1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Marvin, D.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE 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 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 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 N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N O N 21 N O N 22 N O N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N N N 31 S C N 32 N C N 33 N O N 34 N C N 35 N C N 36 N C N 37 N O N 38 N N N 39 N O N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N N N 51 S C N 52 N C N 53 N O N 54 N C N 55 N C N 56 N C N 57 N O N 58 N O N 59 N O N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N N N 70 N C N 71 N C N 72 N O N 73 N O N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N N N 80 S C N 81 N C N 82 N O N 83 S C N 84 N C N 85 N C N 86 N C N 87 N O N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N N N 102 S C N 103 N C N 104 N O N 105 N C N 106 N C N 107 N C N 108 N C N 109 N O N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N N N 124 S C N 125 N C N 126 N O N 127 N C N 128 N C N 129 N C N 130 N C N 131 N N N 132 N O N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N N N 149 S C N 150 N C N 151 N O N 152 N C N 153 N C N 154 N S N 155 N C N 156 N O N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N N N 169 S C N 170 N C N 171 N O N 172 N C Y 173 N C Y 174 N C Y 175 N C Y 176 N C Y 177 N C Y 178 N C N 179 N O N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N N N 192 S C N 193 N C N 194 N O N 195 N C N 196 N C N 197 N C N 198 N O N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N N N 209 S C N 210 N C N 211 N O N 212 N C N 213 N O N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N N N 223 S C N 224 N C N 225 N O N 226 R C N 227 N O N 228 N C N 229 N O N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N N N 240 S C N 241 N C N 242 N O N 243 N C Y 244 N C Y 245 N C Y 246 N C Y 247 N N Y 248 N C Y 249 N C Y 250 N C Y 251 N C Y 252 N C N 253 N O N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N N N 267 S C N 268 N C N 269 N O N 270 N C Y 271 N C Y 272 N C Y 273 N C Y 274 N C Y 275 N C Y 276 N C N 277 N O N 278 N O N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N C N 296 N C N 297 N O N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N doub N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N doub N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing Y 170 N doub Y 171 N sing Y 172 N sing N 173 N sing Y 174 N doub N 175 N sing Y 176 N doub N 177 N sing Y 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N doub N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N doub N 235 N sing N 236 N sing N 237 N sing N 238 N sing Y 239 N doub Y 240 N sing Y 241 N sing N 242 N sing Y 243 N doub Y 244 N sing Y 245 N sing N 246 N sing Y 247 N sing Y 248 N doub N 249 N sing Y 250 N doub N 251 N sing Y 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing Y 267 N doub Y 268 N sing Y 269 N sing N 270 N sing Y 271 N doub N 272 N sing Y 273 N doub N 274 N sing Y 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N doub N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing UK Int.J.Biol.Macromol. IJBMDR 0708 0141-8130 12 125 138 10.1016/0141-8130(90)90064-H 2078529 Model-building studies of Inovirus: genetic variations on a geometric theme. 1990 UK Int.J.Biol.Macromol. IJBMDR 0708 0141-8130 11 159 Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions 1989 II J.Biosci. JOBSDN 1073 0250-4774 8 799 Filamentous Bacterial Viruses 1985 Plenum Press, New York Structural Molecular Biology 2027 0-306-40982-8 3 X-Ray Fiber Diffraction 1982 UK Nature NATUAS 0006 0028-0836 289 814 Structure of the Protein and DNA in Fd Filamentous Bacterial Virus 1981 UK J.Mol.Biol. JMOBAK 0070 0022-2836 88 581 Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class I (Fd, If1, Ike) Virion 1974 1 2 3 10.2210/pdb1ifd/pdb pdb_00001ifd 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 1 1.0 5244.000 INOVIRUS 1 man polymer no no AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS 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 Inovirus Enterobacteria phage M13 sample 10864 Enterobacteria phage fd BACTERIA M13 chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1994-07-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.type Y BNL 1992-02-16 REL INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS I INCLUDES STRAINS FD, IF1 AND IKE. CLASS II INCLUDES STRAINS PF1 AND XF. STRAIN FD BELONGS TO THE FF GROUP WITHIN CLASS I. THE MEMBERS OF THE FF GROUP HAVE VIRTUALLY IDENTICAL COAT PROTEIN SEQUENCES AND ONLY SLIGHTLY DIFFERENT GENOME SEQUENCES. OTHER COMMONLY STUDIED FF STRAINS ARE F1, WHICH HAS THE SAME COAT PROTEIN SEQUENCE AS FD; AND M13, WHICH HAS AN ASP TO ASN EXCHANGE AT POSITION 12. THE COORDINATES OF THE M13 MODEL CAN BE DERIVED BY SUBSTITUTING ASN 12 FOR ASP 12 IN THE FD MODEL. MEMBERS OF THE FF GROUP GROW IN ESCHERICHIA COLI BACTERIA THAT CARRY THE F-FACTOR GENES. SOME OF THESE GENES ARE REQUIRED TO GENERATE THE F-PILI, WHICH ARE PROTEIN APPENDAGES THAT PROTRUDE FROM THE SURFACE OF THE BACTERIA AND ARE NECESSARY FOR ADSORPTION OF FD AS THE FIRST STEP IN INFECTION AND GROWTH. 5 no 1 55 16.000000 -33.230000 ALA 1 n 1 ALA 1 A GLU 2 n 2 GLU 2 A GLY 3 n 3 GLY 3 A ASP 4 n 4 ASP 4 A ASP 5 n 5 ASP 5 A PRO 6 n 6 PRO 6 A ALA 7 n 7 ALA 7 A LYS 8 n 8 LYS 8 A ALA 9 n 9 ALA 9 A ALA 10 n 10 ALA 10 A PHE 11 n 11 PHE 11 A ASP 12 n 12 ASP 12 A SER 13 n 13 SER 13 A LEU 14 n 14 LEU 14 A GLN 15 n 15 GLN 15 A ALA 16 n 16 ALA 16 A SER 17 n 17 SER 17 A ALA 18 n 18 ALA 18 A THR 19 n 19 THR 19 A GLU 20 n 20 GLU 20 A TYR 21 n 21 TYR 21 A ILE 22 n 22 ILE 22 A GLY 23 n 23 GLY 23 A TYR 24 n 24 TYR 24 A ALA 25 n 25 ALA 25 A TRP 26 n 26 TRP 26 A ALA 27 n 27 ALA 27 A MET 28 n 28 MET 28 A VAL 29 n 29 VAL 29 A VAL 30 n 30 VAL 30 A VAL 31 n 31 VAL 31 A ILE 32 n 32 ILE 32 A VAL 33 n 33 VAL 33 A GLY 34 n 34 GLY 34 A ALA 35 n 35 ALA 35 A THR 36 n 36 THR 36 A ILE 37 n 37 ILE 37 A GLY 38 n 38 GLY 38 A ILE 39 n 39 ILE 39 A LYS 40 n 40 LYS 40 A LEU 41 n 41 LEU 41 A PHE 42 n 42 PHE 42 A LYS 43 n 43 LYS 43 A LYS 44 n 44 LYS 44 A PHE 45 n 45 PHE 45 A THR 46 n 46 THR 46 A SER 47 n 47 SER 47 A LYS 48 n 48 LYS 48 A ALA 49 n 49 ALA 49 A SER 50 n 50 SER 50 A representative helical assembly 55 helical helical asymmetric unit 1 monomeric helical asymmetric unit, std helical frame 1 monomeric 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 1_555 x,y,z identity operation 0.00000 0.00000 0.00000 -0.97092575 -0.23938084 0.00000000 0.23938084 -0.97092575 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -80.00000 -0.52769727 0.84943251 0.00000000 -0.84943251 -0.52769727 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -80.00000 0.64479090 0.76435901 0.00000000 -0.76435901 0.64479090 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -80.00000 0.92619996 -0.37703267 0.00000000 0.37703267 0.92619996 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -80.00000 -0.07236785 -0.99737801 0.00000000 0.99737801 -0.07236785 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -80.00000 -0.68097653 -0.73230524 0.00000000 0.73230524 -0.68097653 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -64.00000 -0.90689699 0.42135241 0.00000000 -0.42135241 -0.90689699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -64.00000 0.12048337 0.99271535 0.00000000 -0.99271535 0.12048337 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -64.00000 0.98135981 0.19217942 0.00000000 -0.19217942 0.98135981 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -64.00000 0.48603035 -0.87394193 0.00000000 0.87394193 0.48603035 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -64.00000 -0.16831734 -0.98573286 0.00000000 0.98573286 -0.16831734 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -48.00000 -0.98950058 -0.14452890 0.00000000 0.14452890 -0.98950058 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -48.00000 -0.44322765 0.89640909 0.00000000 -0.89640909 -0.44322765 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -48.00000 0.71557083 0.69854019 0.00000000 -0.69854019 