0.009551 0.005514 0.000000 0.000000 0.011029 0.000000 0.000000 0.000000 0.008764 0.00000 0.00000 0.00000 Sato, H. Takeda, K. Tani, K. Hino, T. Okada, T. Nakasako, M. Kamiya, N. Kouyama, T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 104.700 104.700 114.100 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C46 H96 O11 P2 887.195 PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER DPHPG non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C5 H7 N O3 129.114 n PYROGLUTAMIC ACID L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C20 H28 O 284.436 RETINAL non-polymer C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 55 1251 1256 10.1107/S090744499900503X 10393291 Specific lipid-protein interactions in a novel honeycomb lattice structure of bacteriorhodopsin. 1999 UK J.Mol.Biol. JMOBAK 0070 0022-2836 283 463 A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies 1998 10.2210/pdb1bm1/pdb pdb_00001bm1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 285 1 IMAGE PLATE 1996-11-14 FUJI M x-ray 1 1.012 1.0 BL-18B Photon Factory 1.012 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 26797.381 BACTERIORHODOPSIN 1 nat polymer 284.436 RETINAL 1 syn non-polymer 887.195 PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER 1 syn non-polymer no yes (PCA)AQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQN PIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGF TSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAP EPSAGDGAAATS QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA GDGAAATS A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Halobacterium sample 2242 Halobacterium salinarum JW3 1 3.37 63.47 DATA WERE COLLECTED USING THE WEISSENBERG METHOD 5.2 pH 5.2 database_2 entity_poly pdbx_database_status pdbx_initial_refinement_model struct_conn struct_site repository Initial release Version format compliance Derived calculations Version format compliance Database references Derived calculations Other Polymer sequence Refinement description 1 0 1999-04-27 1 1 2008-03-24 1 2 2011-07-13 2 0 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity_poly.pdbx_seq_one_letter_code_can _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-07-28 REL RET RETINAL DPG PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER 2BRD PDB ENTRY 2BRD PDB experimental model RET 250 2 RET RET 250 A DPG 269 3 DPG DPG 269 A n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A ARG 7 n 7 ARG 7 A PRO 8 n 8 PRO 8 A GLU 9 n 9 GLU 9 A TRP 10 n 10 TRP 10 A ILE 11 n 11 ILE 11 A TRP 12 n 12 TRP 12 A LEU 13 n 13 LEU 13 A ALA 14 n 14 ALA 14 A LEU 15 n 15 LEU 15 A GLY 16 n 16 GLY 16 A THR 17 n 17 THR 17 A ALA 18 n 18 ALA 18 A LEU 19 n 19 LEU 19 A MET 20 n 20 MET 20 A GLY 21 n 21 GLY 21 A LEU 22 n 22 LEU 22 A GLY 23 n 23 GLY 23 A THR 24 n 24 THR 24 A