data_8I2Z # _entry.id 8I2Z # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.368 _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 8I2Z pdb_00008i2z 10.2210/pdb8i2z/pdb WWPDB D_1300033933 ? ? EMDB EMD-35143 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of the zeaxanthin-bound kin4B8' _pdbx_database_related.db_id EMD-35143 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8I2Z _pdbx_database_status.recvd_initial_deposition_date 2023-01-15 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Murakoshi, S.' 1 0000-0001-7019-9332 'Chazan, A.' 2 0000-0002-2768-5818 'Shihoya, W.' 3 0000-0003-4813-5740 'Beja, O.' 4 0000-0001-6629-0192 'Nureki, O.' 5 0000-0003-1813-7008 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 1476-4687 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 615 _citation.language ? _citation.page_first 535 _citation.page_last 540 _citation.title 'Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41586-023-05774-6 _citation.pdbx_database_id_PubMed 36859551 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chazan, A.' 1 ? primary 'Das, I.' 2 0000-0001-6481-7448 primary 'Fujiwara, T.' 3 ? primary 'Murakoshi, S.' 4 ? primary 'Rozenberg, A.' 5 0000-0001-9534-2297 primary 'Molina-Marquez, A.' 6 ? primary 'Sano, F.K.' 7 ? primary 'Tanaka, T.' 8 ? primary 'Gomez-Villegas, P.' 9 0000-0002-0511-8724 primary 'Larom, S.' 10 ? primary 'Pushkarev, A.' 11 0000-0002-5536-9193 primary 'Malakar, P.' 12 ? primary 'Hasegawa, M.' 13 ? primary 'Tsukamoto, Y.' 14 ? primary 'Ishizuka, T.' 15 0000-0002-9952-4685 primary 'Konno, M.' 16 0000-0002-0605-1816 primary 'Nagata, T.' 17 0000-0001-5379-2951 primary 'Mizuno, Y.' 18 0000-0002-4874-0679 primary 'Katayama, K.' 19 0000-0001-8498-4374 primary 'Abe-Yoshizumi, R.' 20 ? primary 'Ruhman, S.' 21 ? primary 'Inoue, K.' 22 0000-0002-6898-4347 primary 'Kandori, H.' 23 0000-0002-4922-1344 primary 'Leon, R.' 24 ? primary 'Shihoya, W.' 25 0000-0003-4813-5740 primary 'Yoshizawa, S.' 26 0000-0001-9667-6010 primary 'Sheves, M.' 27 0000-0002-5048-8169 primary 'Nureki, O.' 28 0000-0003-1813-7008 primary 'Beja, O.' 29 0000-0001-6629-0192 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8I2Z _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8I2Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man Xanthorhodopsin 28745.842 1 ? ? ? ? 2 non-polymer syn RETINAL 284.436 1 ? ? ? ? 3 non-polymer syn Zeaxanthin 568.871 1 ? ? ? ? 4 water nat water 18.015 33 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Kin4B8 # _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 ;MSATTLTLQQFSTVYNMLSFAVASMLGAFAFFVMGRKIVGPKYRLALVVSSLVVLIAGYHYWRIMGSWTAAYALKDGMYV PTGEPFNDAYRYVDWLLTVPLLLTELVLVMKLKKESGSVLAKLILAAIAMIALGYPGEISNPESQAGARLMWGVLSTVPF LYILYVLWVRLGDAIGEHPAKVQVLLKNTRYLILLTWGFYPIVYAMGSYGWLGGAGSVVAVQVGYSIADVTAKALYGVMI FAIAYAKSEADGSLPAHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MSATTLTLQQFSTVYNMLSFAVASMLGAFAFFVMGRKIVGPKYRLALVVSSLVVLIAGYHYWRIMGSWTAAYALKDGMYV PTGEPFNDAYRYVDWLLTVPLLLTELVLVMKLKKESGSVLAKLILAAIAMIALGYPGEISNPESQAGARLMWGVLSTVPF LYILYVLWVRLGDAIGEHPAKVQVLLKNTRYLILLTWGFYPIVYAMGSYGWLGGAGSVVAVQVGYSIADVTAKALYGVMI FAIAYAKSEADGSLPAHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 SER n 1 3 ALA n 1 4 THR n 1 5 THR n 1 6 LEU n 1 7 THR n 1 8 LEU n 1 9 GLN n 1 10 GLN n 1 11 PHE n 1 12 SER n 1 13 THR n 1 14 VAL n 1 15 TYR n 1 16 ASN n 1 17 MET n 1 18 LEU n 1 19 SER n 1 20 PHE n 1 21 ALA n 1 22 VAL n 1 23 ALA n 1 24 SER n 1 25 MET n 1 26 LEU n 1 27 GLY n 1 28 ALA n 1 29 PHE n 1 30 ALA n 1 31 PHE n 1 32 PHE n 1 33 VAL n 1 34 MET n 1 35 GLY n 1 36 ARG n 1 37 LYS n 1 38 ILE n 1 39 VAL n 1 40 GLY n 1 41 PRO n 1 42 LYS n 1 43 TYR n 1 44 ARG n 1 45 LEU n 1 46 ALA n 1 47 LEU n 1 48 VAL n 