data_3JD6 # _entry.id 3JD6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.296 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code RCSB RCSB160552 PDB 3JD6 WWPDB D_1000160552 # _pdbx_database_related.db_name EMDB _pdbx_database_related.db_id EMD-6425 _pdbx_database_related.content_type 'associated EM volume' _pdbx_database_related.details 'Mature retinoschisin with a C-terminal hexahistidine tag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3JD6 _pdbx_database_status.recvd_initial_deposition_date 2016-04-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Tolun, G.' 1 'Vijayasarathy, C.' 2 'Huang, R.' 3 'Zeng, Y.' 4 'Li, Y.' 5 'Steven, A.C.' 6 'Sieving, P.A.' 7 'Heymann, J.B.' 8 # _citation.id primary _citation.title 'Paired octamer rings of retinoschisin suggest a junctional model for cell-cell adhesion in the retina.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 113 _citation.page_first 5287 _citation.page_last 5292 _citation.year 2016 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27114531 _citation.pdbx_database_id_DOI 10.1073/pnas.1519048113 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Tolun, G.' 1 primary 'Vijayasarathy, C.' 2 primary 'Huang, R.' 3 primary 'Zeng, Y.' 4 primary 'Li, Y.' 5 primary 'Steven, A.C.' 6 primary 'Sieving, P.A.' 7 primary 'Heymann, J.B.' 8 # _cell.entry_id 3JD6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3JD6 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description Retinoschisin _entity.formula_weight 23889.830 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'UNP residues 24-224' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'RS1, X-linked juvenile retinoschisis protein' # _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 ;STEDEGEDPWYQKACKCDCQGGPNALWSAGATSLDCIPECPYHKPLGFESGEVTPDQITCSNPEQYVGWYSSWTANKARL NSQGFGCAWLSKFQDSSQWLQIDLKEIKVISGILTQGRCDIDEWMTKYSVQYRTDERLNWIYYKDQTGNNRVFYGNSDRT STVQNLLRPPIISRFIRLIPLGWHVRIAIRMELLECVSKCAHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;STEDEGEDPWYQKACKCDCQGGPNALWSAGATSLDCIPECPYHKPLGFESGEVTPDQITCSNPEQYVGWYSSWTANKARL NSQGFGCAWLSKFQDSSQWLQIDLKEIKVISGILTQGRCDIDEWMTKYSVQYRTDERLNWIYYKDQTGNNRVFYGNSDRT STVQNLLRPPIISRFIRLIPLGWHVRIAIRMELLECVSKCAHHHHHH ; _entity_poly.pdbx_strand_id O _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 SER n 1 2 THR n 1 3 GLU n 1 4 ASP n 1 5 GLU n 1 6 GLY n 1 7 GLU n 1 8 ASP n 1 9 PRO n 1 10 TRP n 1 11 TYR n 1 12 GLN n 1 13 LYS n 1 14 ALA n 1 15 CYS n 1 16 LYS n 1 17 CYS n 1 18 ASP n 1 19 CYS n 1 20 GLN n 1 21 GLY n 1 22 GLY n 1 23 PRO n 1 24 ASN n 1 25 ALA n 1 26 LEU n 1 27 TRP n 1 28 SER n 1 29 ALA n 1 30 GLY n 1 31 ALA n 1 32 THR n 1 33 SER n 1 34 LEU n 1 35 ASP n 1 36 CYS n 1 37 ILE n 1 38 PRO n 1 39 GLU n 1 40 CYS n 1 41 PRO n 1 42 TYR n 1 43 HIS n 1 44 LYS n 1 45 PRO n 1 46 LEU n 1 47 GLY n 1 48 PHE n 1 49 GLU n 1 50 SER n 1 51 GLY n 1 52 GLU n 1 53 VAL n 1 54 THR n 1 55 PRO n 1 56 ASP n 1 57 GLN n 1 58 ILE n 1 59 THR n 1 60 CYS n 1 61 SER n 1 62 ASN n 1 63 PRO n 1 64 GLU n 1 65 GLN n 1 66 TYR n 1 67 VAL n 1 68 GLY n 1 69 TRP n 1 70 TYR n 1 71 SER n 1 72 SER n 1 73 TRP n 1 74 THR n 1 75 ALA n 1 76 ASN n 1 77 LYS n 1 78 ALA n 1 79 ARG n 1 80 LEU n 1 81 ASN n 1 82 SER n 1 83 GLN n 1 84 GLY n 1 85 PHE n 1 86 GLY n 1 87 CYS n 1 88 ALA n 1 89 TRP n 1 90 LEU n 1 91 SER n 1 92 LYS n 1 93 PHE n 1 94 GLN n 1 95 ASP n 1 96 