ALA n 1 91 ASN n 1 92 ASN n 1 93 THR n 1 94 VAL n 1 95 SER n 1 96 GLN n 1 97 GLU n 1 98 GLN n 1 99 ALA n 1 100 ASN n 1 101 LYS n 1 102 TRP n 1 103 LEU n 1 104 THR n 1 105 GLU n 1 106 LEU n 1 107 GLY n 1 108 GLY n 1 109 THR n 1 110 ILE n 1 111 GLY n 1 112 LYS n 1 113 VAL n 1 114 SER n 1 115 GLN n 1 116 LYS n 1 117 ASN n 1 118 GLY n 1 119 GLY n 1 120 TYR n 1 121 VAL n 1 122 VAL n 1 123 SER n 1 124 ILE n 1 125 ASN n 1 126 MET n 1 127 THR n 1 128 PRO n 1 129 ILE n 1 130 ASP n 1 131 ASN n 1 132 MET n 1 133 LEU n 1 134 LYS n 1 135 SER n 1 136 LEU n 1 137 ASP n 1 138 ASN n 1 139 LEU n 1 140 GLY n 1 141 GLY n 1 142 ASN n 1 143 GLY n 1 144 GLU n 1 145 VAL n 1 146 VAL n 1 147 LEU n 1 148 ASP n 1 149 ASN n 1 150 ALA n 1 151 LYS n 1 152 TYR n 1 153 GLN n 1 154 ALA n 1 155 TRP n 1 156 ASN n 1 157 ALA n 1 158 GLY n 1 159 PHE n 1 160 SER n 1 161 ALA n 1 162 GLU n 1 163 ASP n 1 164 GLU n 1 165 THR n 1 166 MET n 1 167 LYS n 1 168 ASN n 1 169 ASN n 1 170 LEU n 1 171 GLN n 1 172 THR n 1 173 LEU n 1 174 VAL n 1 175 GLN n 1 176 LYS n 1 177 TYR n 1 178 SER n 1 179 ASN n 1 180 ALA n 1 181 ASN n 1 182 SER n 1 183 ILE n 1 184 PHE n 1 185 ASP n 1 186 ASN n 1 187 LEU n 1 188 VAL n 1 189 LYS n 1 190 VAL n 1 191 LEU n 1 192 SER n 1 193 SER n 1 194 THR n 1 195 ILE n 1 196 SER n 1 197 SER n 1 198 CYS n 1 199 THR n 1 200 ASP n 1 201 THR n 1 202 ASP n 1 203 LYS n 1 204 LEU n 1 205 PHE n 1 206 LEU n 1 207 HIS n 1 208 PHE n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'SHIGELLA FLEXNERI 5A STR. M90T' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1086030 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 1 125 125 GLY GLY D . n A 1 2 ASP 2 126 126 ASP ASP D . n A 1 3 GLN 3 127 127 GLN GLN D . n A 1 4 MET 4 128 128 MET MET D . n A 1 5 ILE 5 129 129 ILE ILE D . n A 1 6 SER 6 130 130 SER SER D . n A 1 7 HIS 7 131 131 HIS HIS D . n A 1 8 ARG 8 132 132 ARG ARG D . n A 1 9 GLU 9 133 133 GLU GLU D . n A 1 10 LEU 10 134 134 LEU LEU D . n A 1 11 TRP 11 135 135 TRP TRP D . n A 1 12 ALA 12 136 136 ALA ALA D . n A 1 13 LYS 13 137 137 LYS LYS D . n A 1 14 ILE 14 138 138 ILE ILE D . n A 1 15 ALA 15 139 139 ALA ALA D . n A 1 16 ASN 16 140 140 ASN ASN D . n A 1 17 SER 17 141 141 SER SER D . n A 1 18 ILE 18 142 142 ILE ILE D . n A 1 19 ASN 19 143 143 ASN ASN D . n A 1 20 ASP 20 144 144 ASP ASP D . n A 1 21 ILE 21 145 145 ILE ILE D . n A 1 22 ASN 22 146 146 ASN ASN D . n A 1 23 GLU 23 147 147 GLU GLU D . n A 1 24 GLN 24 148 148 GLN GLN D . n A 1 25 TYR 25 149 149 TYR TYR D . n A 1 26 LEU 26 150 150 LEU LEU D . n A 1 27 LYS 27 151 151 LYS LYS D . n A 1 28 VAL 28 152 152 VAL VAL D . n A 1 29 TYR 29 153 153 TYR TYR D . n A 1 30 GLU 30 154 154 GLU GLU D . n A 1 31 HIS 31 155 155 HIS HIS D . n A 1 32 ALA 32 156 156 ALA ALA D . n A 1 33 VAL 33 157 157 VAL VAL D . n A 1 34 SER 34 158 158 SER SER D . n A 1 35 SER 35 159 159 SER SER D . n A 1 36 TYR 36 160 160 TYR TYR D . n A 1 37 THR 37 161 161 THR THR D . n A 1 38 GLN 38 162 162 GLN GLN D . n A 1 39 MET 39 163 163 MET MET D . n A 1 40 TYR 40 164 164 TYR TYR D . n A 1 41 GLN 41 165 165 GLN GLN D . n A 1 42 ASP 42 166 166 ASP ASP D . n A 1 43 PHE 43 167 167 PHE PHE D . n A 1 44 SER 44 168 168 SER SER D . n A 1 45 ALA 45 169 169 ALA ALA D . n A 1 46 VAL 46 170 170 VAL VAL D . n A 1 47 LEU 47 171 171 LEU LEU