1 49 VAL n 1 50 SER n 1 51 SER n 1 52 LEU n 1 53 VAL n 1 54 VAL n 1 55 LEU n 1 56 ILE n 1 57 ALA n 1 58 GLY n 1 59 TYR n 1 60 HIS n 1 61 TYR n 1 62 TRP n 1 63 ARG n 1 64 ILE n 1 65 MET n 1 66 GLY n 1 67 SER n 1 68 TRP n 1 69 THR n 1 70 ALA n 1 71 ALA n 1 72 TYR n 1 73 ALA n 1 74 LEU n 1 75 LYS n 1 76 ASP n 1 77 GLY n 1 78 MET n 1 79 TYR n 1 80 VAL n 1 81 PRO n 1 82 THR n 1 83 GLY n 1 84 GLU n 1 85 PRO n 1 86 PHE n 1 87 ASN n 1 88 ASP n 1 89 ALA n 1 90 TYR n 1 91 ARG n 1 92 TYR n 1 93 VAL n 1 94 ASP n 1 95 TRP n 1 96 LEU n 1 97 LEU n 1 98 THR n 1 99 VAL n 1 100 PRO n 1 101 LEU n 1 102 LEU n 1 103 LEU n 1 104 THR n 1 105 GLU n 1 106 LEU n 1 107 VAL n 1 108 LEU n 1 109 VAL n 1 110 MET n 1 111 LYS n 1 112 LEU n 1 113 LYS n 1 114 LYS n 1 115 GLU n 1 116 SER n 1 117 GLY n 1 118 SER n 1 119 VAL n 1 120 LEU n 1 121 ALA n 1 122 LYS n 1 123 LEU n 1 124 ILE n 1 125 LEU n 1 126 ALA n 1 127 ALA n 1 128 ILE n 1 129 ALA n 1 130 MET n 1 131 ILE n 1 132 ALA n 1 133 LEU n 1 134 GLY n 1 135 TYR n 1 136 PRO n 1 137 GLY n 1 138 GLU n 1 139 ILE n 1 140 SER n 1 141 ASN n 1 142 PRO n 1 143 GLU n 1 144 SER n 1 145 GLN n 1 146 ALA n 1 147 GLY n 1 148 ALA n 1 149 ARG n 1 150 LEU n 1 151 MET n 1 152 TRP n 1 153 GLY n 1 154 VAL n 1 155 LEU n 1 156 SER n 1 157 THR n 1 158 VAL n 1 159 PRO n 1 160 PHE n 1 161 LEU n 1 162 TYR n 1 163 ILE n 1 164 LEU n 1 165 TYR n 1 166 VAL n 1 167 LEU n 1 168 TRP n 1 169 VAL n 1 170 ARG n 1 171 LEU n 1 172 GLY n 1 173 ASP n 1 174 ALA n 1 175 ILE n 1 176 GLY n 1 177 GLU n 1 178 HIS n 1 179 PRO n 1 180 ALA n 1 181 LYS n 1 182 VAL n 1 183 GLN n 1 184 VAL n 1 185 LEU n 1 186 LEU n 1 187 LYS n 1 188 ASN n 1 189 THR n 1 190 ARG n 1 191 TYR n 1 192 LEU n 1 193 ILE n 1 194 LEU n 1 195 LEU n 1 196 THR n 1 197 TRP n 1 198 GLY n 1 199 PHE n 1 200 TYR n 1 201 PRO n 1 202 ILE n 1 203 VAL n 1 204 TYR n 1 205 ALA n 1 206 MET n 1 207 GLY n 1 208 SER n 1 209 TYR n 1 210 GLY n 1 211 TRP n 1 212 LEU n 1 213 GLY n 1 214 GLY n 1 215 ALA n 1 216 GLY n 1 217 SER n 1 218 VAL n 1 219 VAL n 1 220 ALA n 1 221 VAL n 1 222 GLN n 1 223 VAL n 1 224 GLY n 1 225 TYR n 1 226 SER n 1 227 ILE n 1 228 ALA n 1 229 ASP n 1 230 VAL n 1 231 THR n 1 232 ALA n 1 233 LYS n 1 234 ALA n 1 235 LEU n 1 236 TYR n 1 237 GLY n 1 238 VAL n 1 239 MET n 1 240 ILE n 1 241 PHE n 1 242 ALA n 1 243 ILE n 1 244 ALA n 1 245 TYR n 1 246 ALA n 1 247 LYS n 1 248 SER n 1 249 GLU n 1 250 ALA n 1 251 ASP n 1 252 GLY n 1 253 SER n 1 254 LEU n 1 255 PRO n 1 256 ALA n 1 257 HIS n 1 258 HIS n 1 259 HIS n 1 260 HIS n 1 261 HIS n 1 262 HIS 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 262 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene tmp_000014 _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 'uncultured Bdellovibrionales bacterium' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 395355 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A0A977XLG0_9PROT _struct_ref.pdbx_db_accession A0A977XLG0 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSATTLTLQQFSTVYNMLSFAVASMLGAFAFFVMGRKIVGPKYRLALVVSSLVVLIAGYHYWRIMGSWTAAYALKDGMYV PTGEPFNDAYRYVDWLLTVPLLLTELVLVMKLKKESGSVLAKLILAAIAMIALGYPGEISNPESQAGARLMWGVLSTVPF LYILYVLWVRLGDAIGEHPAKVQVLLKNTRYLILLTWGFYPIVYAMGSYGWLGGAGSVVAVQVGYSIADVTAKALYGVMI FAIAYAKSEADGSLPA ; _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8I2Z _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 256 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A0A977XLG0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 256 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 256 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 8I2Z HIS A 257 ? UNP A0A977XLG0 ? ? 'expression tag' 257 1 1 8I2Z HIS A 258 ? UNP A0A977XLG0 ? ? 'expression tag' 258 2 1 8I2Z HIS A 259 ? UNP A0A977XLG0 ? ? 