data_9DKZ # _entry.id 9DKZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.398 _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 9DKZ pdb_00009dkz 10.2210/pdb9dkz/pdb WWPDB D_1000288291 ? ? # 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 2024-09-25 2 'Structure model' 1 1 2024-10-16 3 'Structure model' 1 2 2024-11-13 # _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' 'Structure summary' 2 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' pdbx_entry_details 2 2 'Structure model' pdbx_modification_feature 3 3 'Structure model' citation 4 3 'Structure model' citation_author # 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' '_citation.country' 2 3 'Structure model' '_citation.journal_abbrev' 3 3 'Structure model' '_citation.journal_id_CSD' 4 3 'Structure model' '_citation.journal_id_ISSN' 5 3 'Structure model' '_citation.pdbx_database_id_DOI' 6 3 'Structure model' '_citation.pdbx_database_id_PubMed' 7 3 'Structure model' '_citation.title' 8 3 'Structure model' '_citation.year' 9 3 'Structure model' '_citation_author.identifier_ORCID' 10 3 'Structure model' '_citation_author.name' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9DKZ _pdbx_database_status.recvd_initial_deposition_date 2024-09-10 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 3 _pdbx_contact_author.email erwright2@wisc.edu _pdbx_contact_author.name_first Elizabeth _pdbx_contact_author.name_last Wright _pdbx_contact_author.name_mi R _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-0712-9475 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Yang, J.E.' 1 0000-0002-2438-8156 'Bingman, C.A.' 2 0000-0002-3073-5089 'Mitchell, J.' 3 0000-0003-0092-8522 'Mosher, D.' 4 0000-0002-1233-1005 'Wright, E.R.' 5 0000-0003-0712-9475 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biorxiv _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2692-8205 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'In situ crystalline structure of the human eosinophil major basic protein-1.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1101/2024.10.09.617336 _citation.pdbx_database_id_PubMed 39416224 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yang, J.E.' 1 ? primary 'Mitchell, J.M.' 2 ? primary 'Bingman, C.A.' 3 ? primary 'Mosher, D.F.' 4 ? primary 'Wright, E.R.' 5 0000-0003-0712-9475 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Bone marrow proteoglycan' 13694.769 1 ? ? ? ;The major basic protein-1 structure was directly determined from intragranular nanocrystals inside unperturbed human eosinophil cells obtained from donors. ; 2 water nat water 18.015 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'BMPG,Proteoglycan 2' # _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 ;CRYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWA AHQPWSRGGHCVALCTRGGHWRRAHCLRRLPFICSY ; _entity_poly.pdbx_seq_one_letter_code_can ;CRYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWA AHQPWSRGGHCVALCTRGGHWRRAHCLRRLPFICSY ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CYS n 1 2 ARG n 1 3 TYR n 1 4 LEU n 1 5 LEU n 1 6 VAL n 1 7 ARG n 1 8 SER n 1 9 LEU n 1 10 GLN n 1 11 THR n 1 12 PHE n 1 13 SER n 1 14 GLN n 1 15 ALA n 1 16 TRP n 1 17 PHE n 1 18 THR n 1 19 CYS n 1 20 ARG n 1 21 ARG n 1 22 CYS n 1 23 TYR n 1 24 ARG n 1 25 GLY n 1 26 ASN n 1 27 LEU n 1 28 VAL n 1 29 SER n 1 30 ILE n 1 31 HIS n 1 32 ASN n 1 33 PHE n 1 34 ASN n 1 35 ILE n 1 36 ASN n 1 37 TYR n 1 38 ARG n 1 39 ILE n 1 40 GLN n 1 41 CYS n 1 42 SER n 1 43 VAL n 1 44 SER n 1 45 ALA n 1 46 LEU n 1 47 ASN n 1 48 GLN n 1 49 GLY n 1 50 GLN n 1 51 VAL n 1 52 TRP n 1 53 ILE n 1 54 GLY n 1 55 GLY n 1 56 ARG n 1 57 ILE n 1 58 THR n 1 59 GLY n 1 60 SER n 1 61 GLY n 1 62 ARG n 1 63 CYS n 1 64 ARG n 1 65 ARG n 1 66 PHE n 1 67 GLN n 1 68 TRP n 1 69 VAL n 1 70 ASP n 1 71 GLY n 1 72 SER n 1 73 ARG n 1 74 TRP n 1 75 ASN n 1 76 PHE n 1 77 ALA n 1 78 TYR n 1 79 TRP n 1 80 ALA n 1 81 ALA n 1 82 HIS n 1 83 GLN n 1 84 PRO n 1 85 TRP n 1 86 SER n 1 87 ARG n 1 88 GLY n 1 89 GLY n 1 90 HIS n 1 91 CYS n 1 92 VAL n 1 93 ALA n 1 94 LEU n 1 95 CYS n 1 96 THR n 1 97 ARG n 1 98 GLY n 1 99 GLY n 1 100 HIS n 1 101 TRP n 1 102 ARG n 1 103 ARG n 1 104 ALA n 1 105 HIS n 1 106 CYS n 1 107 LEU n 1 108 ARG n 1 109 ARG n 1 110 LEU n 1 111 PRO n 1 112 PHE n 1 113 ILE n 1 114 CYS n 1 115 SER n 1 116 TYR 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 116 _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'PRG2, MBP' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue blood _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 eosinophil _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 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 CYS 1 107 107 CYS CYS A . n A 1 2 ARG 2 108 108 ARG ARG A . n A 1 3 TYR 3 109 109 TYR TYR A . n A 1 4 LEU 4 110 110 LEU LEU A . n A 1 5 LEU 5 111 111 LEU LEU A . n A 1 6 VAL 6 112 112 VAL VAL A . n A 1 7 ARG 7 113 113 ARG ARG A . n A 1 8 SER 8 114 114 SER SER A . n A 1 9 LEU 9 115 115 LEU LEU A . n A 1 10 GLN 10 116 116 GLN GLN A . n A 1 11 THR 11 117 117 THR THR A . n A 1 12 PHE 12 118 118 PHE PHE A . n A 1 13 SER 13 119 119 SER SER A . n A 1 14 GLN 14 120 120 GLN GLN A . n A 1 15 ALA 15 121 121 ALA ALA A . n A 1 16 TRP 16 122 122 TRP TRP A . n A 1 17 PHE 17 123 123 PHE PHE A . n A 1 18 THR 18 124 124 THR THR A . n A 1 19 CYS 19 125 125 CYS CYS A . n A 1 20 ARG 20 126 126 ARG ARG A . n A 1 21 ARG 21 127 127 ARG ARG A . n A 1 22 CYS 22 128 128 CYS CYS A . n A 1 23 TYR 23 129 129 TYR TYR A . n A 1 24 ARG 24 130 130 ARG ARG A . n A 1 25 GLY 25 131 131 GLY GLY A . n A 1 26 ASN 26 132 132 ASN ASN A . n A 1 27 LEU 27 133 133 LEU LEU A . n A 1 28 VAL 28 134 134 VAL VAL A . n A 1 29 SER 29 135 135 SER SER A . n A 1 30 ILE 30 136 136 ILE ILE A . n A 1 31 HIS 31 137 137 HIS HIS A . n A 1 32 ASN 32 138 138 ASN ASN A . n A 1 33 PHE 33 139 139 PHE PHE A . n A 1 34 ASN 34 140 140 ASN ASN A . n A 1 35 ILE 35 141 141 ILE ILE A . n A 1 36 ASN 36 142 142 ASN ASN A . n A 1 37 TYR 37 143 143 TYR TYR A . n A 1 38 ARG 38 144 144 ARG ARG A . n A 1 39 ILE 39 145 145 ILE ILE A . n A 1 40 GLN 40 146 146 GLN GLN A . n A 1 41 CYS 41 147 147 CYS CYS A . n A 1 42 SER 42 148 148 SER SER A . n A 1 43 VAL 43 149 149 VAL VAL A . n A 1 44 SER 44 150 150 SER SER A . n A 1 45 ALA 45 151 151 ALA ALA A . n A 1 46 LEU 46 152 152 LEU LEU A . n A 1 47 ASN 47 153 153 ASN ASN A . n A 1 48 GLN 48 154 154 GLN GLN A . n A 1 49 GLY 49 155 155 GLY GLY A . n A 1 50 GLN 50 156 156 GLN GLN A . n A 1 51 VAL 51 157 157 VAL VAL A . n A 1 52 TRP 52 158 158 TRP TRP A . n A 1 53 ILE 53 159 159 ILE ILE A . n A 1 54 GLY 54 160 160 GLY GLY A . n A 1 55 GLY 55 161 161 GLY GLY A . n A 1 56 ARG 56 162 162 ARG ARG A . n A 1 57 ILE 57 163 163 ILE ILE A . n A 1 58 THR 58 164 164 THR THR A . n A 1 59 GLY 59 165 165 GLY GLY A . n A 1 60 SER 60 166 166 SER SER A . n A 1 61 GLY 61 167 167 GLY GLY A . n A 1 62 ARG 62 168 168 ARG ARG A . n A 1 63 CYS 63 169 169 CYS CYS A . n A 1 64 ARG 64 170 170 ARG ARG A . n A 1 65 ARG 65 171 171 ARG ARG A . n A 1 66 PHE 66 172 172 PHE PHE A . n A 1 67 GLN 67 173 173 GLN GLN A . n A 1 68 TRP 68 174 174 TRP TRP A . n A 1 69 VAL 69 175 175 VAL VAL A . n A 1 70 ASP 70 176 176 ASP ASP A . n A 1 71 GLY 71 177 177 GLY GLY A . n A 1 72 SER 72 178 178 SER SER A . n A 1 73 ARG 73 179 179 ARG ARG A . n A 1 74 TRP 74 180 180 TRP TRP A . n A 1 75 ASN 75 181 181 ASN ASN A . n A 1 76 PHE 76 182 182 PHE PHE A . n A 1 77 ALA 77 183 183 ALA ALA A . n A 1 78 TYR 78 184 184 TYR TYR A . n A 1 79 TRP 79 185 185 TRP TRP A . n A 1 80 ALA 80 186 186 ALA ALA A . n A 1 81 ALA 81 187 187 ALA ALA A . n A 1 82 HIS 82 188 188 HIS HIS A . n A 1 83 GLN 83 189 189 GLN GLN A . n A 1 84 PRO 84 190 190 PRO PRO A . n A 1 85 TRP 85 191 191 TRP TRP A . n A 1 86 SER 86 192 192 SER SER A . n A 1 87 ARG 87 193 193 ARG ARG A . n A 1 88 GLY 88 194 194 GLY GLY A . n A 1 89 GLY 89 195 195 GLY GLY A . n A 1 90 HIS 90 196 196 HIS HIS A . n A 1 91 CYS 91 197 197 CYS CYS A . n A 1 92 VAL 92 198 198 VAL VAL A . n A 1 93 ALA 93 199 199 ALA ALA A . n A 1 94 LEU 94 200 200 LEU LEU A . n A 1 95 CYS 95 201 201 CYS CYS A . n A 1 96 THR 96 202 202 THR THR A . n A 1 97 ARG 97 203 203 ARG ARG A . n A 1 98 GLY 98 204 204 GLY GLY A . n A 1 99 GLY 99 205 205 GLY GLY A . n A 1 100 HIS 100 206 206 HIS HIS A . n A 1 101 TRP 101 207 207 TRP TRP A . n A 1 102 ARG 102 208 208 ARG ARG A . n A 1 103 ARG 103 209 209 ARG ARG A . n A 1 104 ALA 104 210 210 ALA ALA A . n A 1 105 HIS 105 211 211 HIS HIS A . n A 1 106 CYS 106 212 212 CYS CYS A . n A 1 107 LEU 107 213 213 LEU LEU A . n A 1 108 ARG 108 214 214 ARG ARG A . n A 1 109 ARG 109 215 215 ARG ARG A . n A 1 110 LEU 110 216 216 LEU LEU A . n A 1 111 PRO 111 217 217 PRO PRO A . n A 1 112 PHE 112 218 218 PHE PHE A . n A 1 113 ILE 113 219 219 ILE ILE A . n A 1 114 CYS 114 220 220 CYS CYS A . n A 1 115 SER 115 221 221 SER SER A . n A 1 116 TYR 116 222 222 TYR TYR A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id HOH _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id HOH _pdbx_nonpoly_scheme.auth_mon_id HOH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.dependencies _software.description _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.pdbx_ordinal _software.type _software.version ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? 