D . n A 1 48 SER 48 172 172 SER SER D . n A 1 49 SER 49 173 173 SER SER D . n A 1 50 LEU 50 174 174 LEU LEU D . n A 1 51 ALA 51 175 175 ALA ALA D . n A 1 52 GLY 52 176 176 GLY GLY D . n A 1 53 TRP 53 177 177 TRP TRP D . n A 1 54 ILE 54 178 178 ILE ILE D . n A 1 55 SER 55 179 179 SER SER D . n A 1 56 PRO 56 180 180 PRO PRO D . n A 1 57 GLY 57 181 181 GLY GLY D . n A 1 58 GLY 58 182 182 GLY GLY D . n A 1 59 ASN 59 183 183 ASN ASN D . n A 1 60 ASP 60 184 184 ASP ASP D . n A 1 61 GLY 61 185 185 GLY GLY D . n A 1 62 ASN 62 186 186 ASN ASN D . n A 1 63 SER 63 187 187 SER SER D . n A 1 64 VAL 64 188 188 VAL VAL D . n A 1 65 LYS 65 189 189 LYS LYS D . n A 1 66 LEU 66 190 190 LEU LEU D . n A 1 67 GLN 67 191 191 GLN GLN D . n A 1 68 VAL 68 192 192 VAL VAL D . n A 1 69 ASN 69 193 193 ASN ASN D . n A 1 70 SER 70 194 194 SER SER D . n A 1 71 LEU 71 195 195 LEU LEU D . n A 1 72 LYS 72 196 196 LYS LYS D . n A 1 73 LYS 73 197 197 LYS LYS D . n A 1 74 ALA 74 198 198 ALA ALA D . n A 1 75 LEU 75 199 199 LEU LEU D . n A 1 76 GLU 76 200 200 GLU GLU D . n A 1 77 GLU 77 201 201 GLU GLU D . n A 1 78 LEU 78 202 202 LEU LEU D . n A 1 79 LYS 79 203 203 LYS LYS D . n A 1 80 GLU 80 204 204 GLU GLU D . n A 1 81 LYS 81 205 205 LYS LYS D . n A 1 82 TYR 82 206 206 TYR TYR D . n A 1 83 LYS 83 207 207 LYS LYS D . n A 1 84 ASP 84 208 208 ASP ASP D . n A 1 85 LYS 85 209 209 LYS LYS D . n A 1 86 PRO 86 210 210 PRO PRO D . n A 1 87 LEU 87 211 211 LEU LEU D . n A 1 88 TYR 88 212 212 TYR TYR D . n A 1 89 PRO 89 213 213 PRO PRO D . n A 1 90 ALA 90 214 214 ALA ALA D . n A 1 91 ASN 91 215 215 ASN ASN D . n A 1 92 ASN 92 216 216 ASN ASN D . n A 1 93 THR 93 217 217 THR THR D . n A 1 94 VAL 94 218 218 VAL VAL D . n A 1 95 SER 95 219 219 SER SER D . n A 1 96 GLN 96 220 220 GLN GLN D . n A 1 97 GLU 97 221 221 GLU GLU D . n A 1 98 GLN 98 222 222 GLN GLN D . n A 1 99 ALA 99 223 223 ALA ALA D . n A 1 100 ASN 100 224 224 ASN ASN D . n A 1 101 LYS 101 225 225 LYS LYS D . n A 1 102 TRP 102 226 226 TRP TRP D . n A 1 103 LEU 103 227 227 LEU LEU D . n A 1 104 THR 104 228 228 THR THR D . n A 1 105 GLU 105 229 229 GLU GLU D . n A 1 106 LEU 106 230 230 LEU LEU D . n A 1 107 GLY 107 231 231 GLY GLY D . n A 1 108 GLY 108 232 232 GLY GLY D . n A 1 109 THR 109 233 233 THR THR D . n A 1 110 ILE 110 234 234 ILE ILE D . n A 1 111 GLY 111 235 235 GLY GLY D . n A 1 112 LYS 112 236 236 LYS LYS D . n A 1 113 VAL 113 237 237 VAL VAL D . n A 1 114 SER 114 238 238 SER SER D . n A 1 115 GLN 115 239 239 GLN GLN D . n A 1 116 LYS 116 240 240 LYS LYS D . n A 1 117 ASN 117 241 241 ASN ASN D . n A 1 118 GLY 118 242 242 GLY GLY D . n A 1 119 GLY 119 243 243 GLY GLY D . n A 1 120 TYR 120 244 244 TYR TYR D . n A 1 121 VAL 121 245 245 VAL VAL D . n A 1 122 VAL 122 246 246 VAL VAL D . n A 1 123 SER 123 247 247 SER SER D . n A 1 124 ILE 124 248 248 ILE ILE D . n A 1 125 ASN 125 249 249 ASN ASN D . n A 1 126 MET 126 250 250 MET MET D . n A 1 127 THR 127 251 251 THR THR D . n A 1 128 PRO 128 252 252 PRO PRO D . n A 1 129 ILE 129 253 253 ILE ILE D . n A 1 130 ASP 130 254 254 ASP ASP D . n A 1 131 ASN 131 255 255 ASN ASN D . n A 1 132 MET 132 256 256 MET MET D . n A 1 133 LEU 133 257 257 LEU LEU D . n A 1 134 LYS 134 258 258 LYS LYS D . n A 1 135 SER 135 259 259 SER SER D . n A 1 136 LEU 136 260 260 