'expression tag' 259 3 1 8I2Z HIS A 260 ? UNP A0A977XLG0 ? ? 'expression tag' 260 4 1 8I2Z HIS A 261 ? UNP A0A977XLG0 ? ? 'expression tag' 261 5 1 8I2Z HIS A 262 ? UNP A0A977XLG0 ? ? 'expression tag' 262 6 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 K3I non-polymer . Zeaxanthin zeaxanthin 'C40 H56 O2' 568.871 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 RET non-polymer . RETINAL ? 'C20 H28 O' 284.436 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 # _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 8I2Z _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _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 86.425 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.899 _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 8I2Z _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _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 2.00 _refine.ls_d_res_low 107.90 _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 259007 _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 100.00 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.27887 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.27887 _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 'PARAMETERS FOR MASK CACLULATION' _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 ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.050 _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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 ? _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 ? _refine.overall_SU_B 3.934 _refine.overall_SU_ML 0.087 _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 ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id 1 _refine_hist.details ? _refine_hist.d_res_high . _refine_hist.d_res_low . _refine_hist.number_atoms_solvent ? _refine_hist.number_atoms_total 2050 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand ? _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.010 0.013 2071 ? r_bond_refined_d ? ? 'ELECTRON MICROSCOPY' ? 0.031 0.017 2056 ? r_bond_other_d ? ? 'ELECTRON MICROSCOPY' ? 1.332 1.634 2827 ? r_angle_refined_deg ? ? 'ELECTRON MICROSCOPY' ? 1.613 1.565 4689 ? r_angle_other_deg ? ? 'ELECTRON MICROSCOPY' ? 3.973 5.000 253 ? r_dihedral_angle_1_deg ? ? 'ELECTRON MICROSCOPY' ? 28.529 18.247 97 ? r_dihedral_angle_2_deg ? ? 'ELECTRON MICROSCOPY' ? 15.096 15.000 318 ? r_dihedral_angle_3_deg ? ? 'ELECTRON MICROSCOPY' ? 17.128 15.000 7 ? r_dihedral_angle_4_deg ? ? 'ELECTRON MICROSCOPY' ? 0.084 0.200 261 ? r_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.008 0.020 2313 ? r_gen_planes_refined ? ? 'ELECTRON MICROSCOPY' ? 0.002 0.020 484 ? r_gen_planes_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? 7.852 8.428 1015 ? r_mcbond_it ? ? 'ELECTRON MICROSCOPY' ? 7.837 8.420 1014 ? r_mcbond_other ? ? 'ELECTRON MICROSCOPY' ? 9.626 12.693 1267 ? r_mcangle_it ? ? 'ELECTRON MICROSCOPY' ? 9.630 12.701 1268 ? r_mcangle_other ? ? 'ELECTRON MICROSCOPY' ? 10.043 9.647 1056 ? r_scbond_it ? ? 'ELECTRON MICROSCOPY' ? 10.038 9.646 1057 ? r_scbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_it ? ? 'ELECTRON MICROSCOPY' ? 14.149 14.070 1561 ? r_scangle_other ? ? 'ELECTRON MICROSCOPY' ? 17.889 ? 8919 ? r_long_range_B_refined ? ? 'ELECTRON MICROSCOPY' ? 17.884 ? 