LEU 25 n 25 LEU 25 A TYR 26 n 26 TYR 26 A PHE 27 n 27 PHE 27 A LEU 28 n 28 LEU 28 A VAL 29 n 29 VAL 29 A LYS 30 n 30 LYS 30 A GLY 31 n 31 GLY 31 A MET 32 n 32 MET 32 A GLY 33 n 33 GLY 33 A VAL 34 n 34 VAL 34 A SER 35 n 35 SER 35 A ASP 36 n 36 ASP 36 A PRO 37 n 37 PRO 37 A ASP 38 n 38 ASP 38 A ALA 39 n 39 ALA 39 A LYS 40 n 40 LYS 40 A LYS 41 n 41 LYS 41 A PHE 42 n 42 PHE 42 A TYR 43 n 43 TYR 43 A ALA 44 n 44 ALA 44 A ILE 45 n 45 ILE 45 A THR 46 n 46 THR 46 A THR 47 n 47 THR 47 A LEU 48 n 48 LEU 48 A VAL 49 n 49 VAL 49 A PRO 50 n 50 PRO 50 A ALA 51 n 51 ALA 51 A ILE 52 n 52 ILE 52 A ALA 53 n 53 ALA 53 A PHE 54 n 54 PHE 54 A THR 55 n 55 THR 55 A MET 56 n 56 MET 56 A TYR 57 n 57 TYR 57 A LEU 58 n 58 LEU 58 A SER 59 n 59 SER 59 A MET 60 n 60 MET 60 A LEU 61 n 61 LEU 61 A LEU 62 n 62 LEU 62 A GLY 63 n 63 GLY 63 A TYR 64 n 64 TYR 64 A GLY 65 n 65 GLY 65 A LEU 66 n 66 LEU 66 A THR 67 n 67 THR 67 A MET 68 n 68 MET 68 A VAL 69 n 69 VAL 69 A PRO 70 n 70 PRO 70 A PHE 71 n 71 PHE 71 A GLY 72 n 72 GLY 72 A GLY 73 n 73 GLY 73 A GLU 74 n 74 GLU 74 A GLN 75 n 75 GLN 75 A ASN 76 n 76 ASN 76 A PRO 77 n 77 PRO 77 A ILE 78 n 78 ILE 78 A TYR 79 n 79 TYR 79 A TRP 80 n 80 TRP 80 A ALA 81 n 81 ALA 81 A ARG 82 n 82 ARG 82 A TYR 83 n 83 TYR 83 A ALA 84 n 84 ALA 84 A ASP 85 n 85 ASP 85 A TRP 86 n 86 TRP 86 A LEU 87 n 87 LEU 87 A PHE 88 n 88 PHE 88 A THR 89 n 89 THR 89 A THR 90 n 90 THR 90 A PRO 91 n 91 PRO 91 A LEU 92 n 92 LEU 92 A LEU 93 n 93 LEU 93 A LEU 94 n 94 LEU 94 A LEU 95 n 95 LEU 95 A ASP 96 n 96 ASP 96 A LEU 97 n 97 LEU 97 A ALA 98 n 98 ALA 98 A LEU 99 n 99 LEU 99 A LEU 100 n 100 LEU 100 A VAL 101 n 101 VAL 101 A ASP 102 n 102 ASP 102 A ALA 103 n 103 ALA 103 A ASP 104 n 104 ASP 104 A GLN 105 n 105 GLN 105 A GLY 106 n 106 GLY 106 A THR 107 n 107 THR 107 A ILE 108 n 108 ILE 108 A LEU 109 n 109 LEU 109 A ALA 110 n 110 ALA 110 A LEU 111 n 111 LEU 111 A VAL 112 n 112 VAL 112 A GLY 113 n 113 GLY 113 A ALA 114 n 114 ALA 114 A ASP 115 n 115 ASP 115 A GLY 116 n 116 GLY 116 A ILE 117 n 117 ILE 117 A MET 118 n 118 MET 118 A ILE 119 n 119 ILE 119 A GLY 120 n 120 GLY 120 A THR 121 n 121 THR 121 A GLY 122 n 122 GLY 122 A LEU 123 n 123 LEU 123 A VAL 124 n 124 VAL 124 A GLY 125 n 125 GLY 125 A ALA 126 n 126 ALA 126 A LEU 127 n 127 LEU 127 A THR 128 n 128 THR 128 A LYS 129 n 129 LYS 129 A VAL 130 n 130 VAL 130 A TYR 131 n 131 TYR 131 A SER 132 n 132 SER 132 A TYR 133 n 133 TYR 133 A ARG 134 n 134 ARG 134 A PHE 135 n 135 PHE 135 A VAL 136 n 136 VAL 136 A TRP 137 n 137 TRP 137 A TRP 138 n 138 TRP 138 A ALA 139 n 139 ALA 139 A ILE 140 n 140 ILE 140 A SER 141 n 141 SER 141 A THR 142 n 142 THR 142 A ALA 143 n 143 ALA 143 A ALA 144 n 144 ALA 144 A MET 145 n 145 MET 145 A LEU 146 n 146 LEU 146 A TYR 147 n 147 TYR 147 A ILE 148 n 148 ILE 148 A LEU 149 n 149 LEU 149 A TYR 150 n 150 TYR 150 A VAL 151 n 