LEU LEU D . n A 1 137 ASP 137 261 261 ASP ASP D . n A 1 138 ASN 138 262 262 ASN ASN D . n A 1 139 LEU 139 263 263 LEU LEU D . n A 1 140 GLY 140 264 264 GLY GLY D . n A 1 141 GLY 141 265 265 GLY GLY D . n A 1 142 ASN 142 266 266 ASN ASN D . n A 1 143 GLY 143 267 267 GLY GLY D . n A 1 144 GLU 144 268 268 GLU GLU D . n A 1 145 VAL 145 269 269 VAL VAL D . n A 1 146 VAL 146 270 270 VAL VAL D . n A 1 147 LEU 147 271 271 LEU LEU D . n A 1 148 ASP 148 272 272 ASP ASP D . n A 1 149 ASN 149 273 273 ASN ASN D . n A 1 150 ALA 150 274 274 ALA ALA D . n A 1 151 LYS 151 275 275 LYS LYS D . n A 1 152 TYR 152 276 276 TYR TYR D . n A 1 153 GLN 153 277 277 GLN GLN D . n A 1 154 ALA 154 278 278 ALA ALA D . n A 1 155 TRP 155 279 279 TRP TRP D . n A 1 156 ASN 156 280 280 ASN ASN D . n A 1 157 ALA 157 281 281 ALA ALA D . n A 1 158 GLY 158 282 282 GLY GLY D . n A 1 159 PHE 159 283 283 PHE PHE D . n A 1 160 SER 160 284 284 SER SER D . n A 1 161 ALA 161 285 285 ALA ALA D . n A 1 162 GLU 162 286 286 GLU GLU D . n A 1 163 ASP 163 287 287 ASP ASP D . n A 1 164 GLU 164 288 288 GLU GLU D . n A 1 165 THR 165 289 289 THR THR D . n A 1 166 MET 166 290 290 MET MET D . n A 1 167 LYS 167 291 291 LYS LYS D . n A 1 168 ASN 168 292 292 ASN ASN D . n A 1 169 ASN 169 293 293 ASN ASN D . n A 1 170 LEU 170 294 294 LEU LEU D . n A 1 171 GLN 171 295 295 GLN GLN D . n A 1 172 THR 172 296 296 THR THR D . n A 1 173 LEU 173 297 297 LEU LEU D . n A 1 174 VAL 174 298 298 VAL VAL D . n A 1 175 GLN 175 299 299 GLN GLN D . n A 1 176 LYS 176 300 300 LYS LYS D . n A 1 177 TYR 177 301 301 TYR TYR D . n A 1 178 SER 178 302 302 SER SER D . n A 1 179 ASN 179 303 303 ASN ASN D . n A 1 180 ALA 180 304 304 ALA ALA D . n A 1 181 ASN 181 305 305 ASN ASN D . n A 1 182 SER 182 306 306 SER SER D . n A 1 183 ILE 183 307 307 ILE ILE D . n A 1 184 PHE 184 308 308 PHE PHE D . n A 1 185 ASP 185 309 309 ASP ASP D . n A 1 186 ASN 186 310 310 ASN ASN D . n A 1 187 LEU 187 311 311 LEU LEU D . n A 1 188 VAL 188 312 312 VAL VAL D . n A 1 189 LYS 189 313 313 LYS LYS D . n A 1 190 VAL 190 314 314 VAL VAL D . n A 1 191 LEU 191 315 315 LEU LEU D . n A 1 192 SER 192 316 316 SER SER D . n A 1 193 SER 193 317 317 SER SER D . n A 1 194 THR 194 318 318 THR THR D . n A 1 195 ILE 195 319 319 ILE ILE D . n A 1 196 SER 196 320 320 SER SER D . n A 1 197 SER 197 321 321 SER SER D . n A 1 198 CYS 198 322 322 CYS CYS D . n A 1 199 THR 199 323 323 THR THR D . n A 1 200 ASP 200 324 324 ASP ASP D . n A 1 201 THR 201 325 325 THR THR D . n A 1 202 ASP 202 326 326 ASP ASP D . n A 1 203 LYS 203 327 327 LYS LYS D . n A 1 204 LEU 204 328 328 LEU LEU D . n A 1 205 PHE 205 329 329 PHE PHE D . n A 1 206 LEU 206 330 330 LEU LEU D . n A 1 207 HIS 207 331 331 HIS HIS D . n A 1 208 PHE 208 332 332 PHE PHE D . n # _cell.entry_id 4D3E _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D3E _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 4D3E _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 4D3E _refine.pdbx_diffrn_id 1 _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 24 _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 ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1621 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1621 _refine_hist.d_res_high 2.12 _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 