8903 ? r_long_range_B_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_rigid_bond_restr ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_free ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_ls_shell.d_res_high 2.000 _refine_ls_shell.d_res_low 2.052 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 0 _refine_ls_shell.number_reflns_R_work 19094 _refine_ls_shell.percent_reflns_obs 100.00 _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 0.571 _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 20 _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 0.000 # _struct.entry_id 8I2Z _struct.title 'Cryo-EM structure of the zeaxanthin-bound kin4B8' _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 8I2Z _struct_keywords.text 'Rhodopsin, Cryo-EM, anntena, PROTON TRANSPORT' _struct_keywords.pdbx_keywords 'PROTON TRANSPORT' # 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 ? C N N 3 ? D N N 4 ? # 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 7 ? ARG A 36 ? THR A 7 ARG A 36 1 ? 30 HELX_P HELX_P2 AA2 LYS A 37 ? VAL A 39 ? LYS A 37 VAL A 39 5 ? 3 HELX_P HELX_P3 AA3 TYR A 43 ? ALA A 71 ? TYR A 43 ALA A 71 1 ? 29 HELX_P HELX_P4 AA4 ASP A 88 ? LYS A 111 ? ASP A 88 LYS A 111 1 ? 24 HELX_P HELX_P5 AA5 GLU A 115 ? ILE A 139 ? GLU A 115 ILE A 139 1 ? 25 HELX_P HELX_P6 AA6 GLN A 145 ? VAL A 169 ? GLN A 145 VAL A 169 1 ? 25 HELX_P HELX_P7 AA7 ARG A 170 ? GLY A 176 ? ARG A 170 GLY A 176 1 ? 7 HELX_P HELX_P8 AA8 PRO A 179 ? GLY A 198 ? PRO A 179 GLY A 198 1 ? 20 HELX_P HELX_P9 AA9 GLY A 198 ? TYR A 209 ? GLY A 198 TYR A 209 1 ? 12 HELX_P HELX_P10 AB1 GLY A 214 ? ASP A 251 ? GLY A 214 ASP A 251 1 ? 38 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id covale1 _struct_conn.conn_type_id covale _struct_conn.pdbx_leaving_atom_flag one _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 233 _struct_conn.ptnr1_label_atom_id NZ _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 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_label_atom_id C15 _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 233 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 301 _struct_conn.ptnr2_symmetry 1_555 _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 1.352 _struct_conn.pdbx_value_order ? _struct_conn.pdbx_role ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id AA1 _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense 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 TYR A 72 ? LYS A 75 ? TYR A 72 LYS A 75 AA1 2 MET A 78 ? PRO A 81 ? MET A 78 PRO A 81 # _pdbx_struct_sheet_hbond.sheet_id AA1 _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id LYS _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 75 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id LYS _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 75 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id MET _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 78 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id MET _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 78 # _atom_sites.entry_id 8I2Z _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 ? ? ? A . n A 1 2 SER 2 2 ? ? ? A . n A 1 3 ALA 3 3 3 ALA ALA A . n A 1 4 THR 4 4 4 THR THR A . n A 1 5 THR 5 5 5 THR THR A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 GLN 9 9 9 GLN GLN A . n A 1 10 GLN 10 10 10 GLN GLN A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 THR 13 13 13 THR THR A . n A 1 14 VAL 14 14 14 VAL VAL A . n A 1 15 TYR 15 15 15 TYR TYR A . n A 1 16 ASN 16 16 16 ASN ASN A . n A 1 17 MET 17 17 17 MET MET A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 SER 19 19 19 SER SER A . n A 1 20 PHE 20 20 20 PHE PHE A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 VAL 22 22 22 VAL VAL A . n A 1 23 ALA 23 23 23 ALA ALA A . n A 1 24 SER 24 24 24 SER SER A . n A 1 25 MET 25 25 25 MET MET A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 GLY 27 27 27 GLY GLY A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 PHE 29 29 29 PHE PHE A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 PHE 31 31 31 PHE PHE A . n A 1 32 PHE 32 32 32 PHE