SER n 1 97 SER n 1 98 GLN n 1 99 TRP n 1 100 LEU n 1 101 GLN n 1 102 ILE n 1 103 ASP n 1 104 LEU n 1 105 LYS n 1 106 GLU n 1 107 ILE n 1 108 LYS n 1 109 VAL n 1 110 ILE n 1 111 SER n 1 112 GLY n 1 113 ILE n 1 114 LEU n 1 115 THR n 1 116 GLN n 1 117 GLY n 1 118 ARG n 1 119 CYS n 1 120 ASP n 1 121 ILE n 1 122 ASP n 1 123 GLU n 1 124 TRP n 1 125 MET n 1 126 THR n 1 127 LYS n 1 128 TYR n 1 129 SER n 1 130 VAL n 1 131 GLN n 1 132 TYR n 1 133 ARG n 1 134 THR n 1 135 ASP n 1 136 GLU n 1 137 ARG n 1 138 LEU n 1 139 ASN n 1 140 TRP n 1 141 ILE n 1 142 TYR n 1 143 TYR n 1 144 LYS n 1 145 ASP n 1 146 GLN n 1 147 THR n 1 148 GLY n 1 149 ASN n 1 150 ASN n 1 151 ARG n 1 152 VAL n 1 153 PHE n 1 154 TYR n 1 155 GLY n 1 156 ASN n 1 157 SER n 1 158 ASP n 1 159 ARG n 1 160 THR n 1 161 SER n 1 162 THR n 1 163 VAL n 1 164 GLN n 1 165 ASN n 1 166 LEU n 1 167 LEU n 1 168 ARG n 1 169 PRO n 1 170 PRO n 1 171 ILE n 1 172 ILE n 1 173 SER n 1 174 ARG n 1 175 PHE n 1 176 ILE n 1 177 ARG n 1 178 LEU n 1 179 ILE n 1 180 PRO n 1 181 LEU n 1 182 GLY n 1 183 TRP n 1 184 HIS n 1 185 VAL n 1 186 ARG n 1 187 ILE n 1 188 ALA n 1 189 ILE n 1 190 ARG n 1 191 MET n 1 192 GLU n 1 193 LEU n 1 194 LEU n 1 195 GLU n 1 196 CYS n 1 197 VAL n 1 198 SER n 1 199 LYS n 1 200 CYS n 1 201 ALA n 1 202 HIS n 1 203 HIS n 1 204 HIS n 1 205 HIS n 1 206 HIS n 1 207 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 ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'RS1, XLRS1' _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 '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 ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name 'fall armyworm' _entity_src_gen.pdbx_host_org_scientific_name 'Spodoptera frugiperda' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 7108 _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 Sf9 _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 Bacmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name 11109-E01 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code XLRS1_HUMAN _struct_ref.pdbx_db_accession O15537 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;STEDEGEDPWYQKACKCDCQGGPNALWSAGATSLDCIPECPYHKPLGFESGEVTPDQITCSNPEQYVGWYSSWTANKARL NSQGFGCAWLSKFQDSSQWLQIDLKEIKVISGILTQGRCDIDEWMTKYSVQYRTDERLNWIYYKDQTGNNRVFYGNSDRT STVQNLLRPPIISRFIRLIPLGWHVRIAIRMELLECVSKCA ; _struct_ref.pdbx_align_begin 24 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3JD6 _struct_ref_seq.pdbx_strand_id O _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 201 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O15537 _struct_ref_seq.db_align_beg 24 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 224 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 24 _struct_ref_seq.pdbx_auth_seq_align_end 224 # 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 3JD6 HIS O 202 ? UNP O15537 ? ? 'EXPRESSION TAG' 225 1 1 3JD6 HIS O 203 ? UNP O15537 ? ? 'EXPRESSION TAG' 226 2 1 3JD6 HIS O 204 ? UNP O15537 ? ? 'EXPRESSION TAG' 227 3 1 3JD6 HIS O 205 ? UNP O15537 ? ? 'EXPRESSION TAG' 228 4 1 3JD6 HIS O 206 ? UNP O15537 ? ? 'EXPRESSION TAG' 229 5 1 3JD6 HIS O 207 ? UNP O15537 ? ? 