0.016404 0.009471 0.000000 0.000000 0.018942 0.000000 0.000000 0.000000 0.009093 0.00000 0.00000 0.00000 Royant, A. Edman, K. Ursby, T. Pebay-Peyroula, E. Landau, E.M. Neutze, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 60.960 60.960 109.970 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 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 H2 O 18.015 WATER non-polymer 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 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 UK Nature NATUAS 0006 0028-0836 406 645 10.1038/35020599 10949307 Helix Deformation is Coupled to Vectorial Proton Transport in Bacteriorhodopsin'S Photocycle 2000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 110.0 1 CCD 1999-10-15 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.934 1.0 ID14-1 ESRF 0.934 SYNCHROTRON ESRF BEAMLINE ID14-1 CONFORMER B IS GROUND STATE, CONFORMER A IS THE L-STATE FORM. 24990.535 BACTERIORHODOPSIN, GROUND STATE 1 nat polymer 284.436 RETINAL 1 syn non-polymer 18.015 water 30 nat water no no TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYA DWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYA DWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE 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 sample 2242 HALOBACTERIUM SALINARIUM S9 1 2.36 48 5.60 PROTEIN FROM THE PURPLE MEMBRANE WAS RESOLVED IN OCTYL GLUC, pH 5.60 repository Initial release Version format compliance Version format compliance 1 0 2000-08-19 1 1 2011-05-08 1 2 2011-07-13 X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE PDBE Y PDBE 2000-04-04 REL RET RETINAL HOH water ALTERNATE CONFORMER B GROUND STATE MODEL FROM 1QHJ ALTERNATE CONFORMER A L-STATE MODEL RET 300 2 RET RET 300 A HOH 2001 3 HOH HOH 2001 A HOH 2002 3 HOH HOH 2002 A HOH 2003 3 HOH HOH 2003 A HOH 2004 3 HOH HOH 2004 A HOH 2005 3 HOH HOH 2005 A HOH 2006 3 HOH HOH 2006 A HOH 2007 3 HOH HOH 2007 A HOH 2008 3 HOH HOH 2008 A HOH 2009 3 HOH HOH 2009 A HOH 2010 3 HOH HOH 2010 A HOH 2011 3 HOH HOH 2011 A HOH 2012 3 HOH HOH 2012 A HOH 2013 3 HOH HOH 2013 A HOH 2014 3 HOH HOH 2014 A HOH 2015 3 HOH HOH 2015 A HOH 2016 3 HOH HOH 2016 A HOH 2017 3 HOH HOH 2017 A HOH 2018 3 HOH HOH 2018 A HOH 2019 3 HOH HOH 2019 A HOH 2020 3 HOH HOH 2020 A HOH 2021 3 HOH HOH 2021 A HOH 2022 3 HOH HOH 2022 A HOH 2023 3 HOH HOH 2023 A HOH 2024 3 HOH HOH 2024 A HOH 2025 3 HOH HOH 2025 A HOH 2026 3 HOH HOH 2026 A HOH 2027 3 HOH HOH 2027 A HOH 2028 3 HOH HOH 2028 A HOH 2029 3 HOH HOH 2029 A HOH 2030 3 HOH HOH 2030 A THR 5 n 1 THR 5 A GLY 6 n 2 GLY 6 A ARG 7 n 3 ARG 7 A PRO 8 n 4 PRO 8 A GLU 9 n 5 GLU 9 A TRP 10 n 6 TRP 10 A ILE 11 n 7 ILE 11 A TRP 12 n 8 TRP 12 A LEU 13 n 9 LEU 13 A ALA 14 n 10 ALA 14 A LEU 15 n 11 LEU 15 A GLY 16 n 12 GLY 16 A THR 17 n 13 THR 