PHE A . n A 1 33 VAL 33 33 33 VAL VAL A . n A 1 34 MET 34 34 34 MET MET A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 ARG 36 36 36 ARG ARG A . n A 1 37 LYS 37 37 37 LYS LYS A . n A 1 38 ILE 38 38 38 ILE ILE A . n A 1 39 VAL 39 39 39 VAL VAL A . n A 1 40 GLY 40 40 40 GLY GLY A . n A 1 41 PRO 41 41 41 PRO PRO A . n A 1 42 LYS 42 42 42 LYS LYS A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 ARG 44 44 44 ARG ARG A . n A 1 45 LEU 45 45 45 LEU LEU A . n A 1 46 ALA 46 46 46 ALA ALA A . n A 1 47 LEU 47 47 47 LEU LEU A . n A 1 48 VAL 48 48 48 VAL VAL A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 SER 50 50 50 SER SER A . n A 1 51 SER 51 51 51 SER SER A . n A 1 52 LEU 52 52 52 LEU LEU A . n A 1 53 VAL 53 53 53 VAL VAL A . n A 1 54 VAL 54 54 54 VAL VAL A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 ILE 56 56 56 ILE ILE A . n A 1 57 ALA 57 57 57 ALA ALA A . n A 1 58 GLY 58 58 58 GLY GLY A . n A 1 59 TYR 59 59 59 TYR TYR A . n A 1 60 HIS 60 60 60 HIS HIS A . n A 1 61 TYR 61 61 61 TYR TYR A . n A 1 62 TRP 62 62 62 TRP TRP A . n A 1 63 ARG 63 63 63 ARG ARG A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 MET 65 65 65 MET MET A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 SER 67 67 67 SER SER A . n A 1 68 TRP 68 68 68 TRP TRP A . n A 1 69 THR 69 69 69 THR THR A . n A 1 70 ALA 70 70 70 ALA ALA A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 TYR 72 72 72 TYR TYR A . n A 1 73 ALA 73 73 73 ALA ALA A . n A 1 74 LEU 74 74 74 LEU LEU A . n A 1 75 LYS 75 75 75 LYS LYS A . n A 1 76 ASP 76 76 76 ASP ASP A . n A 1 77 GLY 77 77 77 GLY GLY A . n A 1 78 MET 78 78 78 MET MET A . n A 1 79 TYR 79 79 79 TYR TYR A . n A 1 80 VAL 80 80 80 VAL VAL A . n A 1 81 PRO 81 81 81 PRO PRO A . n A 1 82 THR 82 82 82 THR THR A . n A 1 83 GLY 83 83 83 GLY GLY A . n A 1 84 GLU 84 84 84 GLU GLU A . n A 1 85 PRO 85 85 85 PRO PRO A . n A 1 86 PHE 86 86 86 PHE PHE A . n A 1 87 ASN 87 87 87 ASN ASN A . n A 1 88 ASP 88 88 88 ASP ASP A . n A 1 89 ALA 89 89 89 ALA ALA A . n A 1 90 TYR 90 90 90 TYR TYR A . n A 1 91 ARG 91 91 91 ARG ARG A . n A 1 92 TYR 92 92 92 TYR TYR A . n A 1 93 VAL 93 93 93 VAL VAL A . n A 1 94 ASP 94 94 94 ASP ASP A . n A 1 95 TRP 95 95 95 TRP TRP A . n A 1 96 LEU 96 96 96 LEU LEU A . n A 1 97 LEU 97 97 97 LEU LEU A . n A 1 98 THR 98 98 98 THR THR A . n A 1 99 VAL 99 99 99 VAL VAL A . n A 1 100 PRO 100 100 100 PRO PRO A . n A 1 101 LEU 101 101 101 LEU LEU A . n A 1 102 LEU 102 102 102 LEU LEU A . n A 1 103 LEU 103 103 103 LEU LEU A . n A 1 104 THR 104 104 104 THR THR A . n A 1 105 GLU 105 105 105 GLU GLU A . n A 1 106 LEU 106 106 106 LEU LEU A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 LEU 108 108 108 LEU LEU A . n A 1 109 VAL 109 109 109 VAL VAL A . n A 1 110 MET 110 110 110 MET MET A . n A 1 111 LYS 111 111 111 LYS LYS A . n A 1 112 LEU 112 112 112 LEU LEU A . n A 1 113 LYS 113 113 113 LYS LYS A . n A 1 114 LYS 114 114 114 LYS LYS A . n A 1 115 GLU 115 115 115 GLU GLU A . n A 1 116 SER 116 116 116 SER SER A . n A 1 117 GLY 117 117 117 GLY GLY A . n A 1 118 SER 118 118 118 SER SER A . n A 1 119 VAL 119 119 119 VAL VAL A . n A 1 120 LEU 120 120 120 LEU LEU A . n A 1 121 ALA 121 121 121 ALA ALA A . n A 1 122 LYS 122 122 122 LYS LYS A . n A 1 123 LEU 123 123 123 LEU LEU A . n A 1 124 ILE 124 124 124 ILE ILE A . n A 1 125 LEU 125 125 125 LEU LEU A . n A 1 126 ALA 126 126 126 ALA ALA A . n A 1 127 ALA 127 127 127 ALA ALA A . n A 1 128 ILE 128 128 128 ILE ILE A . n A 1 129 ALA 129 129 129 ALA ALA A . n A 1 130 MET 130 130 130 MET MET A . n A 1 131 ILE 131 131 131 ILE ILE A . n A 1 132 ALA 132 132 132 ALA ALA A . n A 1 133 LEU 133 133 133 LEU LEU A . n A 1 134 GLY 134 134 134 GLY GLY A . n A 1 135 TYR 135 135 135 TYR