0.008873 0.000000 0.000342 0.000000 0.024211 0.000000 0.000000 0.000000 0.016248 0.00000 0.00000 0.00000 Ryu, K.S. Ko, J. Kim, H. Choi, B.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 92.21 90.00 112.700 41.304 61.590 C10 H14 N5 O8 P 363.221 GUANOSINE-5'-MONOPHOSPHATE non-polymer 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 C3 H7 N O2 S 121.158 y CYSTEINE 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 H10 N3 O2 1 156.162 y HISTIDINE L-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 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 P N 2 N O N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C N 18 N C N 19 N O N 20 N N N 21 N C N 22 N N N 23 N N Y 24 N C N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N N N 40 S C N 41 N C N 42 N O N 43 N C N 44 N O N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N C N 59 N N N 60 N C N 61 N N N 62 N N N 63 N O N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H 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 N C N 84 N C N 85 N O N 86 N N 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 N N 97 S C N 98 N C N 99 N O N 100 N C N 101 N C N 102 N O N 103 N O N 104 N O N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N N N 113 R C N 114 N C N 115 N O N 116 N C N 117 N S N 118 N O N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N N N 127 S C N 128 N C N 129 N O N 130 N C N 131 N C N 132 N C N 133 N O N 134 N N N 135 N O 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 N N 147 S C N 148 N C N 149 N O N 150 N C N 151 N C N 152 N C N 153 N O N 154 N O N 155 N O N 156 N H 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 N N 166 N C N 167 N C N 168 N O N 169 N O N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N N N 176 S C N 177 N C N 178 N O N 179 N C Y 180 N C Y 181 N N Y 182 N C Y 183 N C Y 184 N N N 185 N O N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N O N 197 N H N 198 N H N 199 N N N 200 S C N 201 N C N 202 N O N 203 S C N 204 N C N 205 N C N 206 N C N 207 N O N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H 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 N N 222 S C N 223 N C N 224 N O N 225 N C N 226 N C N 227 N C 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 H N 240 N H N 241 N H N 242 N H N 243 N N N 244 S C N 245 N C N 246 N O N 247 N C N 248 N C N 249 N C N 250 N C N 251 N N N 252 N O N 253 N H 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 H N 267 N H N 268 N N N 269 S C N 270 N C N 271 N O N 272 N C N 273 N C N 274 N S N 275 N C N 276 N O N 277 N H N 278 N H 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 N N 289 S C N 290 N C N 291 N O N 292 N C Y 293 N C Y 294 N C Y 295 N C Y 296 N C Y 297 N C Y 298 N C N 299 N O 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 309 N H N 310 N H N 311 N N N 312 S C N 313 N C N 314 N O N 315 N C N 316 N C N 317 N C N 318 N O N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N N N 329 S C N 330 N C N 331 N O N 332 N C N 333 N O N 334 N O N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N N N 343 S C N 344 N C N 345 N