4D3E _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 4D3E _struct.title ;Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4D3E _struct_keywords.pdbx_keywords 'CELL INVASION' _struct_keywords.text 'CELL INVASION, TIP COMPLEX, TYPE III SECRETION SYSTEM, SHIGELLA FLEXNERI, WILD TYPE, IPAD' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code IPAD_SHIFL _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P18013 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4D3E _struct_ref_seq.pdbx_strand_id D _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 208 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P18013 _struct_ref_seq.db_align_beg 125 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 332 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 125 _struct_ref_seq.pdbx_auth_seq_align_end 332 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 x,y,z _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_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 1 SER A 6 ? TYR A 25 ? SER D 130 TYR D 149 1 ? 20 HELX_P HELX_P2 2 TYR A 25 ? GLY A 52 ? TYR D 149 GLY D 176 1 ? 28 HELX_P HELX_P3 3 GLN A 67 ? LYS A 83 ? GLN D 191 LYS D 207 1 ? 17 HELX_P HELX_P4 4 SER A 95 ? LEU A 106 ? SER D 219 LEU D 230 1 ? 12 HELX_P HELX_P5 5 MET A 126 ? GLY A 140 ? MET D 250 GLY D 264 1 ? 15 HELX_P HELX_P6 6 ASP A 148 ? PHE A 208 ? ASP D 272 PHE D 332 1 ? 61 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLY 58 A . ? GLY 182 D ASN 59 A ? ASN 183 D 1 12.75 2 ASN 59 A . ? ASN 183 D ASP 60 A ? ASP 184 D 1 -3.74 3 GLY 61 A . ? GLY 185 D ASN 62 A ? ASN 186 D 1 3.64 4 TYR 88 A . ? TYR 212 D PRO 89 A ? PRO 213 D 1 0.76 5 ASN 142 A . ? ASN 266 D GLY 143 A ? GLY 267 D 1 -1.53 6 GLY 58 A . ? GLY 182 D ASN 59 A ? ASN 183 D 2 12.82 7 ASN 59 A . ? ASN 183 D ASP 60 A ? ASP 184 D 2 -3.70 8 GLY 61 A . ? GLY 185 D ASN 62 A ? ASN 186 D 2 3.68 9 TYR 88 A . ? TYR 212 D PRO 89 A ? PRO 213 D 2 0.72 10 ASN 142 A . ? ASN 266 D GLY 143 A ? GLY 267 D 2 -1.49 11 GLY 58 A . ? GLY 182 D ASN 59 A ? ASN 183 D 3 12.74 12 ASN 59 A . ? ASN 183 D ASP 60 A ? ASP 184 D 3 -3.70 13 GLY 61 A . ? GLY 185 D ASN 62 A ? ASN 186 D 3 3.69 14 TYR 88 A . ? TYR 212 D PRO 89 A ? PRO 213 D 3 0.69 15 ASN 142 A . ? ASN 266 D GLY 143 A ? GLY 267 D 3 -1.46 16 GLY 58 A . ? GLY 182 D ASN 59 A ? ASN 183 D 4 12.76 17 ASN 59 A . ? ASN 183 D ASP 60 A ? ASP 184 D 4 -3.79 18 GLY 61 A . ? GLY 185 D ASN 62 A ? ASN 186 D 4 3.67 19 TYR 88 A . ? TYR 212 D PRO 89 A ? PRO 213 D 4 0.66 20 ASN 142 A . ? ASN 266 D GLY 143 A ? GLY 267 D 4 -1.56 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details DA ? 3 ? DB ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense DA 1 2 ? anti-parallel DA 2 3 ? anti-parallel DB 1 2 ? anti-parallel DB 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id DA 1 ILE A 54 ? PRO A 56 ? ILE D 178 PRO D 180 DA 2 VAL A 64 ? LEU A 66 ? VAL D 188 LEU D 190 DA 3 VAL A 145 ? LEU A 147 ? VAL D 269 LEU D 271 DB 1 PRO A 86 ? TYR A 88 ? PRO D 210 TYR D 212 DB 2 TYR A 120 ? ILE A 124 ? TYR D 244 ILE D 248 DB 3 GLY A 111 ? GLN A 115 ? GLY D 235 GLN D 239 # 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 DA 1 2 N SER A 55 ? N SER D 179 O LYS A 65 ? O LYS D 189 DA 2 3 N LEU A 66 ? N LEU D 190 O VAL A 145 ? O VAL D 269 DB 1 2 N LEU A 87 ? N LEU D 211 O VAL A 122 ? O VAL D 246 DB 2 3 N SER A 123 ? N SER D 247 O LYS A 112 ? O LYS D 236 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O D PHE 329 ? ? CD1 D PHE 332 ? ? 