1 ? 1.21.1_5286 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? 2 ? 2.8.3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? 3 ? 'Jun 30, 2023 BUILT=20230630' ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? 4 ? 'Jun 30, 2023 BUILT=20230630' # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 9DKZ _cell.details ? _cell.formula_units_Z ? _cell.length_a 31.240 _cell.length_a_esd ? _cell.length_b 57.870 _cell.length_b_esd ? _cell.length_c 59.060 _cell.length_c_esd ? _cell.volume 106772.141 _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9DKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab (z,x,y)' _symmetry.space_group_name_H-M 'P 2 21 21' _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 9DKZ _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON CRYSTALLOGRAPHY' _exptl.method_details ? # _reflns.B_iso_Wilson_estimate 85.01 _reflns.entry_id 9DKZ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.2 _reflns.d_resolution_low ? _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 1912 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 96.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 3.20 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.719 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 24817 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.931 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.69 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 3.20 3.29 ? ? ? 2031 ? ? 150 98.0 ? ? ? ? ? ? ? ? ? ? ? ? ? 0.81 4.29 ? ? 1 1 0.559 ? ? ? ? 4.13 ? ? ? ? ? ? ? ? ? 3.29 3.38 ? ? ? 1819 ? ? 130 95.6 ? ? ? ? ? ? ? ? ? ? ? ? ? 0.91 3.663 ? ? 2 1 0.364 ? ? ? ? 3.531 ? ? ? ? ? ? ? ? ? 3.38 3.49 ? ? ? 1843 ? ? 141 95.3 ? ? ? ? ? ? ? ? ? ? ? ? ? 1.53 2.303 ? ? 3 1 0.618 ? ? ? ? 2.217 ? ? ? ? ? ? ? ? ? 3.49 3.6 ? ? ? 1841 ? ? 130 100.0 ? ? ? ? ? ? ? ? ? ? ? ? ? 1.90 1.742 ? ? 4 1 0.699 ? ? ? ? 1.681 ? ? ? ? ? ? ? ? ? 3.60 3.73 ? ? ? 1736 ? ? 127 96.2 ? ? ? ? ? ? ? ? ? ? ? ? ? 1.78 1.594 ? ? 5 1 0.804 ? ? ? ? 1.537 ? ? ? ? ? ? ? ? ? 3.73 3.87 ? ? ? 1712 ? ? 127 94.8 ? ? ? ? ? ? ? ? ? ? ? ? ? 2.71 1.076 ? ? 6 1 0.918 ? ? ? ? 1.037 ? ? ? ? ? ? ? ? ? 3.87 4.03 ? ? ? 1584 ? ? 116 95.9 ? ? ? ? ? ? ? ? ? ? ? ? ? 3.16 0.906 ? ? 7 1 0.861 ? ? ? ? 0.873 ? ? ? ? ? ? ? ? ? 4.03 4.21 ? ? ? 1540 ? ? 117 99.2 ? ? ? ? ? ? ? ? ? ? ? ? ? 3.57 0.674 ? ? 8 1 0.954 ? ? ? ? 0.65 ? ? ? ? ? ? ? ? ? 4.21 4.41 ? ? ? 1485 ? ? 113 94.2 ? ? ? ? ? ? ? ? ? ? ? ? ? 3.70 0.704 ? ? 9 1 0.953 ? ? ? ? 0.678 ? ? ? ? ? ? ? ? ? 4.41 4.65 ? ? ? 1410 ? ? 106 97.2 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.81 0.56 ? ? 10 1 0.929 ? ? ? ? 0.538 ? ? ? ? ? ? ? ? ? 4.65 4.93 ? ? ? 1255 ? ? 98 98.0 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.94 0.502 ? ? 11 1 0.918 ? ? ? ? 0.484 ? ? ? ? ? ? ? ? ? 4.93 5.27 ? ? ? 1200 ? ? 93 92.1 ? ? ? ? ? ? ? ? ? ? ? ? ? 5.07 0.518 ? ? 12 1 0.972 ? ? ? ? 0.498 ? ? ? ? ? ? ? ? ? 5.27 5.69 ? ? ? 1167 ? ? 91 100.0 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.25 0.58 ? ? 13 1 0.931 ? ? ? ? 0.557 ? ? ? ? ? ? ? ? ? 5.69 6.24 ? ? ? 1064 ? ? 86 93.5 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.60 0.566 ? ? 14 1 0.976 ? ? ? ? 0.544 ? ? ? ? ? ? ? ? ? 6.24 6.97 ? ? ? 948 ? ? 74 98.7 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.26 0.626 ? ? 15 1 0.92 ? ? ? ? 0.602 ? ? ? ? ? ? ? ? ? 6.97 8.05 ? ? ? 834 ? ? 69 92.0 ? ? ? ? ? ? ? ? ? ? ? ? ? 5.14 0.497 ? ? 16 1 0.913 ? ? ? ? 0.477 ? ? ? ? ? ? ? ? ? 8.05 9.86 ? ? ? 676 ? ? 65 98.5 ? ? ? ? ? ? ? ? ? ? ? ? ? 5.08 0.439 ? ? 17 1 0.985 ? ? ? ? 0.419 ? ? ? ? ? ? ? ? ? 9.86 13.95 ? ? ? 465 ? ? 49 96.1 ? ? ? ? ? ? ? ? ? ? ? ? ? 5.61 0.478 ? ? 18 1 0.834 ? ? ? ? 0.454 ? ? ? ? ? ? ? ? ? 13.95 ? ? ? ? 207 ? ? 30 81.1 ? ? ? ? ? ? ? ? ? ? ? ? ? 4.14 0.353 ? ? 19 1 0.969 ? ? ? ? 0.326 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 91.79 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9DKZ _refine.pdbx_refine_id 'ELECTRON CRYSTALLOGRAPHY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 3.20 _refine.ls_d_res_low 28.93 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 1882 _refine.ls_number_reflns_R_free 199 _refine.ls_number_reflns_R_work 1683 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 95.58 _refine.ls_percent_reflns_R_free 10.57 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2727 _refine.ls_R_factor_R_free 0.3110 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2679 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details 'Random selection' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 26.1710 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.2682 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # 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 CRYSTALLOGRAPHY' ? 