17 A ALA 18 n 14 ALA 18 A LEU 19 n 15 LEU 19 A MET 20 n 16 MET 20 A GLY 21 n 17 GLY 21 A LEU 22 n 18 LEU 22 A GLY 23 n 19 GLY 23 A THR 24 n 20 THR 24 A LEU 25 n 21 LEU 25 A TYR 26 n 22 TYR 26 A PHE 27 n 23 PHE 27 A LEU 28 n 24 LEU 28 A VAL 29 n 25 VAL 29 A LYS 30 n 26 LYS 30 A GLY 31 n 27 GLY 31 A MET 32 n 28 MET 32 A GLY 33 n 29 GLY 33 A VAL 34 n 30 VAL 34 A SER 35 n 31 SER 35 A ASP 36 n 32 ASP 36 A PRO 37 n 33 PRO 37 A ASP 38 n 34 ASP 38 A ALA 39 n 35 ALA 39 A LYS 40 n 36 LYS 40 A LYS 41 n 37 LYS 41 A PHE 42 n 38 PHE 42 A TYR 43 n 39 TYR 43 A ALA 44 n 40 ALA 44 A ILE 45 n 41 ILE 45 A THR 46 n 42 THR 46 A THR 47 n 43 THR 47 A LEU 48 n 44 LEU 48 A VAL 49 n 45 VAL 49 A PRO 50 n 46 PRO 50 A ALA 51 n 47 ALA 51 A ILE 52 n 48 ILE 52 A ALA 53 n 49 ALA 53 A PHE 54 n 50 PHE 54 A THR 55 n 51 THR 55 A MET 56 n 52 MET 56 A TYR 57 n 53 TYR 57 A LEU 58 n 54 LEU 58 A SER 59 n 55 SER 59 A MET 60 n 56 MET 60 A LEU 61 n 57 LEU 61 A LEU 62 n 58 LEU 62 A GLY 63 n 59 GLY 63 A TYR 64 n 60 TYR 64 A GLY 65 n 61 GLY 65 A LEU 66 n 62 LEU 66 A THR 67 n 63 THR 67 A MET 68 n 64 MET 68 A VAL 69 n 65 VAL 69 A PRO 70 n 66 PRO 70 A PHE 71 n 67 PHE 71 A GLY 72 n 68 GLY 72 A GLY 73 n 69 GLY 73 A GLU 74 n 70 GLU 74 A GLN 75 n 71 GLN 75 A ASN 76 n 72 ASN 76 A PRO 77 n 73 PRO 77 A ILE 78 n 74 ILE 78 A TYR 79 n 75 TYR 79 A TRP 80 n 76 TRP 80 A ALA 81 n 77 ALA 81 A ARG 82 n 78 ARG 82 A TYR 83 n 79 TYR 83 A ALA 84 n 80 ALA 84 A ASP 85 n 81 ASP 85 A TRP 86 n 82 TRP 86 A LEU 87 n 83 LEU 87 A PHE 88 n 84 PHE 88 A THR 89 n 85 THR 89 A THR 90 n 86 THR 90 A PRO 91 n 87 PRO 91 A LEU 92 n 88 LEU 92 A LEU 93 n 89 LEU 93 A LEU 94 n 90 LEU 94 A LEU 95 n 91 LEU 95 A ASP 96 n 92 ASP 96 A LEU 97 n 93 LEU 97 A ALA 98 n 94 ALA 98 A LEU 99 n 95 LEU 99 A LEU 100 n 96 LEU 100 A VAL 101 n 97 VAL 101 A ASP 102 n 98 ASP 102 A ALA 103 n 99 ALA 103 A ASP 104 n 100 ASP 104 A GLN 105 n 101 GLN 105 A GLY 106 n 102 GLY 106 A THR 107 n 103 THR 107 A ILE 108 n 104 ILE 108 A LEU 109 n 105 LEU 109 A ALA 110 n 106 ALA 110 A LEU 111 n 107 LEU 111 A VAL 112 n 108 VAL 112 A GLY 113 n 109 GLY 113 A ALA 114 n 110 ALA 114 A ASP 115 n 111 ASP 115 A GLY 116 n 112 GLY 116 A ILE 117 n 113 ILE 117 A MET 118 n 114 MET 118 A ILE 119 n 115 ILE 119 A GLY 120 n 116 GLY 120 A THR 121 n 117 THR 121 A GLY 122 n 118 GLY 122 A LEU 123 n 119 LEU 123 A VAL 124 n 120 VAL 124 A GLY 125 n 121 GLY 125 A ALA 126 n 122 ALA 126 A LEU 127 n 123 LEU 127 A THR 128 n 124 THR 128 A LYS 129 n 125 LYS 129 A VAL 130 n 126 VAL 130 A TYR 131 n 127 TYR 131 A SER 132 n 128 SER 132 A TYR 133 n 129 TYR 133 A ARG 134 n 130 ARG 134 A PHE 135 n 131 PHE 135 A VAL 136 n 132 VAL 136 A TRP 137 n 133 TRP 137 A TRP 138 n 134 TRP 138 A ALA 139 n 135 ALA 139 A ILE 140 n 136 ILE 140 A SER 141 n 137 SER 141 A THR 142 n 138 THR 