O N 346 R C N 347 N O N 348 N C N 349 N O N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N N N 360 S C N 361 N C N 362 N O N 363 N C Y 364 N C Y 365 N C Y 366 N C Y 367 N N Y 368 N C Y 369 N C Y 370 N C Y 371 N C Y 372 N C N 373 N O N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 N C Y 391 N C Y 392 N C Y 393 N C Y 394 N C Y 395 N C Y 396 N C N 397 N O N 398 N O N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N N N 411 S C N 412 N C N 413 N O N 414 N C N 415 N C N 416 N C N 417 N O N 418 N H N 419 N H N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing 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 sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing N 30 N sing Y 31 N doub N 32 N doub N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N doub N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N doub N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N doub N 60 N sing N 61 N sing 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 sing N 72 N sing N 73 N doub 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 sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N doub N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N doub 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 doub 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 doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing 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 doub 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 doub 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 sing N 147 N sing N 148 N doub 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 doub 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 sing N 166 N doub N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N doub N 176 N sing N 177 N sing N 178 N sing N 179 N sing Y 180 N sing Y 181 N doub Y 182 N doub N 183 N sing Y 184 N sing N 185 N sing Y 186 N sing N 187 N sing N 188 N sing 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 doub 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 sing 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 sing N 219 N doub 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 sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N doub N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 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 sing N 263 N sing N 264 N doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 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 doub N 284 N sing N 285 N sing N 286 N sing N 287 N sing Y 288 N doub Y 289 N sing Y 290 N sing N 291 N sing Y 292 N doub N 293 N sing Y 294 N doub N 295 N sing Y 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N doub N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N doub N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N doub N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N doub N 353 N sing N 354 N sing N 355 N sing N 356 N sing Y 357 N doub Y 358 N sing Y 359 N sing N 360 N sing Y 361 N doub Y 362 N sing Y 363 N sing N 364 N sing Y 365 N sing Y 366 N doub N 367 N sing Y 