0.0055 ? 995 ? f_bond_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 1.0433 ? 1346 ? f_angle_d ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.0573 ? 129 ? f_chiral_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 0.0070 ? 172 ? f_plane_restr ? ? 'ELECTRON CRYSTALLOGRAPHY' ? 12.6272 ? 349 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'ELECTRON CRYSTALLOGRAPHY' 3.20 3.45 . . 37 . 94.6 10 . . 40.99 0.3817 . . . . . . . . . . . 0.4783 'ELECTRON CRYSTALLOGRAPHY' 3.45 3.79 . . 43 . 96.5 10 . . 28.59 0.2724 . . . . . . . . . . . 0.3539 'ELECTRON CRYSTALLOGRAPHY' 3.79 4.34 . . 37 . 95.4 10 . . 22.77 0.2653 . . . . . . . . . . . 0.2882 'ELECTRON CRYSTALLOGRAPHY' 4.34 5.46 . . 39 . 96.2 10 . . 19.19 0.2315 . . . . . . . . . . . 0.3039 'ELECTRON CRYSTALLOGRAPHY' 5.47 28.93 . . 43 . 95.3 9 . . 20.99 0.2650 . . . . . . . . . . . 0.2709 # _struct.entry_id 9DKZ _struct.title 'In situ microED structure of the Eosinophil major basic protein-1' _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 9DKZ _struct_keywords.text 'Effector, Nanocrystal, In-situ, Intracellular, IMMUNE SYSTEM' _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PRG2_HUMAN _struct_ref.pdbx_db_accession P13727 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;CRYLLVRSLQTFSQAWFTCRRCYRGNLVSIHNFNINYRIQCSVSALNQGQVWIGGRITGSGRCRRFQWVDGSRWNFAYWA AHQPWSRGGHCVALCTRGGHWRRAHCLRRLPFICSY ; _struct_ref.pdbx_align_begin 107 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9DKZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 116 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P13727 _struct_ref_seq.db_align_beg 107 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 222 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 107 _struct_ref_seq.pdbx_auth_seq_align_end 222 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,B # _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 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 AA1 THR A 11 ? ARG A 24 ? THR A 117 ARG A 130 1 ? 14 HELX_P HELX_P2 AA2 ASN A 32 ? SER A 44 ? ASN A 138 SER A 150 1 ? 13 HELX_P HELX_P3 AA3 SER A 60 ? ARG A 64 ? SER A 166 ARG A 170 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 19 SG ? ? ? 1_555 A CYS 114 SG ? ? A CYS 125 A CYS 220 1_555 ? ? ? ? ? ? ? 2.036 ? ? disulf2 disulf ? ? A CYS 91 SG ? ? ? 1_555 A CYS 106 SG ? ? A CYS 197 A CYS 212 1_555 ? ? ? ? ? ? ? 2.031 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 CYS A 19 ? CYS A 114 ? CYS A 125 ? 1_555 CYS A 220 ? 1_555 SG SG . . . None 'Disulfide bridge' 2 CYS A 91 ? CYS A 106 ? CYS A 197 ? 1_555 CYS A 212 ? 1_555 SG SG . . . None 'Disulfide bridge' # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLN _struct_mon_prot_cis.label_seq_id 83 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLN _struct_mon_prot_cis.auth_seq_id 189 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 84 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 190 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -10.10 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 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 AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 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 ARG A 2 ? GLN A 10 ? ARG A 108 GLN A 116 AA1 2 LEU A 110 ? TYR A 116 ? LEU A 216 TYR A 222 AA1 3 ASN A 26 ? LEU A 27 ? ASN A 132 LEU A 133 AA2 1 ARG A 65 ? TRP A 68 ? ARG A 171 TRP A 174 AA2 2 GLN A 50 ? THR A 58 ? GLN A 156 THR A 164 AA2 3 CYS A 91 ? CYS A 95 ? CYS A 197 CYS A 201 AA2 4 TRP A 101 ? ALA A 104 ? TRP A 207 ALA A 210 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N LEU A 4 ? N LEU A 110 O CYS A 114 ? O CYS A 220 AA1 2 3 O SER A 115 ? O SER A 221 N ASN A 26 ? N ASN A 132 AA2 1 2 O GLN A 67 ? O GLN A 173 N ARG A 56 ? N ARG A 162 AA2 2 3 N VAL A 51 ? N VAL A 157 O LEU A 94 ? O LEU A 200 AA2 3 4 N ALA A 93 ? N ALA A 199 O ARG A 102 ? O ARG A 208 # _pdbx_entry_details.entry_id 9DKZ _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification Y # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OH _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 TYR _pdbx_validate_symm_contact.auth_seq_id_1 184 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OH _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 TYR _pdbx_validate_symm_contact.auth_seq_id_2 184 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_555 _pdbx_validate_symm_contact.dist 1.80 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id PRO _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 190 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -84.36 _pdbx_validate_torsion.psi -127.89 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x,-y,-z 3 -x,y+1/2,-z+1/2 4 -x,-y+1/2,z+1/2 # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9DKZ _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details 'Alternating rounds of phenix.refine and map filling in Coot' _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space RECIPROCAL _em_3d_fitting.ref_protocol OTHER # loop_ _em_3d_fitting_list.id _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.pdb_entry_id _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.pdb_chain_residue_range _em_3d_fitting_list.details _em_3d_fitting_list.chain_id _em_3d_fitting_list.chain_residue_range _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id 1 1 1h8u A 106-222 ? A 106-222 PDB 'experimental model' 1h8u 1 2 1 . . . ? A 106-222 AlphaFold 'in silico model' AF-P13727-F1-model_v4 2 # _em_3d_reconstruction.entry_id 9DKZ _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 3.2 _em_3d_reconstruction.resolution_method 'DIFFRACTION PATTERN/LAYERLINES' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles ? _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type '3D CRYSTAL' # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details 'secretory granule matrix' _em_buffer.pH 7 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source NATURAL _em_entity_assembly.type CELL _em_entity_assembly.name 'In situ microED structure of the Eosinophil major basic protein-1' _em_entity_assembly.details ;Mature human eosinophil cells were collected and purified from human donor blood. This was followed by eosinophil cell deposition on EM grids, grid plunge-freezing, and cryo-FIB milling of individual eosinophil cells. Cryo-FIB milling of the cells exposed unperturbed cytosolic secretory granules, inside which nanocrystals of the major basic protein-1 were located. Micro-ED data was collected on these crystals for in-situ structure determination. ; _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9DKZ _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode DIFFRACTION _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_min 0 _em_imaging.nominal_defocus_max 0 _em_imaging.calibrated_defocus_min 0 _em_imaging.calibrated_defocus_max 0 _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum 85 _em_imaging.recording_temperature_maximum 100 _em_imaging.alignment_procedure 'COMA FREE' _em_imaging.c2_aperture_diameter 50 _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN # _em_sample_support.id 1 _em_sample_support.film_material ? _em_sample_support.method ? _em_sample_support.grid_material GOLD _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type Quantifoil _em_sample_support.details '10 mA' _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 9DKZ _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 95 _em_vitrification.temp ? _em_vitrification.chamber_temperature 310.15 _em_vitrification.instrument 'LEICA EM GP' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details 'Blot time of 6~8 sec, single-side back blotting' # _em_experiment.entry_id 9DKZ _em_experiment.id 1 _em_experiment.reconstruction_method CRYSTALLOGRAPHY _em_experiment.aggregation_state CELL _em_experiment.entity_assembly_id 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 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 GLY N N N N 108 GLY CA C N N 109 GLY C C N N 110 GLY O O N N 111 GLY OXT O N N 112 GLY H H N N 113 GLY H2 H N N 114 GLY HA2 H N N 115 GLY HA3 H N N 116 GLY HXT H N N 117 HIS N N N N 118 HIS CA C N S 119 HIS C C N N 120 HIS O O N N 121 HIS CB C N N 122 HIS CG C Y N 123 HIS ND1 N Y N 124 HIS CD2 C Y N 125 HIS CE1 C Y N 126 HIS NE2 N Y N 127 HIS OXT O N N 128 HIS H H N N 129 HIS H2 H N N 130 HIS HA H N N 131 HIS HB2 H N N 132 HIS HB3 H N N 133 HIS HD1 H N N 134 HIS HD2 H N N 135 HIS HE1 H N N 136 HIS HE2 H N N 137 HIS HXT H N N 138 HOH O O N N 139 HOH H1 H N N 140 HOH H2 H N N 141 ILE N N N N 142 ILE CA C N S 