TYR A . n A 1 136 PRO 136 136 136 PRO PRO A . n A 1 137 GLY 137 137 137 GLY GLY A . n A 1 138 GLU 138 138 138 GLU GLU A . n A 1 139 ILE 139 139 139 ILE ILE A . n A 1 140 SER 140 140 140 SER SER A . n A 1 141 ASN 141 141 141 ASN ASN A . n A 1 142 PRO 142 142 142 PRO PRO A . n A 1 143 GLU 143 143 143 GLU GLU A . n A 1 144 SER 144 144 144 SER SER A . n A 1 145 GLN 145 145 145 GLN GLN A . n A 1 146 ALA 146 146 146 ALA ALA A . n A 1 147 GLY 147 147 147 GLY GLY A . n A 1 148 ALA 148 148 148 ALA ALA A . n A 1 149 ARG 149 149 149 ARG ARG A . n A 1 150 LEU 150 150 150 LEU LEU A . n A 1 151 MET 151 151 151 MET MET A . n A 1 152 TRP 152 152 152 TRP TRP A . n A 1 153 GLY 153 153 153 GLY GLY A . n A 1 154 VAL 154 154 154 VAL VAL A . n A 1 155 LEU 155 155 155 LEU LEU A . n A 1 156 SER 156 156 156 SER SER A . n A 1 157 THR 157 157 157 THR THR A . n A 1 158 VAL 158 158 158 VAL VAL A . n A 1 159 PRO 159 159 159 PRO PRO A . n A 1 160 PHE 160 160 160 PHE PHE A . n A 1 161 LEU 161 161 161 LEU LEU A . n A 1 162 TYR 162 162 162 TYR TYR A . n A 1 163 ILE 163 163 163 ILE ILE A . n A 1 164 LEU 164 164 164 LEU LEU A . n A 1 165 TYR 165 165 165 TYR TYR A . n A 1 166 VAL 166 166 166 VAL VAL A . n A 1 167 LEU 167 167 167 LEU LEU A . n A 1 168 TRP 168 168 168 TRP TRP A . n A 1 169 VAL 169 169 169 VAL VAL A . n A 1 170 ARG 170 170 170 ARG ARG A . n A 1 171 LEU 171 171 171 LEU LEU A . n A 1 172 GLY 172 172 172 GLY GLY A . n A 1 173 ASP 173 173 173 ASP ASP A . n A 1 174 ALA 174 174 174 ALA ALA A . n A 1 175 ILE 175 175 175 ILE ILE A . n A 1 176 GLY 176 176 176 GLY GLY A . n A 1 177 GLU 177 177 177 GLU GLU A . n A 1 178 HIS 178 178 178 HIS HIS A . n A 1 179 PRO 179 179 179 PRO PRO A . n A 1 180 ALA 180 180 180 ALA ALA A . n A 1 181 LYS 181 181 181 LYS LYS A . n A 1 182 VAL 182 182 182 VAL VAL A . n A 1 183 GLN 183 183 183 GLN GLN A . n A 1 184 VAL 184 184 184 VAL VAL A . n A 1 185 LEU 185 185 185 LEU LEU A . n A 1 186 LEU 186 186 186 LEU LEU A . n A 1 187 LYS 187 187 187 LYS LYS A . n A 1 188 ASN 188 188 188 ASN ASN A . n A 1 189 THR 189 189 189 THR THR A . n A 1 190 ARG 190 190 190 ARG ARG A . n A 1 191 TYR 191 191 191 TYR TYR A . n A 1 192 LEU 192 192 192 LEU LEU A . n A 1 193 ILE 193 193 193 ILE ILE A . n A 1 194 LEU 194 194 194 LEU LEU A . n A 1 195 LEU 195 195 195 LEU LEU A . n A 1 196 THR 196 196 196 THR THR A . n A 1 197 TRP 197 197 197 TRP TRP A . n A 1 198 GLY 198 198 198 GLY GLY A . n A 1 199 PHE 199 199 199 PHE PHE A . n A 1 200 TYR 200 200 200 TYR TYR A . n A 1 201 PRO 201 201 201 PRO PRO A . n A 1 202 ILE 202 202 202 ILE ILE A . n A 1 203 VAL 203 203 203 VAL VAL A . n A 1 204 TYR 204 204 204 TYR TYR A . n A 1 205 ALA 205 205 205 ALA ALA A . n A 1 206 MET 206 206 206 MET MET A . n A 1 207 GLY 207 207 207 GLY GLY A . n A 1 208 SER 208 208 208 SER SER A . n A 1 209 TYR 209 209 209 TYR TYR A . n A 1 210 GLY 210 210 210 GLY GLY A . n A 1 211 TRP 211 211 211 TRP TRP A . n A 1 212 LEU 212 212 212 LEU LEU A . n A 1 213 GLY 213 213 213 GLY GLY A . n A 1 214 GLY 214 214 214 GLY GLY A . n A 1 215 ALA 215 215 215 ALA ALA A . n A 1 216 GLY 216 216 216 GLY GLY A . n A 1 217 SER 217 217 217 SER SER A . n A 1 218 VAL 218 218 218 VAL VAL A . n A 1 219 VAL 219 219 219 VAL VAL A . n A 1 220 ALA 220 220 220 ALA ALA A . n A 1 221 VAL 221 221 221 VAL VAL A . n A 1 222 GLN 222 222 222 GLN GLN A . n A 1 223 VAL 223 223 223 VAL VAL A . n A 1 224 GLY 224 224 224 GLY GLY A . n A 1 225 TYR 225 225 225 TYR TYR A . n A 1 226 SER 226 226 226 SER SER A . n A 1 227 ILE 227 227 227 ILE ILE A . n A 1 228 ALA 228 228 228 ALA ALA A . n A 1 229 ASP 229 229 229 ASP ASP A . n A 1 230 VAL 230 230 230 VAL VAL A . n A 1 231 THR 231 231 231 THR THR A . n A 1 232 ALA 232 232 232 ALA ALA A . n A 1 233 LYS 