'EXPRESSION TAG' 230 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3JD6 _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1367 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1367 _refine_hist.d_res_high . _refine_hist.d_res_low . # _struct.entry_id 3JD6 _struct.title 'Double octamer structure of retinoschisin, a cell-cell adhesion protein of the retina' _struct.pdbx_descriptor Retinoschisin _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3JD6 _struct_keywords.pdbx_keywords 'CELL ADHESION' _struct_keywords.text 'discoidin domain, double octamer, adhesion protein, X-linked retinoschisis, CELL ADHESION' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id THR _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 54 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ASP _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 56 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id THR _struct_conf.beg_auth_asym_id O _struct_conf.beg_auth_seq_id 77 _struct_conf.end_auth_comp_id ASP _struct_conf.end_auth_asym_id O _struct_conf.end_auth_seq_id 79 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 3 # _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 disulf1 disulf ? ? A CYS 40 SG ? ? ? 1_555 A CYS 196 SG ? ? O CYS 63 O CYS 219 1_555 ? ? ? ? ? ? ? 2.038 ? disulf2 disulf ? ? A CYS 87 SG ? ? ? 1_555 A CYS 119 SG ? ? O CYS 110 O CYS 142 1_555 ? ? ? ? ? ? ? 2.036 ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id CYS _struct_mon_prot_cis.label_seq_id 40 _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 CYS _struct_mon_prot_cis.auth_seq_id 63 _struct_mon_prot_cis.auth_asym_id O _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 41 _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 64 _struct_mon_prot_cis.pdbx_auth_asym_id_2 O _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -3.04 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 5 ? # 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 A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? 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 A 1 LYS A 44 ? PRO A 45 ? LYS O 67 PRO O 68 A 2 ARG A 190 ? GLU A 195 ? ARG O 213 GLU O 218 A 3 LEU A 100 ? GLN A 116 ? LEU O 123 GLN O 139 A 4 THR A 162 ? LEU A 181 ? THR O 185 LEU O 204 A 5 LYS A 127 ? ARG A 133 ? LYS O 150 ARG O 156 A 6 ILE A 141 ? TYR A 142 ? ILE O 164 TYR O 165 B 1 ILE A 58 ? CYS A 60 ? ILE O 81 CYS O 83 B 2 LEU A 100 ? GLN A 116 ? LEU O 123 GLN O 139 B 3 THR A 162 ? LEU A 181 ? THR O 185 LEU O 204 B 4 LYS A 127 ? ARG A 133 ? LYS O 150 ARG O 156 B 5 PHE A 153 ? TYR A 154 ? PHE O 176 TYR O 177 # 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 A 1 2 N LYS A 44 ? N LYS O 67 O GLU A 195 ? O GLU O 218 A 2 3 O LEU A 194 ? O LEU O 217 N GLY A 112 ? N GLY O 135 A 3 4 N THR A 115 ? N THR O 138 O VAL A 163 ? O VAL O 186 A 4 5 O LEU A 181 ? O LEU O 204 N LYS A 127 ? N LYS O 150 A 5 6 N TYR A 132 ? N TYR O 155 O ILE A 141 ? O ILE O 164 B 1 2 N THR A 59 ? N THR O 82 O GLN A 101 ? O GLN O 124 B 2 3 N THR A 115 ? N THR O 138 O VAL A 163 ? O VAL O 186 B 3 4 O LEU A 181 ? O LEU O 204 N LYS A 127 ? N LYS O 150 B 4 5 N TYR A 128 ? N TYR O 151 O PHE A 153 ? O PHE O 176 # _database_PDB_matrix.entry_id 3JD6 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3JD6 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H 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 SER 1 24 ? ? ? O . n A 1 2 THR 2 25 ? ? ? O . n A 1 3 GLU 3 26 ? ? ? O . n A 1 4 ASP 4 27 ? ? ? O . n A 1 5 GLU 5 28 ? ? ? O . n A 1 6 GLY 6 29 ? ? ? O . n A 1 7 GLU 7 30 ? ? ? O . n A 1 8 