0.71557083 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -48.00000 0.88547474 -0.46468751 0.00000000 0.46468751 0.88547474 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -48.00000 0.39938920 -0.91678147 0.00000000 0.91678147 0.39938920 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -32.00000 -0.74849294 -0.66314276 0.00000000 0.66314276 -0.74849294 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -32.00000 -0.86198328 0.50693671 0.00000000 -0.50693671 -0.86198328 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -32.00000 0.21575798 0.97644687 0.00000000 -0.97644687 0.21575798 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -32.00000 0.99532904 0.09654065 0.00000000 -0.09654065 0.99532904 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -32.00000 0.83647750 -0.54800128 0.00000000 0.54800128 0.83647750 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -16.00000 -0.26269442 -0.96487908 0.00000000 0.96487908 -0.26269442 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -16.00000 -0.99883158 -0.04832679 0.00000000 0.04832679 -0.99883158 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -16.00000 -0.35461744 0.93501148 0.00000000 -0.93501148 -0.35461744 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -16.00000 0.77966595 0.62619567 0.00000000 -0.62619567 0.77966595 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 -16.00000 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 1_555 x,y,z identity operation 0.00000 0.00000 0.00000 0.30901699 -0.95105652 0.00000000 0.95105652 0.30901699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 0.00000 -0.80901699 -0.58778525 0.00000000 0.58778525 -0.80901699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 0.00000 -0.80901699 0.58778525 0.00000000 -0.58778525 -0.80901699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 0.00000 0.30901699 0.95105652 0.00000000 -0.95105652 0.30901699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 0.00000 0.83647750 0.54800128 0.00000000 -0.54800128 0.83647750 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 16.00000 0.77966595 -0.62619567 0.00000000 0.62619567 0.77966595 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 16.00000 -0.35461744 -0.93501148 0.00000000 0.93501148 -0.35461744 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 16.00000 -0.99883158 0.04832679 0.00000000 -0.04832679 -0.99883158 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 16.00000 -0.26269442 0.96487908 0.00000000 -0.96487908 -0.26269442 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 16.00000 0.39938920 0.91678147 0.00000000 -0.91678147 0.39938920 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 32.00000 0.99532904 -0.09654065 0.00000000 0.09654065 0.99532904 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 32.00000 0.21575798 -0.97644687 0.00000000 0.97644687 0.21575798 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 32.00000 -0.86198328 -0.50693671 0.00000000 0.50693671 -0.86198328 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 32.00000 -0.74849294 0.66314276 0.00000000 -0.66314276 -0.74849294 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 32.00000 -0.16831734 0.98573286 0.00000000 -0.98573286 -0.16831734 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 48.00000 0.88547474 0.46468751 0.00000000 -0.46468751 0.88547474 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 48.00000 0.71557083 -0.69854019 0.00000000 0.69854019 0.71557083 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 48.00000 -0.44322765 -0.89640909 0.00000000 0.89640909 -0.44322765 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 48.00000 -0.98950058 0.14452890 0.00000000 -0.14452890 -0.98950058 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 48.00000 -0.68097653 0.73230524 0.00000000 -0.73230524 -0.68097653 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 64.00000 0.48603035 0.87394193 0.00000000 -0.87394193 0.48603035 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 64.00000 0.98135981 -0.19217942 0.00000000 