143 ILE C C N N 144 ILE O O N N 145 ILE CB C N S 146 ILE CG1 C N N 147 ILE CG2 C N N 148 ILE CD1 C N N 149 ILE OXT O N N 150 ILE H H N N 151 ILE H2 H N N 152 ILE HA H N N 153 ILE HB H N N 154 ILE HG12 H N N 155 ILE HG13 H N N 156 ILE HG21 H N N 157 ILE HG22 H N N 158 ILE HG23 H N N 159 ILE HD11 H N N 160 ILE HD12 H N N 161 ILE HD13 H N N 162 ILE HXT H N N 163 LEU N N N N 164 LEU CA C N S 165 LEU C C N N 166 LEU O O N N 167 LEU CB C N N 168 LEU CG C N N 169 LEU CD1 C N N 170 LEU CD2 C N N 171 LEU OXT O N N 172 LEU H H N N 173 LEU H2 H N N 174 LEU HA H N N 175 LEU HB2 H N N 176 LEU HB3 H N N 177 LEU HG H N N 178 LEU HD11 H N N 179 LEU HD12 H N N 180 LEU HD13 H N N 181 LEU HD21 H N N 182 LEU HD22 H N N 183 LEU HD23 H N N 184 LEU HXT H N N 185 PHE N N N N 186 PHE CA C N S 187 PHE C C N N 188 PHE O O N N 189 PHE CB C N N 190 PHE CG C Y N 191 PHE CD1 C Y N 192 PHE CD2 C Y N 193 PHE CE1 C Y N 194 PHE CE2 C Y N 195 PHE CZ C Y N 196 PHE OXT O N N 197 PHE H H N N 198 PHE H2 H N N 199 PHE HA H N N 200 PHE HB2 H N N 201 PHE HB3 H N N 202 PHE HD1 H N N 203 PHE HD2 H N N 204 PHE HE1 H N N 205 PHE HE2 H N N 206 PHE HZ H N N 207 PHE HXT H N N 208 PRO N N N N 209 PRO CA C N S 210 PRO C C N N 211 PRO O O N N 212 PRO CB C N N 213 PRO CG C N N 214 PRO CD C N N 215 PRO OXT O N N 216 PRO H H N N 217 PRO HA H N N 218 PRO HB2 H N N 219 PRO HB3 H N N 220 PRO HG2 H N N 221 PRO HG3 H N N 222 PRO HD2 H N N 223 PRO HD3 H N N 224 PRO HXT H N N 225 SER N N N N 226 SER CA C N S 227 SER C C N N 228 SER O O N N 229 SER CB C N N 230 SER OG O N N 231 SER OXT O N N 232 SER H H N N 233 SER H2 H N N 234 SER HA H N N 235 SER HB2 H N N 236 SER HB3 H N N 237 SER HG H N N 238 SER HXT H N N 239 THR N N N N 240 THR CA C N S 241 THR C C N N 242 THR O O N N 243 THR CB C N R 244 THR OG1 O N N 245 THR CG2 C N N 246 THR OXT O N N 247 THR H H N N 248 THR H2 H N N 249 THR HA H N N 250 THR HB H N N 251 THR HG1 H N N 252 THR HG21 H N N 253 THR HG22 H N N 254 THR HG23 H N N 255 THR HXT H N N 256 TRP N N N N 257 TRP CA C N S 258 TRP C C N N 259 TRP O O N N 260 TRP CB C N N 261 TRP CG C Y N 262 TRP CD1 C Y N 263 TRP CD2 C Y N 264 TRP NE1 N Y N 265 TRP CE2 C Y N 266 TRP CE3 C Y N 267 TRP CZ2 C Y N 268 TRP CZ3 C Y N 269 TRP CH2 C Y N 270 TRP OXT O N N 271 TRP H H N N 272 TRP H2 H N N 273 TRP HA H N N 274 TRP HB2 H N N 275 TRP HB3 H N N 276 TRP HD1 H N N 277 TRP HE1 H N N 278 TRP HE3 H N N 279 TRP HZ2 H N N 280 TRP HZ3 H N N 281 TRP HH2 H N N 282 TRP HXT H N N 283 TYR N N N N 284 TYR CA C N S 285 TYR C C N N 286 TYR O O N N 287 TYR CB C N N 288 TYR CG C Y N 289 TYR CD1 C Y N 290 TYR CD2 C Y N 291 TYR CE1 C Y N 292 TYR CE2 C Y N 293 TYR CZ C Y N 294 TYR OH O N N 295 TYR OXT O N N 296 TYR H H N N 297 TYR H2 H N N 298 TYR HA H N N 299 TYR HB2 H N N 300 TYR HB3 H N N 301 TYR HD1 H N N 302 TYR HD2 H N N 303 TYR HE1 H N N 304 TYR HE2 H N N 305 TYR HH H N N 306 TYR HXT H N N 307 VAL N N N N 308 VAL CA C N S 309 VAL C C N N 310 VAL O O N N 311 VAL CB C N N 312 VAL CG1 C N N 313 VAL CG2 C N N 314 VAL OXT O N N 315 VAL H H N N 316 VAL H2 H N N 317 VAL HA H N N 318 VAL HB H N N 319 VAL HG11 H N N 320 VAL HG12 H N N 321 VAL HG13 H N N 322 VAL HG21 H N N 323 VAL HG22 H N N 324 VAL HG23 H N N 325 VAL HXT H N N 326 # 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 GLY N CA sing N N 102 GLY N H sing N N 103 GLY N H2 sing N N 104 GLY CA C sing N N 105 GLY CA HA2 sing N N 106 GLY CA HA3 sing N N 107 GLY C O doub N N 108 GLY C OXT sing N N 109 GLY OXT HXT sing N N 110 HIS N CA sing N N 111 HIS N H sing N N 112 HIS N H2 sing N N 113 HIS CA C sing N N 114 HIS CA CB sing N N 115 HIS CA HA sing N N 116 HIS C O doub N N 117 HIS C OXT sing N N 118 HIS CB CG sing N N 119 HIS CB HB2 sing N N 120 HIS CB HB3 sing N N 121 HIS CG ND1 sing Y N 122 HIS CG CD2 doub Y N 123 HIS ND1 CE1 doub Y N 124 HIS ND1 HD1 sing N N 125 HIS CD2 NE2 sing Y N 126 HIS CD2 HD2 sing N N 127 HIS CE1 NE2 sing Y N 128 HIS CE1 HE1 sing N N 129 HIS NE2 HE2 sing N N 130 HIS OXT HXT sing N N 131 HOH O H1 sing N N 132 HOH O H2 sing N N 133 ILE N CA sing N N 134 ILE N H sing N N 135 ILE N H2 sing N N 136 ILE CA C sing N N 137 ILE CA CB sing N N 138 ILE CA HA sing N N 139 ILE C O doub N N 140 ILE C OXT sing N N 141 ILE CB CG1 sing N N 142 ILE CB CG2 sing N N 143 ILE CB HB sing N N 144 ILE CG1 CD1 sing N N 145 ILE CG1 HG12 sing N N 146 ILE CG1 HG13 sing N N 147 ILE CG2 HG21 sing N N 148 ILE CG2 HG22 sing N N 149 ILE CG2 HG23 sing N N 150 ILE CD1 HD11 sing N N 151 ILE CD1 HD12 sing N N 152 ILE CD1 HD13 sing N N 153 ILE OXT HXT sing N N 154 LEU