142 A ALA 143 n 139 ALA 143 A ALA 144 n 140 ALA 144 A MET 145 n 141 MET 145 A LEU 146 n 142 LEU 146 A TYR 147 n 143 TYR 147 A ILE 148 n 144 ILE 148 A LEU 149 n 145 LEU 149 A TYR 150 n 146 TYR 150 A VAL 151 n 147 VAL 151 A LEU 152 n 148 LEU 152 A PHE 153 n 149 PHE 153 A PHE 154 n 150 PHE 154 A GLY 155 n 151 GLY 155 A PHE 156 n 152 PHE 156 A THR 157 n 153 THR 157 A SER 158 n 154 SER 158 A LYS 159 n 155 LYS 159 A ALA 160 n 156 ALA 160 A GLU 161 n 157 GLU 161 A SER 162 n 158 SER 162 A MET 163 n 159 MET 163 A ARG 164 n 160 ARG 164 A PRO 165 n 161 PRO 165 A GLU 166 n 162 GLU 166 A VAL 167 n 163 VAL 167 A ALA 168 n 164 ALA 168 A SER 169 n 165 SER 169 A THR 170 n 166 THR 170 A PHE 171 n 167 PHE 171 A LYS 172 n 168 LYS 172 A VAL 173 n 169 VAL 173 A LEU 174 n 170 LEU 174 A ARG 175 n 171 ARG 175 A ASN 176 n 172 ASN 176 A VAL 177 n 173 VAL 177 A THR 178 n 174 THR 178 A VAL 179 n 175 VAL 179 A VAL 180 n 176 VAL 180 A LEU 181 n 177 LEU 181 A TRP 182 n 178 TRP 182 A SER 183 n 179 SER 183 A ALA 184 n 180 ALA 184 A TYR 185 n 181 TYR 185 A PRO 186 n 182 PRO 186 A VAL 187 n 183 VAL 187 A VAL 188 n 184 VAL 188 A TRP 189 n 185 TRP 189 A LEU 190 n 186 LEU 190 A ILE 191 n 187 ILE 191 A GLY 192 n 188 GLY 192 A SER 193 n 189 SER 193 A GLU 194 n 190 GLU 194 A GLY 195 n 191 GLY 195 A ALA 196 n 192 ALA 196 A GLY 197 n 193 GLY 197 A ILE 198 n 194 ILE 198 A VAL 199 n 195 VAL 199 A PRO 200 n 196 PRO 200 A LEU 201 n 197 LEU 201 A ASN 202 n 198 ASN 202 A ILE 203 n 199 ILE 203 A GLU 204 n 200 GLU 204 A THR 205 n 201 THR 205 A LEU 206 n 202 LEU 206 A LEU 207 n 203 LEU 207 A PHE 208 n 204 PHE 208 A MET 209 n 205 MET 209 A VAL 210 n 206 VAL 210 A LEU 211 n 207 LEU 211 A ASP 212 n 208 ASP 212 A VAL 213 n 209 VAL 213 A SER 214 n 210 SER 214 A ALA 215 n 211 ALA 215 A LYS 216 n 212 LYS 216 A VAL 217 n 213 VAL 217 A GLY 218 n 214 GLY 218 A PHE 219 n 215 PHE 219 A GLY 220 n 216 GLY 220 A LEU 221 n 217 LEU 221 A ILE 222 n 218 ILE 222 A LEU 223 n 219 LEU 223 A LEU 224 n 220 LEU 224 A ARG 225 n 221 ARG 225 A SER 226 n 222 SER 226 A ARG 227 n 223 ARG 227 A ALA 228 n 224 ALA 228 A ILE 229 n 225 ILE 229 A PHE 230 n 226 PHE 230 A GLY 231 n 227 GLY 231 A GLU 232 n 228 GLU 232 A author_and_software_defined_assembly PISA 3 trimeric 6230 -50.93 26190 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 3_565 -x+y,-x+1,z crystal symmetry operation -30.4800000000 52.7929086147 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_665 -y+1,x-y+1,z crystal symmetry operation 30.4800000000 52.7929086147 0.0000000000 A N PHE 71 A N PHE 67 A O GLU 74 A O GLU 70 1 A CG MET 163 A CG MET 159 1 Y 1 A SD MET 163 A SD MET 159 1 Y 1 A CE MET 163 A CE MET 159 1 Y 1 A CG ARG 227 A CG ARG 223 1 Y 1 A CD ARG 227 A CD ARG 223 1 Y 1 A NE ARG 227 A NE ARG 223 1 Y 1 A CZ ARG 227 