368 N doub N 369 N sing Y 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N doub N 381 N sing N 382 N sing N 383 N sing N 384 N sing Y 385 N doub Y 386 N sing Y 387 N sing N 388 N sing Y 389 N doub N 390 N sing Y 391 N doub N 392 N sing Y 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N doub N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 398 97 110 10.1016/j.jmb.2010.03.007 20226196 Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins. 2010 10.2210/pdb3kyf/pdb pdb_00003kyf 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 200 1 CCD SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 4A PAL/PLS 1.5418 SYNCHROTRON PAL/PLS BEAMLINE 4A 26529.023 Putative uncharacterized protein UNP residues 8-238 1 man polymer 363.221 GUANOSINE-5'-MONOPHOSPHATE 4 syn non-polymer 18.015 water 171 nat water PP4397 no no PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDG VRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRF EGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQRE PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDG VRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRF EGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQRE 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 KT2440 sample PP4397 160488 Pseudomonas putida 562 Escherichia coli BL21 (DE3) Plasmid pET15B 1 2.70 54.44 VAPOR DIFFUSION, HANGING DROP 8.5 0.1M Tris-HCl, pH 8.5, 25% PEG 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Data collection Database references Derived calculations 1 0 2010-04-14 1 1 2011-07-13 1 2 2024-03-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y PDBJ 2009-12-06 REL REL 5GP GUANOSINE-5'-MONOPHOSPHATE HOH water 5GP 501 2 5GP 5GP 501 A 5GP 502 2 5GP 5GP 502 A 5GP 503 2 5GP 5GP 503 A 5GP 504 2 5GP 5GP 504 A HOH 1 3 HOH HOH 1 A HOH 2 3 HOH HOH 2 A HOH 3 3 HOH HOH 3 A HOH 4 3 HOH HOH 4 A HOH 5 3 HOH HOH 5 A HOH 6 3 HOH HOH 6 A HOH 7 3 HOH HOH 7 A HOH 8 3 HOH HOH 239 A HOH 9 3 HOH HOH 240 A HOH 10 3 HOH HOH 241 A HOH 11 3 HOH HOH 242 A HOH 12 3 HOH HOH 243 A HOH 13 3 HOH HOH 244 A HOH 14 3 HOH HOH 245 A HOH 15 3 HOH HOH 246 A HOH 16 3 HOH HOH 247 A HOH 17 3 HOH HOH 248 A HOH 18 3 HOH HOH 249 A HOH 19 3 HOH HOH 250 A HOH 20 3 HOH HOH 251 A HOH 21 3 HOH HOH 252 A HOH 22 3 HOH HOH 253 A HOH 23 3 HOH HOH 254 A HOH 24 3 HOH HOH 255 A HOH 25 3 HOH HOH 256 A HOH 26 3 HOH HOH 257 A HOH 27 3 HOH HOH 258 A HOH 28 3 HOH HOH 259 A HOH 29 3 HOH HOH 260 A HOH 30 3 HOH HOH 261 A HOH 31 3 HOH HOH 262 A HOH 32 3 HOH HOH 263 A HOH 33 3 HOH HOH 264 A HOH 34 3 HOH HOH 265 A HOH 35 3 HOH HOH 266 A HOH 36 3 HOH HOH 267 A HOH 37 3 HOH HOH 268 A HOH 38 3 HOH HOH 269 A HOH 39 3 HOH HOH 270 A HOH 40 3 HOH HOH 271 A HOH 41 3 HOH HOH 272 A HOH 42 3 HOH HOH 273 A HOH 43 3 HOH HOH 274 A HOH 44 3 HOH HOH 275 A HOH 45 3 HOH HOH 276 A HOH 46 3 HOH HOH 277 A HOH 47 3 HOH HOH 278 A HOH 48 3 HOH HOH 279 A HOH 49 3 HOH HOH 280 A HOH 50 3 HOH HOH 281 A HOH 51 3 HOH HOH 282 A HOH 52 3 HOH HOH 283 A HOH 53 3 HOH HOH 284 A HOH 54 3 HOH HOH 285 A HOH 55 3 HOH HOH 286 A HOH 56 3 HOH HOH 287 A HOH 57 3 HOH HOH 288 A HOH 58 3 HOH HOH 289 