233 233 233 LYS LYS A . n A 1 234 ALA 234 234 234 ALA ALA A . n A 1 235 LEU 235 235 235 LEU LEU A . n A 1 236 TYR 236 236 236 TYR TYR A . n A 1 237 GLY 237 237 237 GLY GLY A . n A 1 238 VAL 238 238 238 VAL VAL A . n A 1 239 MET 239 239 239 MET MET A . n A 1 240 ILE 240 240 240 ILE ILE A . n A 1 241 PHE 241 241 241 PHE PHE A . n A 1 242 ALA 242 242 242 ALA ALA A . n A 1 243 ILE 243 243 243 ILE ILE A . n A 1 244 ALA 244 244 244 ALA ALA A . n A 1 245 TYR 245 245 245 TYR TYR A . n A 1 246 ALA 246 246 246 ALA ALA A . n A 1 247 LYS 247 247 247 LYS LYS A . n A 1 248 SER 248 248 248 SER SER A . n A 1 249 GLU 249 249 249 GLU GLU A . n A 1 250 ALA 250 250 250 ALA ALA A . n A 1 251 ASP 251 251 251 ASP ASP A . n A 1 252 GLY 252 252 252 GLY GLY A . n A 1 253 SER 253 253 253 SER SER A . n A 1 254 LEU 254 254 254 LEU LEU A . n A 1 255 PRO 255 255 255 PRO PRO A . n A 1 256 ALA 256 256 256 ALA ALA A . n A 1 257 HIS 257 257 ? ? ? A . n A 1 258 HIS 258 258 ? ? ? A . n A 1 259 HIS 259 259 ? ? ? A . n A 1 260 HIS 260 260 ? ? ? A . n A 1 261 HIS 261 261 ? ? ? A . n A 1 262 HIS 262 262 ? ? ? A . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 3 nureki@bs.s.u-tokyo.ac.jp Osamu Nureki ? 'principal investigator/group leader' 0000-0003-1813-7008 4 wtrshh9@gmail.com Wataru Shihoya ? 'principal investigator/group leader' 0000-0003-4813-5740 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 RET 1 301 301 RET RET A . C 3 K3I 1 302 401 K3I ZEA A . D 4 HOH 1 401 9 HOH HOH A . D 4 HOH 2 402 28 HOH HOH A . D 4 HOH 3 403 6 HOH HOH A . D 4 HOH 4 404 27 HOH HOH A . D 4 HOH 5 405 16 HOH HOH A . D 4 HOH 6 406 30 HOH HOH A . D 4 HOH 7 407 14 HOH HOH A . D 4 HOH 8 408 17 HOH HOH A . D 4 HOH 9 409 32 HOH HOH A . D 4 HOH 10 410 33 HOH HOH A . D 4 HOH 11 411 21 HOH HOH A . D 4 HOH 12 412 10 HOH HOH A . D 4 HOH 13 413 39 HOH HOH A . D 4 HOH 14 414 36 HOH HOH A . D 4 HOH 15 415 20 HOH HOH A . D 4 HOH 16 416 35 HOH HOH A . D 4 HOH 17 417 18 HOH HOH A . D 4 HOH 18 418 8 HOH HOH A . D 4 HOH 19 419 37 HOH HOH A . D 4 HOH 20 420 13 HOH HOH A . D 4 HOH 21 421 29 HOH HOH A . D 4 HOH 22 422 2 HOH HOH A . D 4 HOH 23 423 4 HOH HOH A . D 4 HOH 24 424 19 HOH HOH A . D 4 HOH 25 425 40 HOH HOH A . D 4 HOH 26 426 3 HOH HOH A . D 4 HOH 27 427 26 HOH HOH A . D 4 HOH 28 428 25 HOH HOH A . D 4 HOH 29 429 31 HOH HOH A . D 4 HOH 30 430 38 HOH HOH A . D 4 HOH 31 431 5 HOH HOH A . D 4 HOH 32 432 22 HOH HOH A . D 4 HOH 33 433 41 HOH HOH A . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'complete point assembly' ? pentameric 5 2 'point asymmetric unit' ? monomeric 1 3 'point asymmetric unit, std point frame' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-5)' A,B,C,D 2 1 A,B,C,D 3 P A,B,C,D # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? -0.51023496 -0.86003505 0.00000000 204.71833 0.86003505 -0.51023496 0.00000000 -52.26013 0.00000000 0.00000000 1.00000000 -147.78840 1 'identity operation' 1_555 x,y,z 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 2 'point symmetry operation' ? ? 0.30901699 -0.95105652 0.00000000 245.32069 0.95105652 0.30901699 0.00000000 -38.85498 0.00000000 0.00000000 1.00000000 0.00000 3 'point symmetry operation' ? ? -0.80901699 -0.58778525 0.00000000 358.08224 0.58778525 -0.80901699 0.00000000 182.45202 0.00000000 0.00000000 1.00000000 0.00000 4 'point symmetry operation' ? ? -0.80901699 0.58778525 0.00000000 182.45201 -0.58778525 -0.80901699 0.00000000 358.08224 0.00000000 0.00000000 1.00000000 0.00000 5 'point symmetry operation' ? ? 