0.19217942 0.98135981 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 64.00000 0.12048337 -0.99271535 0.00000000 0.99271535 0.12048337 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 64.00000 -0.90689699 -0.42135241 0.00000000 0.42135241 -0.90689699 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 64.00000 -0.97092575 0.23938084 0.00000000 -0.23938084 -0.97092575 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 80.00000 -0.07236785 0.99737801 0.00000000 -0.99737801 -0.07236785 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 80.00000 0.92619996 0.37703267 0.00000000 -0.37703267 0.92619996 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 80.00000 0.64479090 -0.76435901 0.00000000 0.76435901 0.64479090 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 80.00000 -0.52769727 -0.84943251 0.00000000 0.84943251 -0.52769727 0.00000000 0.00000000 0.00000000 1.00000000 helical symmetry operation 0.00000 0.00000 80.00000 1 A A NE1 CE2 TRP TRP 26 26 -0.093 0.013 1.371 1.278 N THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE. THE DNA IS ABOUT 12% BY WEIGHT OF THE FD VIRION, AND PROBABLY HAS NO WELL-DEFINED STRUCTURE OTHER THAN THAT IMPOSED BY ITS SINGLE-STRANDED CIRCULAR TOPOLOGY: TWO OPPOSITELY DIRECTED DNA CHAINS RUN ALONG THE LENGTH OF THE VIRION TO COMPLETE THE CIRCLE. THE DNA MAY BE A LEFT-HANDED HELIX (SEE JRNL REFERENCE). THE TWO ENDS OF THE VIRION ARE CAPPED BY A FEW COPIES OF MINOR COAT PROTEINS, WHOSE STRUCTURE IS NOT KNOWN. THESE PROTEINS INTERACT WITH THE ENDS OF THE MAJOR COAT PROTEIN ASSEMBLY. THE N-TERMINAL END OF INOVIRUS HAS AN OPEN CUP SHAPE, AND THE C-TERMINAL END IS THE COMPLEMENT OF THIS, A POINTED ARROWHEAD SHAPE (SEE REFERENCES 1 AND 2). THE TWO ENDS OF THE FD ASSEMBLY CAN BE GENERATED BY OPERATING REPEATEDLY (SAY 10 - 20 TIMES) ON THE HELIX UNIT CELL CONTENTS (THE GROUP OF 5 ASYMMETRIC UNITS) WITH THE HELIX PARAMETERS, GIVING TWO DIFFERENT ENDS CONNECTED BY A SHORT SHAFT. SINCE THE MAJOR COAT PROTEIN SUBUNITS AT THE ENDS HAVE FEWER NEIGHBORS THAN THOSE IN THE CENTER OF THE ASSEMBLY, THEIR CONFORMATIONS ARE LESS CONSTRAINED AND MAY BE MODIFIED BY INTERACTION WITH THE MINOR COAT PROTEINS. THE HELIX UNIT CELL PARAMETERS ARE AFFECTED BY EXPERIMENTAL CONDITIONS SUCH AS HYDRATION, PH AND TEMPERATURE. BECAUSE OF THE OVERLAPPING INTERDIGITATED NATURE OF THE ASSEMBLY, EVEN SMALL CHANGES IN THE UNIT CELL PARAMETERS ARE ACCOMPANIED BY CHANGES IN THE SHAPE OF THE ASYMMETRIC UNIT. THESE CHANGES DO NOT ALTER THE PATTERN OF SIDE CHAIN INTERLOCKING BETWEEN NEIGHBORING ASYMMETRIC UNITS, BUT THEY CAN ALTER LOCAL NON-BONDED CONTACTS BY SEVERAL TENTHS OF AN ANGSTROM. THE DEPOSITORS DEFINE A CANONICAL HELIX UNIT CELL WITH PARAMETERS T = -33.23 DEGREES, P = 16.0 ANGSTROMS AND GIVE THE ATOMIC COORDINATES FOR THE ASYMMETRIC UNIT IN THIS UNIT CELL. TO DETERMINE THE COORDINATES OF THE ASYMMETRIC UNIT IN A NEW UNIT CELL WITH SLIGHTLY DIFFERENT PARAMETERS (T', P'), CONVERT FROM CARTESIAN COORDINATES TO CYLINDRICAL-POLAR COORDINATES AND USE EQUATION 5 OF THE JRNL REFERENCE. AN EQUIVALENT ALTERNATIVE METHOD IS TO APPLY A VARIABLE MATRIX THAT IS A FUNCTION OF THE Z COORDINATE OF THE ATOMS. DEFINE A SLEW COEFFICIENT S=(T'-T)/P; FOR EXAMPLE, FOR FD AT PH 2, T'=-36.0 DEGREES DEGREES, P'=16.15 ANGSTROMS AND S=-0.173 DEGREE/ANGSTROM. THEN, TO GENERATE THE SLEWED COORDINATES, APPLY THE MATRIX AND VECTOR (RECALCULATED FOR EACH ATOM): | COS(S*Z) -SIN(S*Z) 0 | | 0 | | SIN(S*Z) COS(S*Z) 0 | + | 0 | | 0 0 1 | | (P'/P)*Z | SLEWING THE COORDINATES IN THIS WAY GIVES RISE TO SMALL LOCAL DISTORTIONS IN COVALENT BOND LENGTHS AND BOND ANGLES, WHICH CAN BE CORRECTED BY A FEW CYCLES OF ENERGY MINIMIZATION. THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10. 4.00 1 4.00 0 370 0 0 370 0.004 refinement EREF MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME 1 Y N A ALA 1 A ALA 1 HELX_P A SER 50 A SER 50 1 A 50 VIRUS VIRUS, Helical virus COATB_BPFD UNP 1 1 P69539 MKKSLVLKASVAVATLVPMLSFAAEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS 24 73 1IFD 1 50 P69539 A 1 1 50 1 P 1