ASP 8 31 ? ? ? O . n A 1 9 PRO 9 32 ? ? ? O . n A 1 10 TRP 10 33 ? ? ? O . n A 1 11 TYR 11 34 ? ? ? O . n A 1 12 GLN 12 35 ? ? ? O . n A 1 13 LYS 13 36 ? ? ? O . n A 1 14 ALA 14 37 ? ? ? O . n A 1 15 CYS 15 38 ? ? ? O . n A 1 16 LYS 16 39 ? ? ? O . n A 1 17 CYS 17 40 ? ? ? O . n A 1 18 ASP 18 41 ? ? ? O . n A 1 19 CYS 19 42 ? ? ? O . n A 1 20 GLN 20 43 ? ? ? O . n A 1 21 GLY 21 44 ? ? ? O . n A 1 22 GLY 22 45 ? ? ? O . n A 1 23 PRO 23 46 ? ? ? O . n A 1 24 ASN 24 47 ? ? ? O . n A 1 25 ALA 25 48 ? ? ? O . n A 1 26 LEU 26 49 ? ? ? O . n A 1 27 TRP 27 50 ? ? ? O . n A 1 28 SER 28 51 ? ? ? O . n A 1 29 ALA 29 52 ? ? ? O . n A 1 30 GLY 30 53 ? ? ? O . n A 1 31 ALA 31 54 ? ? ? O . n A 1 32 THR 32 55 ? ? ? O . n A 1 33 SER 33 56 ? ? ? O . n A 1 34 LEU 34 57 ? ? ? O . n A 1 35 ASP 35 58 58 ASP ASP O . n A 1 36 CYS 36 59 59 CYS CYS O . n A 1 37 ILE 37 60 60 ILE ILE O . n A 1 38 PRO 38 61 61 PRO PRO O . n A 1 39 GLU 39 62 62 GLU GLU O . n A 1 40 CYS 40 63 63 CYS CYS O . n A 1 41 PRO 41 64 64 PRO PRO O . n A 1 42 TYR 42 65 65 TYR TYR O . n A 1 43 HIS 43 66 66 HIS HIS O . n A 1 44 LYS 44 67 67 LYS LYS O . n A 1 45 PRO 45 68 68 PRO PRO O . n A 1 46 LEU 46 69 69 LEU LEU O . n A 1 47 GLY 47 70 70 GLY GLY O . n A 1 48 PHE 48 71 71 PHE PHE O . n A 1 49 GLU 49 72 72 GLU GLU O . n A 1 50 SER 50 73 73 SER SER O . n A 1 51 GLY 51 74 74 GLY GLY O . n A 1 52 GLU 52 75 75 GLU GLU O . n A 1 53 VAL 53 76 76 VAL VAL O . n A 1 54 THR 54 77 77 THR THR O . n A 1 55 PRO 55 78 78 PRO PRO O . n A 1 56 ASP 56 79 79 ASP ASP O . n A 1 57 GLN 57 80 80 GLN GLN O . n A 1 58 ILE 58 81 81 ILE ILE O . n A 1 59 THR 59 82 82 THR THR O . n A 1 60 CYS 60 83 83 CYS CYS O . n A 1 61 SER 61 84 84 SER SER O . n A 1 62 ASN 62 85 85 ASN ASN O . n A 1 63 PRO 63 86 86 PRO PRO O . n A 1 64 GLU 64 87 87 GLU GLU O . n A 1 65 GLN 65 88 88 GLN GLN O . n A 1 66 TYR 66 89 89 TYR TYR O . n A 1 67 VAL 67 90 90 VAL VAL O . n A 1 68 GLY 68 91 91 GLY GLY O . n A 1 69 TRP 69 92 92 TRP TRP O . n A 1 70 TYR 70 93 93 TYR TYR O . n A 1 71 SER 71 94 94 SER SER O . n A 1 72 SER 72 95 95 SER SER O . n A 1 73 TRP 73 96 96 TRP TRP O . n A 1 74 THR 74 97 97 THR THR O . n A 1 75 ALA 75 98 98 ALA ALA O . n A 1 76 ASN 76 99 99 ASN ASN O . n A 1 77 LYS 77 100 100 LYS LYS O . n A 1 78 ALA 78 101 101 ALA ALA O . n A 1 79 ARG 79 102 102 ARG ARG O . n A 1 80 LEU 80 103 103 LEU LEU O . n A 1 81 ASN 81 104 104 ASN ASN O . n A 1 82 SER 82 105 105 SER SER O . n A 1 83 GLN 83 106 106 GLN GLN O . n A 1 84 GLY 84 107 107 GLY GLY O . n A 1 85 PHE 85 108 108 PHE PHE O . n A 1 86 GLY 86 109 109 GLY GLY O . n A 1 87 CYS 87 110 110 CYS CYS O . n A 1 88 ALA 88 111 111 ALA ALA O . n A 1 89 TRP 89 112 112 TRP TRP O . n A 1 90 LEU 90 113 113 LEU LEU O . n A 1 91 SER 91 114 114 SER SER O . n A 1 92 LYS 92 115 115 LYS LYS O . n A 1 93 PHE 93 116 116 PHE PHE O . n A 1 94 GLN 94 117 117 GLN GLN O . n A 1 95 ASP 95 118 118 ASP ASP O . n A 1 96 SER 96 119 119 SER SER O . n A 1 97 SER 97 120 120 SER SER O . n A 1 98 GLN 98 121 121 GLN GLN O . n A 1 99 TRP 99 122 122 TRP TRP O . n A 1 100 LEU 100 123 123 LEU LEU O . n A 1 101 GLN 101 124 124 GLN GLN O . n A 1 102 ILE 102 125 125 ILE ILE O . n A 1 103 ASP 103 126 126 ASP ASP O . n A 1 104 LEU 104 127 127 LEU LEU O . n A 1 105 LYS 105 128 128 LYS LYS O . n A 1 106 GLU 106 129 129 GLU GLU O . n A 1 107 ILE 107 130 130 ILE ILE O . n A 1 108 LYS 108 131 131 LYS LYS O . n A 1 109 VAL 109 132 132 VAL VAL O . n A 1 110 ILE 110 133 133 ILE ILE O . n A 1 111 SER 111 134 134 SER SER O . n A 1 112 GLY 112 135 135 GLY GLY O . n A 1 113 ILE 113 136 136 ILE ILE O . n A 1 114 LEU 114 137 137 LEU LEU O . n A 1 115 THR 115 138 138 THR THR O . n A 1 116 GLN 116 139 139 GLN GLN O . n A 1 117 GLY 117 140 140 GLY GLY O . n A 1 118 ARG 118 141 141 ARG ARG O . n A 1 119 CYS 119 142 142 CYS CYS O . n A 1 120 ASP 120 143 143 ASP ASP O . n A 1 121 ILE 121 144 144 ILE ILE O . n A 1 122 ASP 122 145 145 ASP ASP O . n A 1 123 GLU 123 146 146 GLU GLU O . n A 1 124 TRP 124 147 147 TRP TRP O . n A 1 125 MET 125 148 148 MET MET O . n A 1 126 THR 126 149 149 THR THR O . n A 1 127 LYS 127 150 150 LYS LYS O . n A 1 128 TYR 128 151 151 TYR TYR O . n A 1 129 SER 129 152 152 SER SER O . n A 1 130 VAL 130 153 153 VAL VAL O . n A 1 131 GLN 131 154 154 GLN GLN O . n A 1 132 TYR 132 155 155 TYR TYR O . n A 1 133 ARG 133 156 156 ARG ARG O . n A 1 134 THR 134 157 157 THR THR O . n A 1 135 ASP 135 158 158 ASP ASP O . n A 1 136 GLU 136 159 159 GLU GLU O . n A 1 137 ARG 137 160 160 ARG ARG O . n A 1 138 LEU 138 161 161 LEU LEU O . n A 1 139 ASN 139 162 162 ASN ASN O . n A 1 140 TRP 140 163 163 TRP TRP O . n A 1 141 ILE 141 164 164 ILE ILE O . n A 1 142 TYR 142 165 165 TYR TYR O . n A 1 143 TYR 143 166 166 TYR TYR O . n A 1 144 LYS 144 167 167 LYS LYS O . n A 1 145 ASP 145 168 168 ASP ASP O . n A 1 146 GLN 146 169 169 GLN GLN O . n A 1 147 THR 147 170 170 THR THR O . n A 1 148 GLY 148 171 171 GLY GLY O . n A 1 149 ASN 149 172 172 ASN ASN O . n A 1 150 ASN 150 173 173 ASN ASN O . n A 1 151 ARG 151 174 174 ARG ARG O . n A 1 152 VAL 152 175 175 VAL VAL O . n A 1 153 PHE 153 176 176 PHE PHE O . n A 1 154 TYR 154 177 177 TYR TYR O . n A 1 155 GLY 155 178 178 GLY GLY O . n A 1 156 ASN 156 179 179 ASN ASN O . n A 1 157 SER 157 180 180 SER SER O . n A 1 158 ASP 158 181 181 ASP ASP O . n A 1 159 ARG 159 182 182 ARG ARG O . n A 1 160 THR 160 183 183 THR THR O . n A 1 161 SER 161 184 184 SER SER O . n A 1 162 THR 162 185 185 THR THR O . n A 1 163 VAL 163 186 186 VAL VAL O . n A 1 164 GLN 164 187 187 GLN GLN O . n A 1 165 ASN 165 188 188 ASN ASN O . n A 1 166 LEU 166 189 189 LEU LEU O . n A 1 167 LEU 167 190 190 LEU LEU O . n A 1 168 ARG 168 191 191 ARG ARG O . n A 1 169 PRO 169 192 192 PRO PRO O . n A 1 170 PRO 170 193 193 PRO PRO O . n A 1 171 ILE 171 194 194 ILE ILE O . n A 1 172 ILE 172 195 195 ILE ILE O . n A 1 173 SER 173 196 196 SER SER O . n A 1 174 ARG 174 197 197 ARG ARG O . n A 1 175 PHE 175 198 198 PHE PHE O . n A 1 176 ILE 176 199 199 ILE ILE O . n A 1 177 ARG 177 200 200 ARG ARG O . n A 1 178 LEU 178 201 201 LEU LEU O . n A 1 179 ILE 179 202 202 ILE ILE O . n A 1 180 PRO 180 203 203 PRO PRO O . n A 1 181 LEU 181 204 204 LEU LEU O . n A 1 182 GLY 182 205 205 GLY GLY O . n A 1 183 TRP 183 206 206 TRP TRP O . n A 1 184 HIS 184 207 207 HIS HIS O . n A 1 185 VAL 185 208 208 VAL VAL O . n A 1 186 ARG 186 209 209 ARG ARG O . n A 1 187 ILE 187 210 210 ILE ILE O . n A 1 188 ALA 188 211 211 ALA ALA O . n A 1 189 ILE 189 212 212 ILE ILE O . n A 1 190 ARG 190 213 213 ARG ARG O . n A 1 191 MET 191 214 214 MET MET O . n A 1 192 GLU 192 215 215 GLU GLU O . n A 1 193 LEU 193 216 216 LEU LEU O . n A 1 194 LEU 194 217 217 LEU LEU O . n A 1 195 GLU 195 218 218 GLU GLU O . n A 1 196 CYS 196 219 219 CYS CYS O . n A 1 197 VAL 197 220 220 VAL VAL O . n A 1 198 SER 198 221 221 SER SER O . n A 1 199 LYS 199 222 222 LYS LYS O . n A 1 200 CYS 200 223 223 CYS CYS O . n A 1 201 ALA 201 224 224 ALA ALA O . n A 1 202 HIS 202 225 ? ? ? O . n A 1 203 HIS 203 226 ? ? ? O . n A 1 204 HIS 204 227 ? ? ? O . n A 1 205 HIS 205 228 ? ? ? O . n A 1 206 HIS 206 229 ? ? ? O . n A 1 207 HIS 207 230 ? ? ? O . n # 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' ? 16-MERIC 16 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 '(1-16)' A 2 1 A 3 P A # 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' ? ? 0.70710678 0.70710678 0.00000000 0.00000 0.70710678 -0.70710678 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 1 'point symmetry operation' ? ? 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' ? ? 0.70710678 0.70710678 0.00000000 0.00000 -0.70710678 0.70710678 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 3 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 4 'point symmetry operation' ? ? -0.70710678 0.70710678 0.00000000 0.00000 -0.70710678 -0.70710678 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 5 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 6 'point symmetry operation' ? ? -0.70710678 -0.70710678 0.00000000 0.00000 0.70710678 -0.70710678 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 7 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 8 'point symmetry operation' ? ? 0.70710678 -0.70710678 0.00000000 0.00000 0.70710678 0.70710678 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 9 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 10 'point symmetry operation' ? ? -0.70710678 0.70710678 0.00000000 0.00000 0.70710678 0.70710678 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 11 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 12 'point symmetry operation' ? ? -0.70710678 -0.70710678 0.00000000 0.00000 -0.70710678 0.70710678 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 13 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 14 'point symmetry operation' ? ? 0.70710678 -0.70710678 0.00000000 0.00000 -0.70710678 -0.70710678 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 15 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 16 'point symmetry operation' ? ? 0.70710678 0.70710678 0.00000000 0.00000 0.70710678 -0.70710678 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 0.00000 # _pdbx_point_symmetry.entry_id 3JD6 _pdbx_point_symmetry.Schoenflies_symbol D _pdbx_point_symmetry.circular_symmetry 8 # 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 2016-05-11 2 'Structure model' 1 1 2016-05-25 3 'Structure model' 1 2 2018-07-18 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category em_software # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_em_software.image_processing_id' 2 3 'Structure model' '_em_software.name' # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 3JD6 _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' _em_3d_fitting.ref_space REAL _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria 'FSC(0.5) = 4.7' _em_3d_fitting.details 'METHOD--Flexible fitting REFINEMENT PROTOCOL--FLEXIBLE' _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.pdb_entry_id 1SDD _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.details ? # _em_3d_reconstruction.entry_id 3JD6 _em_3d_reconstruction.id 1 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method 'Bayesian orientation refinement with iterative gridded reconstruction' _em_3d_reconstruction.nominal_pixel_size 1.03 _em_3d_reconstruction.actual_pixel_size 1.03 _em_3d_reconstruction.resolution 4.1 _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 9096 _em_3d_reconstruction.algorithm ? # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name '20 mM Tris-HCl, 150 mM NaCl' _em_buffer.pH 7.5 _em_buffer.details '20 mM Tris-HCl, 150 mM NaCl' # _em_entity_assembly.id 1 _em_entity_assembly.name 'Purified Retinoschisin: residues 24-224 + 6xHis' _em_entity_assembly.type COMPLEX _em_entity_assembly.parent_id 0 _em_entity_assembly.synonym RS1 _em_entity_assembly.details ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 3JD6 _em_image_scans.id 1 _em_image_scans.image_recording_id 1 _em_image_scans.number_digital_images 19 _em_image_scans.citation_id ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.details ? # _em_imaging.entry_id 3JD6 _em_imaging.id 1 _em_imaging.microscope_model 'FEI POLARA 300' _em_imaging.specimen_id 1 _em_imaging.date 2014-06-03 _em_imaging.temperature ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_cs 2.0 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.nominal_magnification 39000 _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.accelerating_voltage 300 _em_imaging.details '10 frames over 3 seconds' _em_imaging.specimen_holder_type 'FEI Polara specimen loader' _em_imaging.specimen_holder_model OTHER _em_imaging.citation_id ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'Plasma-cleaned 2.0 um hole, 2.0 um space C-flat holey carbon grids (Protochips)' _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? _em_sample_support.method ? # _em_vitrification.entry_id 3JD6 _em_vitrification.id 1 _em_vitrification.details 'Ambient temperature 23 degrees C. Plunged into liquid ethane (LEICA EM GP).' _em_vitrification.citation_id ? _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 90 _em_vitrification.instrument 'LEICA EM GP' _em_vitrification.method ? _em_vitrification.specimen_id 1 _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 3JD6 _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' # _em_single_particle_entity.entry_id 3JD6 _em_single_particle_entity.id 1 _em_single_particle_entity.point_symmetry D8 _em_single_particle_entity.image_processing_id 1 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CD2 _pdbx_validate_rmsd_bond.auth_asym_id_1 O _pdbx_validate_rmsd_bond.auth_comp_id_1 TRP _pdbx_validate_rmsd_bond.auth_seq_id_1 112 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CE3 _pdbx_validate_rmsd_bond.auth_asym_id_2 O _pdbx_validate_rmsd_bond.auth_comp_id_2 TRP _pdbx_validate_rmsd_bond.auth_seq_id_2 112 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.303 _pdbx_validate_rmsd_bond.bond_target_value 1.399 _pdbx_validate_rmsd_bond.bond_deviation -0.096 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.015 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N O ALA 111 ? ? CA O ALA 111 ? ? CB O ALA 111 ? ? 119.37 110.10 9.27 1.40 N 2 1 NE O ARG 156 ? ? CZ O ARG 156 ? ? NH1 O ARG 156 ? ? 123.53 120.30 3.23 0.50 N 3 1 NE O ARG 156 ? ? CZ O ARG 156 ? ? NH2 O ARG 156 ? ? 117.04 120.30 -3.26 0.50 N 4 1 N O VAL 220 ? ? CA O VAL 220 ? ? C O VAL 220 ? ? 93.86 111.00 -17.14 2.70 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 CYS O 59 ? ? 178.43 151.45 2 1 ASN O 85 ? ? 73.38 79.01 3 1 SER O 95 ? ? -172.26 81.88 4 1 PHE O 108 ? ? -155.19 23.31 5 1 ALA O 111 ? ? 76.41 -176.83 6 1 GLN O 117 ? ? -171.71 117.03 7 1 SER O 120 ? ? -142.85 33.17 8 1 GLU O 129 ? ? -173.30 132.87 9 1 ASP O 158 ? ? 76.68 -23.59 10 1 LEU O 161 ? ? 66.95 -138.08 11 1 GLN O 169 ? ? 63.45 -175.72 12 1 VAL O 208 ? ? 78.27 -54.87 13 1 ALA O 211 ? ? -173.32 97.70 14 1 GLU O 218 ? ? -126.38 -159.23 15 1 CYS O 223 ? ? 84.72 144.29 # loop_ _pdbx_validate_peptide_omega.id _pdbx_validate_peptide_omega.PDB_model_num _pdbx_validate_peptide_omega.auth_comp_id_1 _pdbx_validate_peptide_omega.auth_asym_id_1 _pdbx_validate_peptide_omega.auth_seq_id_1 _pdbx_validate_peptide_omega.PDB_ins_code_1 _pdbx_validate_peptide_omega.label_alt_id_1 _pdbx_validate_peptide_omega.auth_comp_id_2 _pdbx_validate_peptide_omega.auth_asym_id_2 _pdbx_validate_peptide_omega.auth_seq_id_2 _pdbx_validate_peptide_omega.PDB_ins_code_2 _pdbx_validate_peptide_omega.label_alt_id_2 _pdbx_validate_peptide_omega.omega 1 1 GLU O 62 ? ? CYS O 63 ? ? -70.57 2 1 SER O 95 ? ? TRP O 96 ? ? 59.35 3 1 SER O 221 ? ? LYS O 222 ? ? -71.18 # 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 O SER 24 ? A SER 1 2 1 Y 1 O THR 25 ? A THR 2 3 1 Y 1 O GLU 26 ? A GLU 3 4 1 Y 1 O ASP 27 ? A ASP 4 5 1 Y 1 O GLU 28 ? A GLU 5 6 1 Y 1 O GLY 29 ? A GLY 6 7 1 Y 1 O GLU 30 ? A GLU 7 8 1 Y 1 O ASP 31 ? A ASP 8 9 1 Y 1 O PRO 32 ? A PRO 9 10 1 Y 1 O TRP 33 ? A TRP 10 11 1 Y 1 O TYR 34 ? A TYR 11 12 1 Y 1 O GLN 35 ? A GLN 12 13 1 Y 1 O LYS 36 ? A LYS 13 14 1 Y 1 O ALA 37 ? A ALA 14 15 1 Y 1 O CYS 38 ? A CYS 15 16 1 Y 1 O LYS 39 ? A LYS 16 17 1 Y 1 O CYS 40 ? A CYS 17 18 1 Y 1 O ASP 41 ? A ASP 18 19 1 Y 1 O CYS 42 ? A CYS 19 20 1 Y 1 O GLN 43 ? A GLN 20 21 1 Y 1 O GLY 44 ? A GLY 21 22 1 Y 1 O GLY 45 ? A GLY 22 23 1 Y 1 O PRO 46 ? A PRO 23 24 1 Y 1 O ASN 47 ? A ASN 24 25 1 Y 1 O ALA 48 ? A ALA 25 26 1 Y 1 O LEU 49 ? A LEU 26 27 1 Y 1 O TRP 50 ? A TRP 27 28 1 Y 1 O SER 51 ? A SER 28 29 1 Y 1 O ALA 52 ? A ALA 29 30 1 Y 1 O GLY 53 ? A GLY 30 31 1 Y 1 O ALA 54 ? A ALA 31 32 1 Y 1 O THR 55 ? A THR 32 33 1 Y 1 O SER 56 ? A SER 33 34 1 Y 1 O LEU 57 ? A LEU 34 35 1 Y 1 O HIS 225 ? A HIS 202 36 1 Y 1 O HIS 226 ? A HIS 203 37 1 Y 1 O HIS 227 ? A HIS 204 38 1 Y 1 O HIS 228 ? A HIS 205 39 1 Y 1 O HIS 229 ? A HIS 206 40 1 Y 1 O HIS 230 ? A HIS 207 # _em_ctf_correction.id 1 _em_ctf_correction.details 'Included in iterative refinement' _em_ctf_correction.type . # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.avg_electron_dose_per_image 30 _em_image_recording.details 'Counting mode' _em_image_recording.id 1 _em_image_recording.film_or_detector_model 'GATAN K2 (4k x 4k)' _em_image_recording.imaging_id 1 _em_image_recording.detector_mode ? _em_image_recording.average_exposure_time ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.id _em_software.name _em_software.version _em_software.category _em_software.details _em_software.image_processing_id 1 Coot ? 'MODEL FITTING' ? ? 2 Foldit ? 'MODEL FITTING' ? ? 3 MDFF ? 'MODEL FITTING' ? ? 4 EMAN 2 RECONSTRUCTION ? 1 5 RELION ? RECONSTRUCTION ? 1 # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration 0.2 _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? #