N CA sing N N 155 LEU N H sing N N 156 LEU N H2 sing N N 157 LEU CA C sing N N 158 LEU CA CB sing N N 159 LEU CA HA sing N N 160 LEU C O doub N N 161 LEU C OXT sing N N 162 LEU CB CG sing N N 163 LEU CB HB2 sing N N 164 LEU CB HB3 sing N N 165 LEU CG CD1 sing N N 166 LEU CG CD2 sing N N 167 LEU CG HG sing N N 168 LEU CD1 HD11 sing N N 169 LEU CD1 HD12 sing N N 170 LEU CD1 HD13 sing N N 171 LEU CD2 HD21 sing N N 172 LEU CD2 HD22 sing N N 173 LEU CD2 HD23 sing N N 174 LEU OXT HXT sing N N 175 PHE N CA sing N N 176 PHE N H sing N N 177 PHE N H2 sing N N 178 PHE CA C sing N N 179 PHE CA CB sing N N 180 PHE CA HA sing N N 181 PHE C O doub N N 182 PHE C OXT sing N N 183 PHE CB CG sing N N 184 PHE CB HB2 sing N N 185 PHE CB HB3 sing N N 186 PHE CG CD1 doub Y N 187 PHE CG CD2 sing Y N 188 PHE CD1 CE1 sing Y N 189 PHE CD1 HD1 sing N N 190 PHE CD2 CE2 doub Y N 191 PHE CD2 HD2 sing N N 192 PHE CE1 CZ doub Y N 193 PHE CE1 HE1 sing N N 194 PHE CE2 CZ sing Y N 195 PHE CE2 HE2 sing N N 196 PHE CZ HZ sing N N 197 PHE OXT HXT sing N N 198 PRO N CA sing N N 199 PRO N CD sing N N 200 PRO N H sing N N 201 PRO CA C sing N N 202 PRO CA CB sing N N 203 PRO CA HA sing N N 204 PRO C O doub N N 205 PRO C OXT sing N N 206 PRO CB CG sing N N 207 PRO CB HB2 sing N N 208 PRO CB HB3 sing N N 209 PRO CG CD sing N N 210 PRO CG HG2 sing N N 211 PRO CG HG3 sing N N 212 PRO CD HD2 sing N N 213 PRO CD HD3 sing N N 214 PRO OXT HXT sing N N 215 SER N CA sing N N 216 SER N H sing N N 217 SER N H2 sing N N 218 SER CA C sing N N 219 SER CA CB sing N N 220 SER CA HA sing N N 221 SER C O doub N N 222 SER C OXT sing N N 223 SER CB OG sing N N 224 SER CB HB2 sing N N 225 SER CB HB3 sing N N 226 SER OG HG sing N N 227 SER OXT HXT sing N N 228 THR N CA sing N N 229 THR N H sing N N 230 THR N H2 sing N N 231 THR CA C sing N N 232 THR CA CB sing N N 233 THR CA HA sing N N 234 THR C O doub N N 235 THR C OXT sing N N 236 THR CB OG1 sing N N 237 THR CB CG2 sing N N 238 THR CB HB sing N N 239 THR OG1 HG1 sing N N 240 THR CG2 HG21 sing N N 241 THR CG2 HG22 sing N N 242 THR CG2 HG23 sing N N 243 THR OXT HXT sing N N 244 TRP N CA sing N N 245 TRP N H sing N N 246 TRP N H2 sing N N 247 TRP CA C sing N N 248 TRP CA CB sing N N 249 TRP CA HA sing N N 250 TRP C O doub N N 251 TRP C OXT sing N N 252 TRP CB CG sing N N 253 TRP CB HB2 sing N N 254 TRP CB HB3 sing N N 255 TRP CG CD1 doub Y N 256 TRP CG CD2 sing Y N 257 TRP CD1 NE1 sing Y N 258 TRP CD1 HD1 sing N N 259 TRP CD2 CE2 doub Y N 260 TRP CD2 CE3 sing Y N 261 TRP NE1 CE2 sing Y N 262 TRP NE1 HE1 sing N N 263 TRP CE2 CZ2 sing Y N 264 TRP CE3 CZ3 doub Y N 265 TRP CE3 HE3 sing N N 266 TRP CZ2 CH2 doub Y N 267 TRP CZ2 HZ2 sing N N 268 TRP CZ3 CH2 sing Y N 269 TRP CZ3 HZ3 sing N N 270 TRP CH2 HH2 sing N N 271 TRP OXT HXT sing N N 272 TYR N CA sing N N 273 TYR N H sing N N 274 TYR N H2 sing N N 275 TYR CA C sing N N 276 TYR CA CB sing N N 277 TYR CA HA sing N N 278 TYR C O doub N N 279 TYR C OXT sing N N 280 TYR CB CG sing N N 281 TYR CB HB2 sing N N 282 TYR CB HB3 sing N N 283 TYR CG CD1 doub Y N 284 TYR CG CD2 sing Y N 285 TYR CD1 CE1 sing Y N 286 TYR CD1 HD1 sing N N 287 TYR CD2 CE2 doub Y N 288 TYR CD2 HD2 sing N N 289 TYR CE1 CZ doub Y N 290 TYR CE1 HE1 sing N N 291 TYR CE2 CZ sing Y N 292 TYR CE2 HE2 sing N N 293 TYR CZ OH sing N N 294 TYR OH HH sing N N 295 TYR OXT HXT sing N N 296 VAL N CA sing N N 297 VAL N H sing N N 298 VAL N H2 sing N N 299 VAL CA C sing N N 300 VAL CA CB sing N N 301 VAL CA HA sing N N 302 VAL C O doub N N 303 VAL C OXT sing N N 304 VAL CB CG1 sing N N 305 VAL CB CG2 sing N N 306 VAL CB HB sing N N 307 VAL CG1 HG11 sing N N 308 VAL CG1 HG12 sing N N 309 VAL CG1 HG13 sing N N 310 VAL CG2 HG21 sing N N 311 VAL CG2 HG22 sing N N 312 VAL CG2 HG23 sing N N 313 VAL OXT HXT sing N N 314 # _em_3d_crystal_entity.angle_alpha 90 _em_3d_crystal_entity.angle_beta 90 _em_3d_crystal_entity.angle_gamma 90 _em_3d_crystal_entity.image_processing_id 1 _em_3d_crystal_entity.id 1 _em_3d_crystal_entity.length_a 31.24 _em_3d_crystal_entity.length_b 57.87 _em_3d_crystal_entity.length_c 59.06 _em_3d_crystal_entity.space_group_name 'P2 21 21' _em_3d_crystal_entity.space_group_num 18 # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type NONE # _em_diffraction_shell.em_diffraction_stats_id 1 _em_diffraction_shell.fourier_space_coverage 95.6 _em_diffraction_shell.high_resolution 3.2 _em_diffraction_shell.id 1 _em_diffraction_shell.low_resolution 28.93 _em_diffraction_shell.multiplicity 7.5 _em_diffraction_shell.num_structure_factors 