151 VAL 151 A LEU 152 n 152 LEU 152 A PHE 153 n 153 PHE 153 A PHE 154 n 154 PHE 154 A GLY 155 n 155 GLY 155 A PHE 156 n 156 PHE 156 A THR 157 n 157 THR 157 A SER 158 n 158 SER 158 A LYS 159 n 159 LYS 159 A ALA 160 n 160 ALA 160 A GLU 161 n 161 GLU 161 A SER 162 n 162 SER 162 A MET 163 n 163 MET 163 A ARG 164 n 164 ARG 164 A PRO 165 n 165 PRO 165 A GLU 166 n 166 GLU 166 A VAL 167 n 167 VAL 167 A ALA 168 n 168 ALA 168 A SER 169 n 169 SER 169 A THR 170 n 170 THR 170 A PHE 171 n 171 PHE 171 A LYS 172 n 172 LYS 172 A VAL 173 n 173 VAL 173 A LEU 174 n 174 LEU 174 A ARG 175 n 175 ARG 175 A ASN 176 n 176 ASN 176 A VAL 177 n 177 VAL 177 A THR 178 n 178 THR 178 A VAL 179 n 179 VAL 179 A VAL 180 n 180 VAL 180 A LEU 181 n 181 LEU 181 A TRP 182 n 182 TRP 182 A SER 183 n 183 SER 183 A ALA 184 n 184 ALA 184 A TYR 185 n 185 TYR 185 A PRO 186 n 186 PRO 186 A VAL 187 n 187 VAL 187 A VAL 188 n 188 VAL 188 A TRP 189 n 189 TRP 189 A LEU 190 n 190 LEU 190 A ILE 191 n 191 ILE 191 A GLY 192 n 192 GLY 192 A SER 193 n 193 SER 193 A GLU 194 n 194 GLU 194 A GLY 195 n 195 GLY 195 A ALA 196 n 196 ALA 196 A GLY 197 n 197 GLY 197 A ILE 198 n 198 ILE 198 A VAL 199 n 199 VAL 199 A PRO 200 n 200 PRO 200 A LEU 201 n 201 LEU 201 A ASN 202 n 202 ASN 202 A ILE 203 n 203 ILE 203 A GLU 204 n 204 GLU 204 A THR 205 n 205 THR 205 A LEU 206 n 206 LEU 206 A LEU 207 n 207 LEU 207 A PHE 208 n 208 PHE 208 A MET 209 n 209 MET 209 A VAL 210 n 210 VAL 210 A LEU 211 n 211 LEU 211 A ASP 212 n 212 ASP 212 A VAL 213 n 213 VAL 213 A SER 214 n 214 SER 214 A ALA 215 n 215 ALA 215 A LYS 216 n 216 LYS 216 A VAL 217 n 217 VAL 217 A GLY 218 n 218 GLY 218 A PHE 219 n 219 PHE 219 A GLY 220 n 220 GLY 220 A LEU 221 n 221 LEU 221 A ILE 222 n 222 ILE 222 A LEU 223 n 223 LEU 223 A LEU 224 n 224 LEU 224 A ARG 225 n 225 ARG 225 A SER 226 n 226 SER 226 A ARG 227 n 227 ARG 227 A n 228 228 A n 229 229 A n 230 230 A n 231 231 A n 232 232 A n 233 233 A n 234 234 A n 235 235 A n 236 236 A n 237 237 A n 238 238 A n 239 239 A n 240 240 A n 241 241 A n 242 242 A n 243 243 A n 244 244 A n 245 245 A n 246 246 A n 247 247 A n 248 248 A author_and_software_defined_assembly PISA,PQS 3 trimeric 11090 -87 26690 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_655 -y+1,x-y,z crystal symmetry operation 104.7000000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_665 -x+y+1,-x+1,z crystal symmetry operation 52.3500000000 90.6728597762 0.0000000000 A O VAL 69 A O VAL 69 A N ASN 76 A N ASN 76 1 A C22 DPG 269 C C22 DPG 1 1 N 1 A C23 DPG 269 C C23 DPG 1 1 N 1 A C24 DPG 269 C C24 DPG 1 1 N 1 A C25 DPG 269 C C25 DPG 1 1 N 1 A C26 DPG 269 C C26 DPG 1 1 N 1 A C27 DPG 269 C C27 DPG 1 1 N 1 A C28 DPG 269 C C28 DPG 1 1 N 1 A C29 DPG 269 C C29 DPG 1 1 N 1 A C30 DPG 269 C C30 DPG 1 1 N 1 A PCA 1 A PCA 1 1 Y 1 A ALA 2 A ALA 2 1 Y 1 A GLN 3 A GLN 3 1 Y 