A CZ ARG 223 1 Y 1 A NH1 ARG 227 A NH1 ARG 223 1 Y 1 A NH2 ARG 227 A NH2 ARG 223 1 Y 1 A CG GLU 232 A CG GLU 228 1 Y 1 A CD GLU 232 A CD GLU 228 1 Y 1 A OE1 GLU 232 A OE1 GLU 228 1 Y 1 A OE2 GLU 232 A OE2 GLU 228 1 Y 1 A ARG 7 B -155.47 -71.22 1 A PHE 71 B -177.53 149.62 1 A PHE 156 A -129.32 -61.80 1 A PHE 156 B -127.29 -64.70 1 A LYS 216 B -107.55 -62.53 1 A VAL 217 A -122.08 -56.19 PROTEIN_REP.PARAM PROTEIN.TOP WATER_REP.PARAM WATER.TOP RETFIN-CIS.PAR RETFIN.TOP 40.0 -3.96 -0.40 0.00 -3.96 0.00 7.91 THE COORDINATE FILE CONTAINS 2 MODELS CHAINS A AND B, ONLY A WAS REFINED, B WAS FIXED DURING THE WHOLE REFINEMENT. THE NUMBER OF ATOMS USED IN THE REFINEMENT REFERES TO CHAIN A. FREE R VALUE TEST SET SAME AS PREVIOUS REFINEMENTS 1QHJ, 1QKP, 1QKO 0.288 0.012 0.265 0.265 2.1 30.5 593 12912 4.6 95.4 RANDOM 2443186 1 RESTRAINED THROUGHOUT 0.0 OTHER FLAT MODEL 75.56 0.404 0.35 0.32 5.00 0.23 0.31 2.1 30.5 30 1802 20 0 1752 0.008 1.1 18.7 0.77 0.286 0.031 0.289 2.23 87 2111 6 4.0 98.9 19.4 2.100 30.500 1E0P 13088 0.06300 1 9.0000 5.600 96.6 2.10 2.21 1.400 0.52100 1 5.80 99.2 refinement CNS 1.0 data reduction DENZO data scaling SCALA data scaling SCALEPACK phasing CNS 1.0 BACTERIORHODOPSIN, GROUND STATE L intermediate of bacteriorhodopsin 1 N N 2 N N 3 N N A GLU 9 A GLU 5 HELX_P A GLY 31 A GLY 27 1 1 23 A MET 32 A MET 28 HELX_P A VAL 34 A VAL 30 5 2 3 A ASP 36 A ASP 32 HELX_P A LEU 62 A LEU 58 1 3 27 A TYR 79 A TYR 75 HELX_P A ASP 102 A ASP 98 1 4 24 A ASP 104 A ASP 100 HELX_P A THR 128 A THR 124 1 5 25 A VAL 130 A VAL 126 HELX_P A GLY 155 A GLY 151 1 6 26 A PHE 156 A PHE 152 HELX_P A GLU 161 A GLU 157 1 7 6 A ARG 164 A ARG 160 HELX_P A GLY 192 A GLY 188 1 8 29 A PRO 200 A PRO 196 HELX_P A VAL 217 A VAL 213 1 9 18 A VAL 217 A VAL 213 HELX_P A LEU 224 A LEU 220 1 10 8 A ARG 225 A ARG 221 HELX_P A PHE 230 A PHE 226 5 11 6 covale 1.308 B B A LYS 216 A NZ LYS 212 1_555 A RET 300 B C15 RET 1_555 covale 1.283 A A A LYS 216 A NZ LYS 212 1_555 A RET 300 B C15 RET 1_555 TRANSPORT TRANSPORT, ION TRANSPORT, PHOTORECEPTOR, TRANSMEMBRANE, RETINAL PROTEIN HYDROGEN ION TRANSPORT BACR_HALHA UNP 1 P02945 18 245 1E0P 5 232 P02945 A 1 1 228 2 anti-parallel A THR 67 A THR 63 A PHE 71 A PHE 67 A GLU 74 A GLU 70 A ILE 78 A ILE 74 BINDING SITE FOR RESIDUE RET A 300 Software 16 A TRP 86 A TRP 82 16 1_555 A THR 89 A THR 85 16 1_555 A THR 90 A THR 86 16 1_555 A LEU 93 A LEU 89 16 1_555 A MET 118 A MET 114 16 1_555 A GLY 122 A GLY 118 16 1_555 A TRP 138 A TRP 134 16 1_555 A SER 141 A SER 137 16 1_555 A THR 142 A THR 138 16 1_555 A TRP 182 A TRP 178 16 1_555 A TYR 185 A TYR 181 16 1_555 A PRO 186 A PRO 182 16 1_555 A TRP 189 A TRP 185 16 1_555 A ASP 212 A ASP 208 16 1_555 A ALA 215 A ALA 211 16 1_555 A LYS 216 A LYS 212 16 1_555 173 P 63