1912 _em_diffraction_shell.phase_residual 26.33 # _em_diffraction_stats.details ? _em_diffraction_stats.fourier_space_coverage 95.6 _em_diffraction_stats.high_resolution 3.2 _em_diffraction_stats.id 1 _em_diffraction_stats.image_processing_id 1 _em_diffraction_stats.num_intensities_measured 24722 _em_diffraction_stats.num_structure_factors 3303 _em_diffraction_stats.overall_phase_error 26.33 _em_diffraction_stats.overall_phase_residual ? _em_diffraction_stats.phase_error_rejection_criteria 0 _em_diffraction_stats.r_merge 67.29 _em_diffraction_stats.r_sym ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location cytoplasm _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 9606 _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.organelle 'mature eosinophil secretory granule' _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue blood _em_entity_assembly_naturalsource.details ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time 1 _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 0.15 _em_image_recording.details ;The final dataset was merged from six crystals, each with 40 images. Tilt was -20 to +20 degrees, 1 degree per frame, 1 second per frame ; _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'FEI CETA (4k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images 40 _em_image_recording.num_grids_imaged 3 _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'IMAGE ACQUISITION' ? 1 ? ? 1 EPU 1.13 MASKING ? 2 ? ? ? ? ? 'CTF CORRECTION' ? 3 1 ? ? ? ? 'LAYERLINE INDEXING' ? 4 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 5 ? ? ? ? ? 'MODEL FITTING' ? 6 ? 1 ? Coot 0.9.8.92 OTHER ? 7 ? ? ? ? ? 'MOLECULAR REPLACEMENT' ? 8 1 ? ? PHENIX 1.21.1-5286 'LATTICE DISTORTION CORRECTION' ? 9 1 ? ? ? ? 'SYMMETRY DETERMINATION' ? 10 1 ? ? ? ? 'CRYSTALLOGRAPHY MERGING' ? 11 1 ? ? ? ? RECONSTRUCTION ? 12 1 ? ? PHENIX 1.21.1-5286 'MODEL REFINEMENT' ? 13 ? 1 ? PHENIX 1.21.1_5286 # _em_specimen.concentration 1000000 _em_specimen.details ;Human eosinophil cells were collected from human donor blood. The cells were rested in 1640 RPMI medium supplemented with 0.1% human serum albumin, before direct deposition onto gold EM grids and plunge freezing. Subsequently, cryo-FIB milling was used to expose unperturbed intragranular major basic protien-1 nanocrystals present within the cytosolic secretory granules. ; _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'R01 GM114561' 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'U24 GM139168' 2 'National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)' 'United States' 'P01 HL088594' 3 'Department of Energy (DOE, United States)' 'United States' DE-SC0023013 4 'Department of Energy (DOE, United States)' 'United States' DE-SC0018409 5 # loop_ _pdbx_initial_refinement_model.id _pdbx_initial_refinement_model.type _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.accession_code _pdbx_initial_refinement_model.entity_id_list _pdbx_initial_refinement_model.details 1 'experimental model' PDB 1h8u ? ? 2 'in silico model' AlphaFold AF-P13727-F1-model_v4 ? ? # _space_group.name_H-M_alt 'P 2 21 21' _space_group.name_Hall 'P 2 2ab (z,x,y)' _space_group.IT_number 18 _space_group.crystal_system orthorhombic _space_group.id 1 # _atom_sites.entry_id 9DKZ _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.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.032010 _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] 0.017280 _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] 0.016932 _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 _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.pdbx_scat_Cromer_Mann_a5 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.pdbx_scat_Cromer_Mann_b5 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 0.08930 0.25630 0.75700 1.04870 0.35750 0.24650 1.71000 6.40940 18.61130 50.25230 0.0 ;5-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.03490 0.12010 0.19700 0.05730 0.11950 0.53470 3.58670 12.34710 18.95250 38.62690 0.0 ;5-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 0.10220 0.32190 0.79820 0.81970 0.17150 0.24510 1.74810 6.19250 17.38940 48.14310 0.0 ;5-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 0.09740 0.29210 0.69100 0.69900 0.20390 0.20670 1.38150 4.69430 12.71050 32.47260 0.0 ;5-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? S ? ? 0.24970 0.56280 1.38990 2.18650 0.77150 0.26810 1.67110 7.02670 19.53770 50.38880 0.0 ;5-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ #