data_1AP9 # _entry.id 1AP9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 1AP9 pdb_00001ap9 10.2210/pdb1ap9/pdb WWPDB D_1000171089 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1AP9 _pdbx_database_status.recvd_initial_deposition_date 1997-07-26 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pebay-Peyroula, E.' 1 'Rummel, G.' 2 'Rosenbusch, J.P.' 3 'Landau, E.M.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases.' Science 277 1676 1681 1997 SCIEAS US 0036-8075 0038 ? 9287223 10.1126/science.277.5332.1676 1 'Crystallisation of a Polar Protein and Small Molecules from the Aqueous Compartment of Lipidic Cubic Phases' J.Phys.Chem.B 101 1935 ? 1997 JPCBFK US 1089-5647 1278 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pebay-Peyroula, E.' 1 ? primary 'Rummel, G.' 2 ? primary 'Rosenbusch, J.P.' 3 ? primary 'Landau, E.M.' 4 ? 1 'Landau, E.M.' 5 ? 1 'Rummel, G.' 6 ? 1 'Cowan-Jacob, S.W.' 7 ? 1 'Rosenbusch, J.P.' 8 ? # _cell.entry_id 1AP9 _cell.length_a 61.760 _cell.length_b 61.760 _cell.length_c 104.160 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AP9 _symmetry.space_group_name_H-M 'P 63' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 # 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 nat BACTERIORHODOPSIN 26814.412 1 ? ? ? 'RETINAL LINKED TO LYS 216 VIA A SCHIFF BASE' 2 non-polymer syn RETINAL 284.436 1 ? ? ? ? 3 water nat water 18.015 26 ? ? ? ? # _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 ;QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA GDGAAATS ; _entity_poly.pdbx_seq_one_letter_code_can ;QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA GDGAAATS ; _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 GLN n 1 2 ALA n 1 3 GLN n 1 4 ILE n 1 5 THR n 1 6 GLY n 1 7 ARG n 1 8 PRO n 1 9 GLU n 1 10 TRP n 1 11 ILE n 1 12 TRP n 1 13 LEU n 1 14 ALA n 1 15 LEU n 1 16 GLY n 1 17 THR n 1 18 ALA n 1 19 LEU n 1 20 MET n 1 21 GLY n 1 22 LEU n 1 23 GLY n 1 24 THR n 1 25 LEU n 1 26 TYR n 1 27 PHE n 1 28 LEU n 1 29 VAL n 1 30 LYS n 1 31 GLY n 1 32 MET n 1 33 GLY n 1 34 VAL n 1 35 SER n 1 36 ASP n 1 37 PRO n 1 38 ASP n 1 39 ALA n 1 40 LYS n 1 41 LYS n 1 42 PHE n 1 43 TYR n 1 44 ALA n 1 45 ILE n 1 46 THR n 1 47 THR n 1 48 LEU n 1 49 VAL n 1 50 PRO n 1 51 ALA n 1 52 ILE n 1 53 ALA n 1 54 PHE n 1 55 THR n 1 56 MET n 1 57 TYR n 1 58 LEU n 1 59 SER n 1 60 MET n 1 61 LEU n 1 62 LEU n 1 63 GLY n 1 64 TYR n 1 65 GLY n 1 66 LEU n 1 67 THR n 1 68 MET n 1 69 VAL n 1 70 PRO n 1 71 PHE n 1 72 GLY n 1 73 GLY n 1 74 GLU n 1 75 GLN n 1 76 ASN n 1 77 PRO n 1 78 ILE n 1 79 TYR n 1 80 TRP n 1 81 ALA n 1 82 ARG n 1 83 TYR n 1 84 ALA n 1 85 ASP n 1 86 TRP n 1 87 LEU n 1 88 PHE n 1 89 THR n 1 90 THR n 1 91 PRO n 1 92 LEU n 1 93 LEU n 1 94 LEU n 1 95 LEU n 1 96 ASP n 1 97 LEU n 1 98 ALA n 1 99 LEU n 1 100 LEU n 1 101 VAL n 1 102 ASP n 1 103 ALA n 1 104 ASP n 1 105 GLN n 1 106 GLY n 1 107 THR n 1 108 ILE n 1 109 LEU n 1 110 ALA n 1 111 LEU n 1 112 VAL n 1 113 GLY n 1 114 ALA n 1 115 ASP n 1 116 GLY n 1 117 ILE n 1 118 MET n 1 119 ILE n 1 120 GLY n 1 121 THR n 1 122 GLY n 1 123 LEU n 1 124 VAL n 1 125 GLY n 1 126 ALA n 1 127 LEU n 1 128 THR n 1 129 LYS n 1 130 VAL n 1 131 TYR n 1 132 SER n 1 133 TYR n 1 134 ARG n 1 135 PHE n 1 136 VAL n 1 137 TRP n 1 138 TRP n 1 139 ALA n 1 140 ILE n 1 141 SER n 1 142 THR n 1 143 ALA n 1 144 ALA n 1 145 MET n 1 146 LEU n 1 147 TYR n 1 148 ILE n 1 149 LEU n 1 150 TYR n 1 151 VAL n 1 152 LEU n 1 153 PHE n 1 154 PHE n 1 155 GLY n 1 156 PHE n 1 157 THR n 1 158 SER n 1 159 LYS n 1 160 ALA n 1 161 GLU n 1 162 SER n 1 163 MET n 1 164 ARG n 1 165 PRO n 1 166 GLU n 1 167 VAL n 1 168 ALA n 1 169 SER n 1 170 THR n 1 171 PHE n 1 172 LYS n 1 173 VAL n 1 174 LEU n 1 175 ARG n 1 176 ASN n 1 177 VAL n 1 178 THR n 1 179 VAL n 1 180 VAL n 1 181 LEU n 1 182 TRP n 1 183 SER n 1 184 ALA n 1 185 TYR n 1 186 PRO n 1 187 VAL n 1 188 VAL n 1 189 TRP n 1 190 LEU n 1 191 ILE n 1 192 GLY n 1 193 SER n 1 194 GLU n 1 195 GLY n 1 196 ALA n 1 197 GLY n 1 198 ILE n 1 199 VAL n 1 200 PRO n 1 201 LEU n 1 202 ASN n 1 203 ILE n 1 204 GLU n 1 205 THR n 1 206 LEU n 1 207 LEU n 1 208 PHE n 1 209 MET n 1 210 VAL n 1 211 LEU n 1 212 ASP n 1 213 VAL n 1 214 SER n 1 215 ALA n 1 216 LYS n 1 217 VAL n 1 218 GLY n 1 219 PHE n 1 220 GLY n 1 221 LEU n 1 222 ILE n 1 223 LEU n 1 224 LEU n 1 225 ARG n 1 226 SER n 1 227 ARG n 1 228 ALA n 1 229 ILE n 1 230 PHE n 1 231 GLY n 1 232 GLU n 1 233 ALA n 1 234 GLU n 1 235 ALA n 1 236 PRO n 1 237 GLU n 1 238 PRO n 1 239 SER n 1 240 ALA n 1 241 GLY n 1 242 ASP n 1 243 GLY n 1 244 ALA n 1 245 ALA n 1 246 ALA n 1 247 THR n 1 248 SER n # _entity_src_nat.entity_id 1 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Halobacterium salinarum' _entity_src_nat.pdbx_ncbi_taxonomy_id 2242 _entity_src_nat.genus Halobacterium _entity_src_nat.species ? _entity_src_nat.strain S9 _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location 'PLASMA MEMBRANE' _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code BACR_HALN1 _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession P02945 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ;MLELLPTAVEGVSQAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT MVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLY ILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSR AIFGEAEAPEPSAGDGAAATSD ; _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1AP9 _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 248 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P02945 _struct_ref_seq.db_align_beg 14 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 261 _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 248 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 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.entry_id 1AP9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.39 _exptl_crystal.density_percent_sol 48.0 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER AT PH 5.6, AT 20C AND IN THE DARK. THE MIXTURE WAS CENTRIFUGED AT 10000G FOR 150 MN PRIOR TO CRYSTALLISATION. ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1996-08 _diffrn_detector.details 'ELLIPSOIDAL MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI(111)' _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.688 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID13' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 _diffrn_source.pdbx_wavelength 0.688 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1AP9 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 10.0 _reflns.d_resolution_high 2.35 _reflns.number_obs 8045 _reflns.number_all ? _reflns.percent_possible_obs 91.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.1000000 _reflns.pdbx_netI_over_sigmaI 4.7 _reflns.B_iso_Wilson_estimate 45.5 _reflns.pdbx_redundancy 2.0 _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.35 _reflns_shell.d_res_low 2.56 _reflns_shell.percent_possible_all 90.4 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.2660000 _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_redundancy 1.6 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1AP9 _refine.ls_number_reflns_obs 6564 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.5 _refine.pdbx_data_cutoff_high_absF 10000000.00 _refine.pdbx_data_cutoff_low_absF 0.001 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 5.00 _refine.ls_d_res_high 2.35 _refine.ls_percent_reflns_obs 77.8 _refine.ls_R_factor_obs 0.2582000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2582000 _refine.ls_R_factor_R_free 0.3170000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5 _refine.ls_number_reflns_R_free 300 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 75 _refine.aniso_B[1][1] 0 _refine.aniso_B[2][2] 0 _refine.aniso_B[3][3] 0 _refine.aniso_B[1][2] 0 _refine.aniso_B[1][3] 0 _refine.aniso_B[2][3] 0 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2BRD' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1AP9 _refine_analyze.Luzzati_coordinate_error_obs 0.40 _refine_analyze.Luzzati_sigma_a_obs 0.62 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.51 _refine_analyze.Luzzati_sigma_a_free 0.76 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1694 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 26 _refine_hist.number_atoms_total 1740 _refine_hist.d_res_high 2.35 _refine_hist.d_res_low 5.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.491 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 20.82 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 1.188 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.35 _refine_ls_shell.d_res_low 2.48 _refine_ls_shell.number_reflns_R_work 957 _refine_ls_shell.R_factor_R_work 0.3947000 _refine_ls_shell.percent_reflns_obs 67.0 _refine_ls_shell.R_factor_R_free 0.3840000 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free 5.0 _refine_ls_shell.number_reflns_R_free 49 _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PARHCSDX.PRO TOPHCSDX.PRO 'X-RAY DIFFRACTION' 2 PARAM19.SOL RETINAL.TOP 'X-RAY DIFFRACTION' 3 RETINAL.PAR ? 'X-RAY DIFFRACTION' # _struct.entry_id 1AP9 _struct.title 'X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1AP9 _struct_keywords.pdbx_keywords PHOTORECEPTOR _struct_keywords.text 'PHOTORECEPTOR, PROTON PUMP, MEMBRANE PROTEIN, RETINAL PROTEIN, MICROCRYSTALS, MICROFOCUS BEAM, LIPIDIC CUBIC PHASES' # 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 ? # _struct_biol.id 1 # 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 A1 TRP A 10 ? MET A 20 ? TRP A 10 MET A 20 1 ? 11 HELX_P HELX_P2 A2 GLY A 23 ? LYS A 30 ? GLY A 23 LYS A 30 1 ? 8 HELX_P HELX_P3 B PRO A 37 ? LEU A 61 ? PRO A 37 LEU A 61 1 ? 25 HELX_P HELX_P4 C1 TYR A 83 ? TRP A 86 ? TYR A 83 TRP A 86 1 ? 4 HELX_P HELX_P5 C2 THR A 90 ? LEU A 93 ? THR A 90 LEU A 93 1 ? 4 HELX_P HELX_P6 D GLN A 105 ? ALA A 126 ? GLN A 105 ALA A 126 1 ? 22 HELX_P HELX_P7 E ARG A 134 ? LEU A 152 ? ARG A 134 LEU A 152 1 ? 19 HELX_P HELX_P8 F1 GLU A 166 ? SER A 169 ? GLU A 166 SER A 169 1 ? 4 HELX_P HELX_P9 F2 LYS A 172 ? TRP A 189 ? LYS A 172 TRP A 189 1 ? 18 HELX_P HELX_P10 G ASN A 202 ? GLY A 220 ? ASN A 202 GLY A 220 1 ? 19 # _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 216 _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 216 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 300 _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 1.264 _struct_conn.pdbx_value_order ? _struct_conn.pdbx_role ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details SFF Unknown ? ? ? ? 1 'SCHIFF BASE' AC1 Software A RET 300 ? 13 'BINDING SITE FOR RESIDUE RET A 300' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 SFF 1 LYS A 216 ? LYS A 216 . ? 1_555 ? 2 AC1 13 TYR A 83 ? TYR A 83 . ? 1_555 ? 3 AC1 13 TRP A 86 ? TRP A 86 . ? 1_555 ? 4 AC1 13 THR A 89 ? THR A 89 . ? 1_555 ? 5 AC1 13 THR A 90 ? THR A 90 . ? 1_555 ? 6 AC1 13 MET A 118 ? MET A 118 . ? 1_555 ? 7 AC1 13 ILE A 119 ? ILE A 119 . ? 1_555 ? 8 AC1 13 TRP A 138 ? TRP A 138 . ? 1_555 ? 9 AC1 13 SER A 141 ? SER A 141 . ? 1_555 ? 10 AC1 13 MET A 145 ? MET A 145 . ? 1_555 ? 11 AC1 13 TRP A 182 ? TRP A 182 . ? 1_555 ? 12 AC1 13 TYR A 185 ? TYR A 185 . ? 1_555 ? 13 AC1 13 ASP A 212 ? ASP A 212 . ? 1_555 ? 14 AC1 13 LYS A 216 ? LYS A 216 . ? 1_555 ? # _database_PDB_matrix.entry_id 1AP9 _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 1AP9 _atom_sites.fract_transf_matrix[1][1] 0.016192 _atom_sites.fract_transf_matrix[1][2] 0.009348 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.018697 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.009601 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # loop_ _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 GLN 1 1 ? ? ? A . n A 1 2 ALA 2 2 ? ? ? A . n A 1 3 GLN 3 3 ? ? ? A . n A 1 4 ILE 4 4 ? ? ? A . n A 1 5 THR 5 5 ? ? ? A . n A 1 6 GLY 6 6 ? ? ? A . n A 1 7 ARG 7 7 7 ARG ARG A . n A 1 8 PRO 8 8 8 PRO PRO A . n A 1 9 GLU 9 9 9 GLU GLU A . n A 1 10 TRP 10 10 10 TRP TRP A . n A 1 11 ILE 11 11 11 ILE ILE A . n A 1 12 TRP 12 12 12 TRP TRP A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 LEU 15 15 15 LEU LEU A . n A 1 16 GLY 16 16 16 GLY GLY A . n A 1 17 THR 17 17 17 THR THR A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 MET 20 20 20 MET MET A . n A 1 21 GLY 21 21 21 GLY GLY A . n A 1 22 LEU 22 22 22 LEU LEU A . n A 1 23 GLY 23 23 23 GLY GLY A . n A 1 24 THR 24 24 24 THR THR A . n A 1 25 LEU 25 25 25 LEU LEU A . n A 1 26 TYR 26 26 26 TYR TYR A . n A 1 27 PHE 27 27 27 PHE PHE A . n A 1 28 LEU 28 28 28 LEU LEU A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 LYS 30 30 30 LYS LYS A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 MET 32 32 32 MET MET A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 VAL 34 34 34 VAL VAL A . n A 1 35 SER 35 35 35 SER SER A . n A 1 36 ASP 36 36 36 ASP ASP A . n A 1 37 PRO 37 37 37 PRO PRO A . n A 1 38 ASP 38 38 38 ASP ASP A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 LYS 40 40 40 LYS LYS A . n A 1 41 LYS 41 41 41 LYS LYS A . n A 1 42 PHE 42 42 42 PHE PHE A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 ALA 44 44 44 ALA ALA A . n A 1 45 ILE 45 45 45 ILE ILE A . n A 1 46 THR 46 46 46 THR THR A . n A 1 47 THR 47 47 47 THR THR A . n A 1 48 LEU 48 48 48 LEU LEU A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 PRO 50 50 50 PRO PRO A . n A 1 51 ALA 51 51 51 ALA ALA A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 PHE 54 54 54 PHE PHE A . n A 1 55 THR 55 55 55 THR THR A . n A 1 56 MET 56 56 56 MET MET A . n A 1 57 TYR 57 57 57 TYR TYR A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 SER 59 59 59 SER SER A . n A 1 60 MET 60 60 60 MET MET A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 LEU 62 62 62 LEU LEU A . n A 1 63 GLY 63 63 63 GLY GLY A . n A 1 64 TYR 64 64 64 TYR TYR A . n A 1 65 GLY 65 65 65 GLY GLY A . n A 1 66 LEU 66 66 66 LEU LEU A . n A 1 67 THR 67 67 67 THR THR A . n A 1 68 MET 68 68 68 MET MET A . n A 1 69 VAL 69 69 69 VAL VAL A . n A 1 70 PRO 70 70 70 PRO PRO A . n A 1 71 PHE 71 71 71 PHE PHE A . n A 1 72 GLY 72 72 72 GLY GLY A . n A 1 73 GLY 73 73 73 GLY GLY A . n A 1 74 GLU 74 74 74 GLU GLU A . n A 1 75 GLN 75 75 75 GLN GLN A . n A 1 76 ASN 76 76 76 ASN ASN A . n A 1 77 PRO 77 77 77 PRO PRO A . n A 1 78 ILE 78 78 78 ILE ILE A . n A 1 79 TYR 79 79 79 TYR TYR A . n A 1 80 TRP 80 80 80 TRP TRP A . n A 1 81 ALA 81 81 81 ALA ALA A . n A 1 82 ARG 82 82 82 ARG ARG A . n A 1 83 TYR 83 83 83 TYR TYR A . n A 1 84 ALA 84 84 84 ALA ALA A . n A 1 85 ASP 85 85 85 ASP ASP A . n A 1 86 TRP 86 86 86 TRP TRP A . n A 1 87 LEU 87 87 87 LEU LEU A . n A 1 88 PHE 88 88 88 PHE PHE A . n A 1 89 THR 89 89 89 THR THR A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 PRO 91 91 91 PRO PRO A . n A 1 92 LEU 92 92 92 LEU LEU A . n A 1 93 LEU 93 93 93 LEU LEU A . n A 1 94 LEU 94 94 94 LEU LEU A . n A 1 95 LEU 95 95 95 LEU LEU A . n A 1 96 ASP 96 96 96 ASP ASP A . n A 1 97 LEU 97 97 97 LEU LEU A . n A 1 98 ALA 98 98 98 ALA ALA A . n A 1 99 LEU 99 99 99 LEU LEU A . n A 1 100 LEU 100 100 100 LEU LEU A . n A 1 101 VAL 101 101 101 VAL VAL A . n A 1 102 ASP 102 102 102 ASP ASP A . n A 1 103 ALA 103 103 103 ALA ALA A . n A 1 104 ASP 104 104 104 ASP ASP A . n A 1 105 GLN 105 105 105 GLN GLN A . n A 1 106 GLY 106 106 106 GLY GLY A . n A 1 107 THR 107 107 107 THR THR A . n A 1 108 ILE 108 108 108 ILE ILE A . n A 1 109 LEU 109 109 109 LEU LEU A . n A 1 110 ALA 110 110 110 ALA ALA A . n A 1 111 LEU 111 111 111 LEU LEU A . n A 1 112 VAL 112 112 112 VAL VAL A . n A 1 113 GLY 113 113 113 GLY GLY A . n A 1 114 ALA 114 114 114 ALA ALA A . n A 1 115 ASP 115 115 115 ASP ASP A . n A 1 116 GLY 116 116 116 GLY GLY A . n A 1 117 ILE 117 117 117 ILE ILE A . n A 1 118 MET 118 118 118 MET MET A . n A 1 119 ILE 119 119 119 ILE ILE A . n A 1 120 GLY 120 120 120 GLY GLY A . n A 1 121 THR 121 121 121 THR THR A . n A 1 122 GLY 122 122 122 GLY GLY A . n A 1 123 LEU 123 123 123 LEU LEU A . n A 1 124 VAL 124 124 124 VAL VAL A . n A 1 125 GLY 125 125 125 GLY GLY A . n A 1 126 ALA 126 126 126 ALA ALA A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 THR 128 128 128 THR THR A . n A 1 129 LYS 129 129 129 LYS LYS A . n A 1 130 VAL 130 130 130 VAL VAL A . n A 1 131 TYR 131 131 131 TYR TYR A . n A 1 132 SER 132 132 132 SER SER A . n A 1 133 TYR 133 133 133 TYR TYR A . n A 1 134 ARG 134 134 134 ARG ARG A . n A 1 135 PHE 135 135 135 PHE PHE A . n A 1 136 VAL 136 136 136 VAL VAL A . n A 1 137 TRP 137 137 137 TRP TRP A . n A 1 138 TRP 138 138 138 TRP TRP A . n A 1 139 ALA 139 139 139 ALA ALA A . n A 1 140 ILE 140 140 140 ILE ILE A . n A 1 141 SER 141 141 141 SER SER A . n A 1 142 THR 142 142 142 THR THR A . n A 1 143 ALA 143 143 143 ALA ALA A . n A 1 144 ALA 144 144 144 ALA ALA A . n A 1 145 MET 145 145 145 MET MET A . n A 1 146 LEU 146 146 146 LEU LEU A . n A 1 147 TYR 147 147 147 TYR TYR A . n A 1 148 ILE 148 148 148 ILE ILE A . n A 1 149 LEU 149 149 149 LEU LEU A . n A 1 150 TYR 150 150 150 TYR TYR A . n A 1 151 VAL 151 151 151 VAL VAL A . n A 1 152 LEU 152 152 152 LEU LEU A . n A 1 153 PHE 153 153 153 PHE PHE A . n A 1 154 PHE 154 154 154 PHE PHE A . n A 1 155 GLY 155 155 155 GLY GLY A . n A 1 156 PHE 156 156 156 PHE PHE A . n A 1 157 THR 157 157 157 THR THR A . n A 1 158 SER 158 158 158 SER SER A . n A 1 159 LYS 159 159 159 LYS LYS A . n A 1 160 ALA 160 160 160 ALA ALA A . n A 1 161 GLU 161 161 161 GLU GLU A . n A 1 162 SER 162 162 162 SER SER A . n A 1 163 MET 163 163 163 MET MET A . n A 1 164 ARG 164 164 164 ARG ARG A . n A 1 165 PRO 165 165 165 PRO PRO A . n A 1 166 GLU 166 166 166 GLU GLU A . n A 1 167 VAL 167 167 167 VAL VAL A . n A 1 168 ALA 168 168 168 ALA ALA A . n A 1 169 SER 169 169 169 SER SER A . n A 1 170 THR 170 170 170 THR THR A . n A 1 171 PHE 171 171 171 PHE PHE A . n A 1 172 LYS 172 172 172 LYS LYS A . n A 1 173 VAL 173 173 173 VAL VAL A . n A 1 174 LEU 174 174 174 LEU LEU A . n A 1 175 ARG 175 175 175 ARG ARG A . n A 1 176 ASN 176 176 176 ASN ASN A . n A 1 177 VAL 177 177 177 VAL VAL A . n A 1 178 THR 178 178 178 THR THR A . n A 1 179 VAL 179 179 179 VAL VAL A . n A 1 180 VAL 180 180 180 VAL VAL A . n A 1 181 LEU 181 181 181 LEU LEU A . n A 1 182 TRP 182 182 182 TRP TRP A . n A 1 183 SER 183 183 183 SER SER A . n A 1 184 ALA 184 184 184 ALA ALA A . n A 1 185 TYR 185 185 185 TYR TYR A . n A 1 186 PRO 186 186 186 PRO PRO A . n A 1 187 VAL 187 187 187 VAL VAL A . n A 1 188 VAL 188 188 188 VAL VAL A . n A 1 189 TRP 189 189 189 TRP TRP A . n A 1 190 LEU 190 190 190 LEU LEU A . n A 1 191 ILE 191 191 191 ILE ILE A . n A 1 192 GLY 192 192 192 GLY GLY A . n A 1 193 SER 193 193 193 SER SER A . n A 1 194 GLU 194 194 194 GLU GLU A . n A 1 195 GLY 195 195 195 GLY GLY A . n A 1 196 ALA 196 196 196 ALA ALA A . n A 1 197 GLY 197 197 197 GLY GLY A . n A 1 198 ILE 198 198 198 ILE ILE A . n A 1 199 VAL 199 199 199 VAL VAL A . n A 1 200 PRO 200 200 200 PRO PRO A . n A 1 201 LEU 201 201 201 LEU LEU A . n A 1 202 ASN 202 202 202 ASN ASN A . n A 1 203 ILE 203 203 203 ILE ILE A . n A 1 204 GLU 204 204 204 GLU GLU A . n A 1 205 THR 205 205 205 THR THR A . n A 1 206 LEU 206 206 206 LEU LEU A . n A 1 207 LEU 207 207 207 LEU LEU A . n A 1 208 PHE 208 208 208 PHE PHE A . n A 1 209 MET 209 209 209 MET MET A . n A 1 210 VAL 210 210 210 VAL VAL A . n A 1 211 LEU 211 211 211 LEU LEU A . n A 1 212 ASP 212 212 212 ASP ASP A . n A 1 213 VAL 213 213 213 VAL VAL A . n A 1 214 SER 214 214 214 SER SER A . n A 1 215 ALA 215 215 215 ALA ALA A . n A 1 216 LYS 216 216 216 LYS LYS A . n A 1 217 VAL 217 217 217 VAL VAL A . n A 1 218 GLY 218 218 218 GLY GLY A . n A 1 219 PHE 219 219 219 PHE PHE A . n A 1 220 GLY 220 220 220 GLY GLY A . n A 1 221 LEU 221 221 221 LEU LEU A . n A 1 222 ILE 222 222 222 ILE ILE A . n A 1 223 LEU 223 223 223 LEU LEU A . n A 1 224 LEU 224 224 224 LEU LEU A . n A 1 225 ARG 225 225 225 ARG ARG A . n A 1 226 SER 226 226 ? ? ? A . n A 1 227 ARG 227 227 ? ? ? A . n A 1 228 ALA 228 228 ? ? ? A . n A 1 229 ILE 229 229 ? ? ? A . n A 1 230 PHE 230 230 ? ? ? A . n A 1 231 GLY 231 231 ? ? ? A . n A 1 232 GLU 232 232 ? ? ? A . n A 1 233 ALA 233 233 ? ? ? A . n A 1 234 GLU 234 234 ? ? ? A . n A 1 235 ALA 235 235 ? ? ? A . n A 1 236 PRO 236 236 ? ? ? A . n A 1 237 GLU 237 237 ? ? ? A . n A 1 238 PRO 238 238 ? ? ? A . n A 1 239 SER 239 239 ? ? ? A . n A 1 240 ALA 240 240 ? ? ? A . n A 1 241 GLY 241 241 ? ? ? A . n A 1 242 ASP 242 242 ? ? ? A . n A 1 243 GLY 243 243 ? ? ? A . n A 1 244 ALA 244 244 ? ? ? A . n A 1 245 ALA 245 245 ? ? ? A . n A 1 246 ALA 246 246 ? ? ? A . n A 1 247 THR 247 247 ? ? ? A . n A 1 248 SER 248 248 ? ? ? A . n # 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 1 300 300 RET RET A . C 3 HOH 1 400 400 HOH HOH A . C 3 HOH 2 401 401 HOH HOH A . C 3 HOH 3 402 402 HOH HOH A . C 3 HOH 4 403 403 HOH HOH A . C 3 HOH 5 404 404 HOH HOH A . C 3 HOH 6 405 405 HOH HOH A . C 3 HOH 7 406 406 HOH HOH A . C 3 HOH 8 407 407 HOH HOH A . C 3 HOH 9 408 408 HOH HOH A . C 3 HOH 10 409 409 HOH HOH A . C 3 HOH 11 410 410 HOH HOH A . C 3 HOH 12 411 411 HOH HOH A . C 3 HOH 13 412 412 HOH HOH A . C 3 HOH 14 413 413 HOH HOH A . C 3 HOH 15 414 414 HOH HOH A . C 3 HOH 16 415 415 HOH HOH A . C 3 HOH 17 416 416 HOH HOH A . C 3 HOH 18 417 417 HOH HOH A . C 3 HOH 19 418 418 HOH HOH A . C 3 HOH 20 419 419 HOH HOH A . C 3 HOH 21 420 420 HOH HOH A . C 3 HOH 22 421 421 HOH HOH A . C 3 HOH 23 422 422 HOH HOH A . C 3 HOH 24 423 423 HOH HOH A . C 3 HOH 25 424 424 HOH HOH A . C 3 HOH 26 425 425 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 6840 ? 1 MORE -56 ? 1 'SSA (A^2)' 29080 ? # 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] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 30.8800000000 0.8660254038 -0.5000000000 0.0000000000 53.4857289377 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5000000000 0.8660254038 0.0000000000 -30.8800000000 -0.8660254038 -0.5000000000 0.0000000000 53.4857289377 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # 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 1998-09-16 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_initial_refinement_model 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.8 ? 1 X-PLOR refinement 3.8 ? 2 DENZO 'data reduction' . ? 3 CCP4 'data scaling' . ? 4 X-PLOR phasing 3.8 ? 5 # 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 LEU A 22 ? ? -166.65 -53.18 2 1 VAL A 34 ? ? -68.18 90.28 3 1 THR A 47 ? ? -164.30 -24.17 4 1 LEU A 66 ? ? -152.50 -62.51 5 1 THR A 67 ? ? -12.77 101.83 6 1 MET A 68 ? ? -40.73 170.56 7 1 VAL A 69 ? ? -120.70 -148.12 8 1 PRO A 70 ? ? -56.67 97.78 9 1 PHE A 71 ? ? 62.88 107.80 10 1 GLN A 75 ? ? -154.79 -81.16 11 1 ASN A 76 ? ? -37.94 99.79 12 1 THR A 89 ? ? -147.88 -49.50 13 1 THR A 128 ? ? 60.08 -147.78 14 1 LYS A 129 ? ? -168.29 38.26 15 1 VAL A 130 ? ? -45.90 90.09 16 1 TYR A 131 ? ? 57.79 -10.18 17 1 PHE A 153 ? ? -94.90 35.21 18 1 PHE A 154 ? ? -144.46 -63.21 19 1 SER A 158 ? ? -77.19 22.13 20 1 LYS A 159 ? ? -151.23 -10.96 21 1 GLU A 161 ? ? 174.52 -75.83 22 1 MET A 163 ? ? 65.81 -7.29 23 1 VAL A 167 ? ? -58.95 3.08 24 1 LEU A 190 ? ? -78.92 26.47 25 1 ALA A 196 ? ? -73.29 -105.38 26 1 ILE A 198 ? ? -90.72 -62.86 27 1 PRO A 200 ? ? -42.49 -132.71 28 1 LEU A 224 ? ? -166.34 -34.95 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ARG 7 ? CD ? A ARG 7 CD 2 1 Y 1 A ARG 7 ? NE ? A ARG 7 NE 3 1 Y 1 A ARG 7 ? CZ ? A ARG 7 CZ 4 1 Y 1 A ARG 7 ? NH1 ? A ARG 7 NH1 5 1 Y 1 A ARG 7 ? NH2 ? A ARG 7 NH2 6 1 Y 1 A ARG 225 ? O ? A ARG 225 O # 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 GLN 1 ? A GLN 1 2 1 Y 1 A ALA 2 ? A ALA 2 3 1 Y 1 A GLN 3 ? A GLN 3 4 1 Y 1 A ILE 4 ? A ILE 4 5 1 Y 1 A THR 5 ? A THR 5 6 1 Y 1 A GLY 6 ? A GLY 6 7 1 Y 1 A SER 226 ? A SER 226 8 1 Y 1 A ARG 227 ? A ARG 227 9 1 Y 1 A ALA 228 ? A ALA 228 10 1 Y 1 A ILE 229 ? A ILE 229 11 1 Y 1 A PHE 230 ? A PHE 230 12 1 Y 1 A GLY 231 ? A GLY 231 13 1 Y 1 A GLU 232 ? A GLU 232 14 1 Y 1 A ALA 233 ? A ALA 233 15 1 Y 1 A GLU 234 ? A GLU 234 16 1 Y 1 A ALA 235 ? A ALA 235 17 1 Y 1 A PRO 236 ? A PRO 236 18 1 Y 1 A GLU 237 ? A GLU 237 19 1 Y 1 A PRO 238 ? A PRO 238 20 1 Y 1 A SER 239 ? A SER 239 21 1 Y 1 A ALA 240 ? A ALA 240 22 1 Y 1 A GLY 241 ? A GLY 241 23 1 Y 1 A ASP 242 ? A ASP 242 24 1 Y 1 A GLY 243 ? A GLY 243 25 1 Y 1 A ALA 244 ? A ALA 244 26 1 Y 1 A ALA 245 ? A ALA 245 27 1 Y 1 A ALA 246 ? A ALA 246 28 1 Y 1 A THR 247 ? A THR 247 29 1 Y 1 A SER 248 ? A SER 248 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 RETINAL RET 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2BRD _pdbx_initial_refinement_model.details 'PDB ENTRY 2BRD' #