A HOH 59 3 HOH HOH 290 A HOH 60 3 HOH HOH 291 A HOH 61 3 HOH HOH 292 A HOH 62 3 HOH HOH 293 A HOH 63 3 HOH HOH 294 A HOH 64 3 HOH HOH 295 A HOH 65 3 HOH HOH 296 A HOH 66 3 HOH HOH 297 A HOH 67 3 HOH HOH 298 A HOH 68 3 HOH HOH 299 A HOH 69 3 HOH HOH 300 A HOH 70 3 HOH HOH 301 A HOH 71 3 HOH HOH 302 A HOH 72 3 HOH HOH 303 A HOH 73 3 HOH HOH 304 A HOH 74 3 HOH HOH 305 A HOH 75 3 HOH HOH 306 A HOH 76 3 HOH HOH 307 A HOH 77 3 HOH HOH 308 A HOH 78 3 HOH HOH 309 A HOH 79 3 HOH HOH 310 A HOH 80 3 HOH HOH 311 A HOH 81 3 HOH HOH 312 A HOH 82 3 HOH HOH 313 A HOH 83 3 HOH HOH 314 A HOH 84 3 HOH HOH 315 A HOH 85 3 HOH HOH 316 A HOH 86 3 HOH HOH 317 A HOH 87 3 HOH HOH 318 A HOH 88 3 HOH HOH 319 A HOH 89 3 HOH HOH 320 A HOH 90 3 HOH HOH 321 A HOH 91 3 HOH HOH 322 A HOH 92 3 HOH HOH 323 A HOH 93 3 HOH HOH 324 A HOH 94 3 HOH HOH 325 A HOH 95 3 HOH HOH 326 A HOH 96 3 HOH HOH 327 A HOH 97 3 HOH HOH 328 A HOH 98 3 HOH HOH 329 A HOH 99 3 HOH HOH 330 A HOH 100 3 HOH HOH 331 A HOH 101 3 HOH HOH 332 A HOH 102 3 HOH HOH 333 A HOH 103 3 HOH HOH 334 A HOH 104 3 HOH HOH 335 A HOH 105 3 HOH HOH 336 A HOH 106 3 HOH HOH 337 A HOH 107 3 HOH HOH 338 A HOH 108 3 HOH HOH 339 A HOH 109 3 HOH HOH 340 A HOH 110 3 HOH HOH 341 A HOH 111 3 HOH HOH 342 A HOH 112 3 HOH HOH 343 A HOH 113 3 HOH HOH 344 A HOH 114 3 HOH HOH 345 A HOH 115 3 HOH HOH 346 A HOH 116 3 HOH HOH 347 A HOH 117 3 HOH HOH 348 A HOH 118 3 HOH HOH 349 A HOH 119 3 HOH HOH 350 A HOH 120 3 HOH HOH 351 A HOH 121 3 HOH HOH 352 A HOH 122 3 HOH HOH 353 A HOH 123 3 HOH HOH 354 A HOH 124 3 HOH HOH 355 A HOH 125 3 HOH HOH 356 A HOH 126 3 HOH HOH 357 A HOH 127 3 HOH HOH 358 A HOH 128 3 HOH HOH 359 A HOH 129 3 HOH HOH 360 A HOH 130 3 HOH HOH 361 A HOH 131 3 HOH HOH 362 A HOH 132 3 HOH HOH 363 A HOH 133 3 HOH HOH 364 A HOH 134 3 HOH HOH 365 A HOH 135 3 HOH HOH 366 A HOH 136 3 HOH HOH 367 A HOH 137 3 HOH HOH 368 A HOH 138 3 HOH HOH 369 A HOH 139 3 HOH HOH 370 A HOH 140 3 HOH HOH 371 A HOH 141 3 HOH HOH 372 A HOH 142 3 HOH HOH 373 A HOH 143 3 HOH HOH 374 A HOH 144 3 HOH HOH 375 A HOH 145 3 HOH HOH 376 A HOH 146 3 HOH HOH 377 A HOH 147 3 HOH HOH 378 A HOH 148 3 HOH HOH 379 A HOH 149 3 HOH HOH 380 A HOH 150 3 HOH HOH 381 A HOH 151 3 HOH HOH 382 A HOH 152 3 HOH HOH 383 A HOH 153 3 HOH HOH 384 A HOH 154 3 HOH HOH 385 A HOH 155 3 HOH HOH 386 A HOH 156 3 HOH HOH 387 A HOH 157 3 HOH HOH 388 A HOH 158 3 HOH HOH 389 A HOH 159 3 HOH HOH 390 A HOH 160 3 HOH HOH 391 A HOH 161 3 HOH HOH 392 A HOH 162 3 HOH HOH 393 A HOH 163 3 HOH HOH 394 A HOH 164 3 HOH HOH 395 A HOH 165 3 HOH HOH 396 A HOH 166 3 HOH HOH 397 A HOH 167 3 HOH HOH 398 A HOH 168 3 HOH HOH 399 A HOH 169 3 HOH HOH 400 A HOH 170 3 HOH HOH 401 A HOH 171 3 HOH HOH 402 A PRO 8 n 1 PRO 8 A GLN 9 n 2 GLN 9 A PRO 10 n 3 PRO 10 A PRO 11 n 4 PRO 11 A LYS 12 n 5 LYS 12 A VAL 13 n 6 VAL 13 A LEU 14 n 7 LEU 14 A SER 15 n 8 SER 15 A THR 16 n 9 THR 16 A PRO 17 n 10 PRO 17 A LEU 18 n 11 LEU 18 A GLU 19 n 12 GLU 19 A ILE 20 n 13 ILE 20 A ALA 21 n 14 ALA 21 A ALA 22 n 15 ALA 22 A ASN 23 n 16 ASN 23 A LEU 24 n 17 LEU 24 A ARG 25 n 18 ARG 25 A GLN 26 n 19 GLN 26 A LEU 27 n 20 LEU 27 A GLN 28 n 