0.30901699 0.95105652 0.00000000 -38.85498 -0.95105652 0.30901699 0.00000000 245.32069 0.00000000 0.00000000 1.00000000 0.00000 # _pdbx_point_symmetry.entry_id 8I2Z _pdbx_point_symmetry.Schoenflies_symbol C _pdbx_point_symmetry.circular_symmetry 5 # 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 2023-03-29 2 'Structure model' 1 1 2023-04-19 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Structure summary' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category audit_author # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_audit_author.name' # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name REFMAC _software.os ? _software.os_version ? _software.type ? _software.version 5.8.0267 _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 8I2Z _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8I2Z _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 8I2Z _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 2.3 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 4337540 _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 POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details '150 mM NaCl, 20 mM Tris-HCl' _em_buffer.pH 8.0 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT' _em_entity_assembly.name Kin4B8 _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 8I2Z _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 ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 600 _em_imaging.nominal_defocus_max 1600 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _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 ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _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 300 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.details ? _em_sample_support.specimen_id 1 _em_sample_support.citation_id ? # _em_vitrification.entry_id 8I2Z _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 277 _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details 'Vitrification carried out in ethane atmosphere.' # _em_experiment.entry_id 8I2Z _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MET 1 ? A MET 1 2 1 Y 1 A SER 2 ? A SER 2 3 1 Y 1 A HIS 257 ? A HIS 257 4 1 Y 1 A HIS 258 ? A HIS 258 5 1 Y 1 A HIS 259 ? A HIS 259 6 1 Y 1 A HIS 260 ? A HIS 260 7 1 Y 1 A HIS 261 ? A HIS 261 8 1 Y 1 A HIS 262 ? A HIS 262 # loop_ _em_buffer_component.buffer_id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.id _em_buffer_component.name 1 150 mM NaCl 1 'sodium chloride' 1 20 mM C4H11NO3 2 'tris hydroxymethyl aminomethane' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 395355 _em_entity_assembly_naturalsource.organism 'uncultured Bdellovibrionales bacterium' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 562 _em_entity_assembly_recombinant.organism 'Escherichia coli' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 50.140 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _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 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? RELION 3.1 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? cryoSPARC 2.0 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? cryoSPARC 2.0 CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? 'VOLUME SELECTION' ? 14 1 1 1 ? ? 'SERIES ALIGNMENT' ? 15 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 16 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 17 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 18 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 19 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _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 # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 RET ? ? RET ? ? 'SUBJECT OF INVESTIGATION' ? 2 K3I ? ? K3I ? ? 'SUBJECT OF INVESTIGATION' ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 RETINAL RET 3 Zeaxanthin K3I 4 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details ? #