1.33 2 1 CE D MET 128 ? ? CD2 D PHE 329 ? ? 1.34 3 1 CA D LEU 230 ? ? CE D LYS 300 ? ? 1.42 4 1 CA D THR 323 ? ? OD2 D ASP 326 ? ? 1.49 5 1 O D PHE 329 ? ? CE1 D PHE 332 ? ? 1.67 6 1 CB D LEU 230 ? ? CE D LYS 300 ? ? 1.73 7 1 CD1 D ILE 138 ? ? CD1 D ILE 319 ? ? 1.73 8 1 O D GLU 229 ? ? NZ D LYS 300 ? ? 1.79 9 1 SD D MET 128 ? ? CE2 D PHE 329 ? ? 1.86 10 1 CE D MET 128 ? ? CG D PHE 329 ? ? 1.90 11 1 CA D LEU 230 ? ? NZ D LYS 300 ? ? 1.98 12 1 O D THR 325 ? ? CD1 D PHE 329 ? ? 1.99 13 1 C D THR 323 ? ? OD2 D ASP 326 ? ? 2.03 14 1 O D CYS 322 ? ? N D ASP 326 ? ? 2.06 15 1 CG D MET 128 ? ? CE2 D PHE 329 ? ? 2.07 16 1 C D PHE 329 ? ? CD1 D PHE 332 ? ? 2.09 17 1 CE2 D TYR 149 ? ? CG2 D ILE 307 ? ? 2.09 18 1 OG D SER 141 ? ? CD2 D LEU 315 ? ? 2.11 19 1 N D THR 323 ? ? OD2 D ASP 326 ? ? 2.13 20 1 SD D MET 128 ? ? CD2 D PHE 329 ? ? 2.13 21 1 O D CYS 322 ? ? OD2 D ASP 326 ? ? 2.15 22 1 O D THR 325 ? ? CE1 D PHE 329 ? ? 2.17 23 1 O D THR 323 ? ? OD2 D ASP 326 ? ? 2.18 24 2 O D PHE 329 ? ? CD1 D PHE 332 ? ? 1.33 25 2 CE D MET 128 ? ? CD2 D PHE 329 ? ? 1.34 26 2 CA D LEU 230 ? ? CE D LYS 300 ? ? 1.41 27 2 CA D THR 323 ? ? OD2 D ASP 326 ? ? 1.49 28 2 O D PHE 329 ? ? CE1 D PHE 332 ? ? 1.67 29 2 CB D LEU 230 ? ? CE D LYS 300 ? ? 1.73 30 2 CD1 D ILE 138 ? ? CD1 D ILE 319 ? ? 1.73 31 2 O D GLU 229 ? ? NZ D LYS 300 ? ? 1.79 32 2 SD D MET 128 ? ? CE2 D PHE 329 ? ? 1.86 33 2 CE D MET 128 ? ? CG D PHE 329 ? ? 1.90 34 2 CA D LEU 230 ? ? NZ D LYS 300 ? ? 1.98 35 2 O D THR 325 ? ? CD1 D PHE 329 ? ? 1.99 36 2 C D THR 323 ? ? OD2 D ASP 326 ? ? 2.03 37 2 O D CYS 322 ? ? N D ASP 326 ? ? 2.06 38 2 CG D MET 128 ? ? CE2 D PHE 329 ? ? 2.07 39 2 C D PHE 329 ? ? CD1 D PHE 332 ? ? 2.09 40 2 CE2 D TYR 149 ? ? CG2 D ILE 307 ? ? 2.10 41 2 OG D SER 141 ? ? CD2 D LEU 315 ? ? 2.11 42 2 N D THR 323 ? ? OD2 D ASP 326 ? ? 2.12 43 2 SD D MET 128 ? ? CD2 D PHE 329 ? ? 2.13 44 2 O D CYS 322 ? ? OD2 D ASP 326 ? ? 2.15 45 2 O D THR 325 ? ? CE1 D PHE 329 ? ? 2.17 46 2 O D THR 323 ? ? OD2 D ASP 326 ? ? 2.18 47 3 O D PHE 329 ? ? CD1 D PHE 332 ? ? 1.33 48 3 CE D MET 128 ? ? CD2 D PHE 329 ? ? 1.34 49 3 CA D LEU 230 ? ? CE D LYS 300 ? ? 1.42 50 3 CA D THR 323 ? ? OD2 D ASP 326 ? ? 1.49 51 3 O D PHE 329 ? ? CE1 D PHE 332 ? ? 1.67 52 3 CB D LEU 230 ? ? CE D LYS 300 ? ? 1.73 53 3 CD1 D ILE 138 ? ? CD1 D ILE 319 ? ? 1.73 54 3 O D GLU 229 ? ? NZ D LYS 300 ? ? 1.79 55 3 SD D MET 128 ? ? CE2 D PHE 329 ? ? 1.86 56 3 CE D MET 128 ? ? CG D PHE 329 ? ? 1.90 57 3 CA D LEU 230 ? ? NZ D LYS 300 ? ? 1.98 58 3 O D THR 325 ? ? CD1 D PHE 329 ? ? 1.99 59 3 C D THR 323 ? ? OD2 D ASP 326 ? ? 2.03 60 3 O D CYS 322 ? ? N D ASP 326 ? ? 2.06 61 3 CG D MET 128 ? ? CE2 D PHE 329 ? ? 2.07 62 3 C D PHE 329 ? ? CD1 D PHE 332 ? ? 2.09 63 3 CE2 D TYR 149 ? ? CG2 D ILE 307 ? ? 2.10 64 3 OG D SER 141 ? ? CD2 D LEU 315 ? ? 2.11 65 3 N D THR 323 ? ? OD2 D ASP 326 ? ? 2.13 66 3 SD D MET 128 ? ? CD2 D PHE 329 ? ? 2.13 67 3 O D CYS 322 ? ? OD2 D ASP 326 ? ? 2.15 68 3 O D THR 325 ? ? CE1 D PHE 329 ? ? 2.17 69 3 O D THR 323 ? ? OD2 D ASP 326 ? ? 2.18 70 4 O D PHE 329 ? ? CD1 D PHE 332 ? ? 1.33 71 4 CE D MET 128 ? ? CD2 D PHE 329 ? ? 1.34 72 4 CA D LEU 230 ? ? CE D LYS 300 ? ? 1.42 73 4 CA D THR 323 ? ? OD2 D ASP 326 ? ? 1.49 74 4 O D PHE 329 ? ? CE1 D PHE 332 ? ? 1.67 75 4 CB D LEU 230 ? ? CE D LYS 300 ? ? 1.73 76 4 CD1 D ILE 138 ? ? CD1 D ILE 319 ? ? 1.73 77 4 O D GLU 229 ? ? NZ D LYS 300 ? ? 1.79 78 4 SD D MET 128 ? ? CE2 D PHE 329 ? ? 1.86 79 4 CE D MET 128 ? ? CG D PHE 329 ? ? 1.90 80 4 CA D LEU 230 ? ? NZ D LYS 300 ? ? 1.98 81 4 O D THR 325 ? ? CD1 D PHE 329 ? ? 1.99 82 4 C D THR 323 ? ? OD2 D ASP 326 ? ? 2.03 83 4 O D CYS 322 ? ? N D ASP 326 ? ? 2.06 84 4 CG D MET 128 ? ? CE2 D PHE 329 ? ? 2.07 85 4 C D PHE 329 ? ? CD1 D PHE 332 ? ? 2.09 86 4 CE2 D TYR 149 ? ? CG2 D ILE 307 ? ? 2.09 87 4 OG D SER 141 ? ? CD2 D LEU 315 ? ? 2.11 88 4 N D THR 323 ? ? OD2 D ASP 326 ? ? 2.13 89 4 SD D MET 128 ? ? CD2 D PHE 329 ? ? 2.13 90 4 O D CYS 322 ? ? OD2 D ASP 326 ? ? 2.15 91 4 O D THR 325 ? ? CE1 D PHE 329 ? ? 2.17 92 4 O D THR 323 ? ? OD2 D ASP 326 ? ? 2.18 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C D SER 321 ? ? N D CYS 322 ? ? 1.193 1.336 -0.143 0.023 Y 2 2 C D SER 321 ? ? N D CYS 322 ? ? 1.192 1.336 -0.144 0.023 Y 3 3 C D SER 321 ? ? N D CYS 322 ? ? 1.193 1.336 -0.143 0.023 Y 4 4 C D SER 321 ? ? N D CYS 322 ? ? 1.192 1.336 -0.144 0.023 Y # 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 ASP D 126 ? ? 156.44 136.69 2 1 GLN D 127 ? ? -155.65 0.64 3 1 SER D 130 ? ? -48.15 155.09 4 1 LEU D 150 ? ? -54.05 -71.05 5 1 ASN D 215 ? ? -146.98 48.66 6 1 LYS D 240 ? ? -97.85 -77.54 7 1 ASN D 241 ? ? 162.68 125.91 8 2 ASP D 126 ? ? 156.40 136.65 9 2 GLN D 127 ? ? -155.71 0.77 10 2 SER D 130 ? ? -48.08 155.12 11 2 LEU D 150 ? ? -53.99 -71.04 12 2 ASN D 215 ? ? -147.02 48.70 13 2 LYS D 240 ? ? -97.84 -77.61 14 2 ASN D 241 ? ? 162.67 125.91 15 3 ASP D 126 ? ? 156.41 136.62 16 3 GLN D 127 ? ? -155.67 0.73 17 3 SER D 130 ? ? -48.10 155.08 18 3 LEU D 150 ? ? -53.98 -71.06 19 3 ASN D 215 ? ? -147.00 48.66 20 3 LYS D 240 ? ? -97.79 -77.59 21 3 ASN D 241 ? ? 162.66 125.93 22 4 ASP D 126 ? ? 156.43 136.68 23 4 GLN D 127 ? ? -155.71 0.72 24 4 SER D 130 ? ? -48.10 155.05 25 4 LEU D 150 ? ? -54.10 -70.98 26 4 ASN D 215 ? ? -147.01 48.69 27 4 LYS D 240 ? ? -97.85 -77.57 28 4 ASN D 241 ? ? 162.64 125.96 # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C D SER 321 ? ? N D CYS 322 ? ? 1.19 2 2 C D SER 321 ? ? N D CYS 322 ? ? 1.19 3 3 C D SER 321 ? ? N D CYS 322 ? ? 1.19 4 4 C D SER 321 ? ? N D CYS 322 ? ? 1.19 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 4D3E _em_3d_fitting.ref_protocol OTHER _em_3d_fitting.ref_space REAL _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details 'METHOD--SEE PUBLICATION REFINEMENT PROTOCOL--X-RAY' _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.pdb_entry_id 2J0O _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.details ? _em_3d_fitting_list.initial_refinement_model_id 1 _em_3d_fitting_list.chain_id ? _em_3d_fitting_list.chain_residue_range ? _em_3d_fitting_list.pdb_chain_residue_range ? _em_3d_fitting_list.source_name PDB _em_3d_fitting_list.type 'experimental model' _em_3d_fitting_list.accession_code 2J0O # _em_3d_reconstruction.entry_id 4D3E _em_3d_reconstruction.id 1 _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.num_particles 2963 _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method 'MIX OF SINGLE PARTICLE AND HELICAL RECONSTRUCTION METHODS' _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size 2.12 _em_3d_reconstruction.resolution 24 _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.details ;THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT DOES NOT SUPPORT ATOMISTIC INTERPRETATIONS BECAUSE OF LACK OF RESOLUTION. ; _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.resolution_method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.refinement_type ? # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name '0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA' _em_buffer.pH 8 _em_buffer.details '0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA' # _em_entity_assembly.id 1 _em_entity_assembly.name 'WILD-TYPE T3SS NEEDLE COMPLEX' _em_entity_assembly.type COMPLEX _em_entity_assembly.parent_id 0 _em_entity_assembly.synonym ? _em_entity_assembly.details 'FIRST ZERO OF CTF SET TO 19A FOR ALL MICROGRAPHS' _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 4D3E _em_image_scans.id 1 _em_image_scans.image_recording_id 1 _em_image_scans.number_digital_images 300 _em_image_scans.citation_id ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.details ? # _em_imaging.entry_id 4D3E _em_imaging.id 1 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.specimen_id 1 _em_imaging.date 2011-08-31 _em_imaging.temperature ? _em_imaging.microscope_model 'FEI TECNAI 20' _em_imaging.nominal_defocus_min 1200 _em_imaging.nominal_defocus_max 1600 _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_cs 2 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_magnification 50000 _em_imaging.calibrated_magnification 70754 _em_imaging.electron_source LAB6 _em_imaging.accelerating_voltage 200 _em_imaging.details ? _em_imaging.specimen_holder_type . _em_imaging.specimen_holder_model . _em_imaging.citation_id ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details CARBON _em_sample_support.method ? _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? # _em_experiment.entry_id 4D3E _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' # _em_single_particle_entity.entry_id 4D3E _em_single_particle_entity.id 1 _em_single_particle_entity.point_symmetry C1 _em_single_particle_entity.image_processing_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 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 TRP N N N N 318 TRP CA C N S 319 TRP C C N N 320 TRP O O N N 321 TRP CB C N N 322 TRP CG C Y N 323 TRP CD1 C Y N 324 TRP CD2 C Y N 325 TRP NE1 N Y N 326 TRP CE2 C Y N 327 TRP CE3 C Y N 328 TRP CZ2 C Y N 329 TRP CZ3 C Y N 330 TRP CH2 C Y N 331 TRP OXT O N N 332 TRP H H N N 333 TRP H2 H N N 334 TRP HA H N N 335 TRP HB2 H N N 336 TRP HB3 H N N 337 TRP HD1 H N N 338 TRP HE1 H N N 339 TRP HE3 H N N 340 TRP HZ2 H N N 341 TRP HZ3 H N N 342 TRP HH2 H N N 343 TRP HXT H N N 344 TYR N N N N 345 TYR CA C N S 346 TYR C C N N 347 TYR O O N N 348 TYR CB C N N 349 TYR CG C Y N 350 TYR CD1 C Y N 351 TYR CD2 C Y N 352 TYR CE1 C Y N 353 TYR CE2 C Y N 354 TYR CZ C Y N 355 TYR OH O N N 356 TYR OXT O N N 357 TYR H H N N 358 TYR H2 H N N 359 TYR HA H N N 360 TYR HB2 H N N 361 TYR HB3 H N N 362 TYR HD1 H N N 363 TYR HD2 H N N 364 TYR HE1 H N N 365 TYR HE2 H N N 366 TYR HH H N N 367 TYR HXT H N N 368 VAL N N N N 369 VAL CA C N S 370 VAL C C N N 371 VAL O O N N 372 VAL CB C N N 373 VAL CG1 C N N 374 VAL CG2 C N N 375 VAL OXT O N N 376 VAL H H N N 377 VAL H2 H N N 378 VAL HA H N N 379 VAL HB H N N 380 VAL HG11 H N N 381 VAL HG12 H N N 382 VAL HG13 H N N 383 VAL HG21 H N N 384 VAL HG22 H N N 385 VAL HG23 H N N 386 VAL HXT H N N 387 # 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 TRP N CA sing N N 304 TRP N H sing N N 305 TRP N H2 sing N N 306 TRP CA C sing N N 307 TRP CA CB sing N N 308 TRP CA HA sing N N 309 TRP C O doub N N 310 TRP C OXT sing N N 311 TRP CB CG sing N N 312 TRP CB HB2 sing N N 313 TRP CB HB3 sing N N 314 TRP CG CD1 doub Y N 315 TRP CG CD2 sing Y N 316 TRP CD1 NE1 sing Y N 317 TRP CD1 HD1 sing N N 318 TRP CD2 CE2 doub Y N 319 TRP CD2 CE3 sing Y N 320 TRP NE1 CE2 sing Y N 321 TRP NE1 HE1 sing N N 322 TRP CE2 CZ2 sing Y N 323 TRP CE3 CZ3 doub Y N 324 TRP CE3 HE3 sing N N 325 TRP CZ2 CH2 doub Y N 326 TRP CZ2 HZ2 sing N N 327 TRP CZ3 CH2 sing Y N 328 TRP CZ3 HZ3 sing N N 329 TRP CH2 HH2 sing N N 330 TRP OXT HXT sing N N 331 TYR N CA sing N N 332 TYR N H sing N N 333 TYR N H2 sing N N 334 TYR CA C sing N N 335 TYR CA CB sing N N 336 TYR CA HA sing N N 337 TYR C O doub N N 338 TYR C OXT sing N N 339 TYR CB CG sing N N 340 TYR CB HB2 sing N N 341 TYR CB HB3 sing N N 342 TYR CG CD1 doub Y N 343 TYR CG CD2 sing Y N 344 TYR CD1 CE1 sing Y N 345 TYR CD1 HD1 sing N N 346 TYR CD2 CE2 doub Y N 347 TYR CD2 HD2 sing N N 348 TYR CE1 CZ doub Y N 349 TYR CE1 HE1 sing N N 350 TYR CE2 CZ sing Y N 351 TYR CE2 HE2 sing N N 352 TYR CZ OH sing N N 353 TYR OH HH sing N N 354 TYR OXT HXT sing N N 355 VAL N CA sing N N 356 VAL N H sing N N 357 VAL N H2 sing N N 358 VAL CA C sing N N 359 VAL CA CB sing N N 360 VAL CA HA sing N N 361 VAL C O doub N N 362 VAL C OXT sing N N 363 VAL CB CG1 sing N N 364 VAL CB CG2 sing N N 365 VAL CB HB sing N N 366 VAL CG1 HG11 sing N N 367 VAL CG1 HG12 sing N N 368 VAL CG1 HG13 sing N N 369 VAL CG2 HG21 sing N N 370 VAL CG2 HG22 sing N N 371 VAL CG2 HG23 sing N N 372 VAL OXT HXT sing N N 373 # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.avg_electron_dose_per_image 90 _em_image_recording.details ? _em_image_recording.id 1 _em_image_recording.film_or_detector_model 'FEI EAGLE (4k x 4k)' _em_image_recording.imaging_id 1 _em_image_recording.detector_mode ? _em_image_recording.average_exposure_time ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.name _em_software.version _em_software.category _em_software.details _em_software.image_processing_id _em_software.imaging_id _em_software.fitting_id 1 'UCSF Chimera' ? 'MODEL FITTING' ? ? ? 1 2 ? ? OTHER 'BESPOKE: Particle 2D and X-Y shift alignment' ? ? ? 3 EMAN 2 RECONSTRUCTION ? 1 ? ? 4 SPIDER ? RECONSTRUCTION ? 1 ? ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration 0.1 _em_specimen.vitrification_applied NO _em_specimen.staining_applied YES _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? # _em_staining.id 1 _em_staining.specimen_id 1 _em_staining.material 'uranyl acetate' _em_staining.type NEGATIVE # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2J0O # _atom_sites.entry_id 4D3E _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 # loop_ _atom_type.symbol C N O S # loop_