1 A ILE 4 A ILE 4 1 Y 1 A THR 5 A THR 5 1 Y 1 A GLY 6 A GLY 6 1 Y 1 A ALA 228 A ALA 228 1 Y 1 A ILE 229 A ILE 229 1 Y 1 A PHE 230 A PHE 230 1 Y 1 A GLY 231 A GLY 231 1 Y 1 A GLU 232 A GLU 232 1 Y 1 A ALA 233 A ALA 233 1 Y 1 A GLU 234 A GLU 234 1 Y 1 A ALA 235 A ALA 235 1 Y 1 A PRO 236 A PRO 236 1 Y 1 A GLU 237 A GLU 237 1 Y 1 A PRO 238 A PRO 238 1 Y 1 A SER 239 A SER 239 1 Y 1 A ALA 240 A ALA 240 1 Y 1 A GLY 241 A GLY 241 1 Y 1 A ASP 242 A ASP 242 1 Y 1 A GLY 243 A GLY 243 1 Y 1 A ALA 244 A ALA 244 1 Y 1 A ALA 245 A ALA 245 1 Y 1 A ALA 246 A ALA 246 1 Y 1 A THR 247 A THR 247 1 Y 1 A SER 248 A SER 248 1 Y 1 A ARG 164 0.275 SIDE CHAIN 1 A VAL 34 -53.56 103.39 1 A PHE 71 178.43 123.11 1 A TYR 79 -116.86 69.63 1 A LEU 100 -66.96 -70.59 1 A ASP 102 -19.63 102.12 1 A LYS 129 -22.93 -77.01 1 A VAL 130 -157.87 -14.52 1 A SER 132 -77.86 34.53 1 A PHE 153 -51.45 -80.93 1 A SER 193 -31.19 -82.67 1 A SER 226 -23.40 124.71 PROTEIN_REP.PARAM TOPHCSDX.PRO RET.PAR RET.TOP DPG.PAR DPG.TOP 0.3110000 0.2600000 0.2600000 3.5 8 3534 10 72.1 RANDOM 1 2 MOLECULAR REPLACEMENT PDB ENTRY 2BRD 3.5 8 0 1787 70 0 1717 0.009 1.359 20.07 1.301 22 3.5 50 1BM1 4000 2 0.1030000 0.1030000 1 7.4 80.2 0.1590000 3.5 3.65 0.1590000 1 4.8 45.2 model building X-PLOR 3.851 refinement X-PLOR 3.851 data reduction WEIS data scaling CCP4 (SCALA) phasing X-PLOR 3.851 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE 1 N N 2 N N 3 N N A GLU 9 A GLU 9 HELX_P A GLY 31 A GLY 31 1 A 23 A ASP 38 A ASP 38 HELX_P A LEU 62 A LEU 62 1 B 25 A ALA 81 A ALA 81 HELX_P A LEU 100 A LEU 100 1 C 20 A GLN 105 A GLN 105 HELX_P A LEU 127 A LEU 127 1 D 23 A ARG 134 A ARG 134 HELX_P A GLY 155 A GLY 155 1 E 22 A GLU 166 A GLU 166 HELX_P A ILE 191 A ILE 191 1 F 26 A ASN 202 A ASN 202 HELX_P A LEU 223 A LEU 223 1 G 22 covale 1.526 one A LYS 216 A NZ LYS 216 1_555 A RET 250 B C15 RET 1_555 PHOTORECEPTOR PROTON PUMP, MEMBRANE PROTEIN, RETINAL PROTEIN, PHOTORECEPTOR BACR_HALN1 UNP 1 14 P02945 14 253 1BM1 2 248 P02945 A 1 2 248 2 anti-parallel A LEU 66 A LEU 66 A PHE 71 A PHE 71 A GLU 74 A GLU 74 A TYR 79 A TYR 79 BINDING SITE FOR RESIDUE RET A 250 A RET 250 Software 9 BINDING SITE FOR RESIDUE DPG A 269 A DPG 269 Software 13 A TRP 86 A TRP 86 9 1_555 A THR 89 A THR 89 9 1_555 A LEU 93 A LEU 93 9 1_555 A MET 118 A MET 118 9 1_555 A SER 141 A SER 141 9 1_555 A TRP 182 A TRP 182 9 1_555 A TRP 189 A TRP 189 9 1_555 A ASP 212 A ASP 212 9 1_555 A LYS 216 A LYS 216 9 1_555 A LEU 28 A LEU 28 13 1_555 A GLY 31 A GLY 31 13 1_555 A MET 32 A MET 32 13 1_555 A VAL 34 A VAL 34 13 1_555 A SER 35 A SER 35 13 1_555 A LYS 40 A LYS 40 13 1_555 A TYR 43 A TYR 43 13 1_555 A ALA 44 A ALA 44 13 1_555 A THR 47 A THR 47 13 1_555 A ALA 110 A ALA 110 13 3_665 A ALA 143 A ALA 143 13 3_665 A TYR 147 A TYR 147 13 3_665 A TYR 150 A TYR 150 13 3_665 177 P 6 2 2