21 GLN 28 A GLU 29 n 22 GLU 29 A SER 30 n 23 SER 30 A HIS 31 n 24 HIS 31 A ASP 32 n 25 ASP 32 A PRO 33 n 26 PRO 33 A LEU 34 n 27 LEU 34 A ILE 35 n 28 ILE 35 A ILE 36 n 29 ILE 36 A THR 37 n 30 THR 37 A PHE 38 n 31 PHE 38 A HIS 39 n 32 HIS 39 A ASP 40 n 33 ASP 40 A ARG 41 n 34 ARG 41 A SER 42 n 35 SER 42 A HIS 43 n 36 HIS 43 A ARG 44 n 37 ARG 44 A PHE 45 n 38 PHE 45 A GLN 46 n 39 GLN 46 A SER 47 n 40 SER 47 A TYR 48 n 41 TYR 48 A VAL 49 n 42 VAL 49 A VAL 50 n 43 VAL 50 A HIS 51 n 44 HIS 51 A VAL 52 n 45 VAL 52 A ASP 53 n 46 ASP 53 A ARG 54 n 47 ARG 54 A GLU 55 n 48 GLU 55 A SER 56 n 49 SER 56 A ASN 57 n 50 ASN 57 A THR 58 n 51 THR 58 A LEU 59 n 52 LEU 59 A ALA 60 n 53 ALA 60 A LEU 61 n 54 LEU 61 A ASP 62 n 55 ASP 62 A GLU 63 n 56 GLU 63 A MET 64 n 57 MET 64 A ILE 65 n 58 ILE 65 A PRO 66 n 59 PRO 66 A ARG 67 n 60 ARG 67 A ASP 68 n 61 ASP 68 A GLY 69 n 62 GLY 69 A GLU 70 n 63 GLU 70 A LYS 71 n 64 LYS 71 A PHE 72 n 65 PHE 72 A ILE 73 n 66 ILE 73 A GLU 74 n 67 GLU 74 A ASN 75 n 68 ASN 75 A GLY 76 n 69 GLY 76 A GLU 77 n 70 GLU 77 A HIS 78 n 71 HIS 78 A PHE 79 n 72 PHE 79 A ARG 80 n 73 ARG 80 A VAL 81 n 74 VAL 81 A GLU 82 n 75 GLU 82 A GLY 83 n 76 GLY 83 A PHE 84 n 77 PHE 84 A HIS 85 n 78 HIS 85 A ASP 86 n 79 ASP 86 A GLY 87 n 80 GLY 87 A VAL 88 n 81 VAL 88 A ARG 89 n 82 ARG 89 A ILE 90 n 83 ILE 90 A ALA 91 n 84 ALA 91 A TRP 92 n 85 TRP 92 A GLU 93 n 86 GLU 93 A CYS 94 n 87 CYS 94 A ASP 95 n 88 ASP 95 A HIS 96 n 89 HIS 96 A ALA 97 n 90 ALA 97 A LEU 98 n 91 LEU 98 A LYS 99 n 92 LYS 99 A ILE 100 n 93 ILE 100 A SER 101 n 94 SER 101 A GLU 102 n 95 GLU 102 A VAL 103 n 96 VAL 103 A ASP 104 n 97 ASP 104 A GLY 105 n 98 GLY 105 A HIS 106 n 99 HIS 106 A ARG 107 n 100 ARG 107 A CYS 108 n 101 CYS 108 A TYR 109 n 102 TYR 109 A SER 110 n 103 SER 110 A GLY 111 n 104 GLY 111 A PRO 112 n 105 PRO 112 A LEU 113 n 106 LEU 113 A PRO 114 n 107 PRO 114 A GLN 115 n 108 GLN 115 A GLU 116 n 109 GLU 116 A VAL 117 n 110 VAL 117 A THR 118 n 111 THR 118 A TYR 119 n 112 TYR 119 A HIS 120 n 113 HIS 120 A GLN 121 n 114 GLN 121 A ARG 122 n 115 ARG 122 A ARG 123 n 116 ARG 123 A ASN 124 n 117 ASN 124 A ALA 125 n 118 ALA 125 A PHE 126 n 119 PHE 126 A ARG 127 n 120 ARG 127 A ALA 128 n 121 ALA 128 A ALA 129 n 122 ALA 129 A LEU 130 n 123 LEU 130 A LYS 131 n 124 LYS 131 A LEU 132 n 125 LEU 132 A SER 133 n 126 SER 133 A GLN 134 n 127 GLN 134 A LEU 135 n 128 LEU 135 A VAL 136 n 129 VAL 136 A ASP 137 n 130 ASP 137 A ILE 138 n 131 ILE 138 A ILE 139 n 132 ILE 139 A LEU 140 n 133 LEU 140 A ASP 141 n 134 ASP 141 A GLY 142 n 135 GLY 142 A ALA 143 n 136 ALA 143 A HIS 144 n 137 HIS 144 A LEU 145 n 138 LEU 145 A LYS 146 n 139 LYS 146 A GLY 147 n 140 GLY 147 A ASN 148 n 141 ASN 148 A GLY 149 n 142 GLY 149 A ALA 150 n 143 ALA 150 A MET 151 n 144 MET 151 A ARG 152 n 145 ARG 152 A GLY 153 n 146 GLY 153 A LYS 154 n 147 LYS 154 A LEU 155 n 148 LEU 155 A LEU 156 n 149 LEU 156 A ASP 157 n 150 ASP 157 A ILE 158 n 151 ILE 158 A SER 159 n 152 SER 159 A ALA 160 n 153 ALA 160 A THR 161 n 154 THR 161 A GLY 162 n 155 GLY 162 A CYS 163 n 156 CYS 163 A LYS 164 n 157 LYS 164 A LEU 165 n 158 LEU 165 A ARG 166 n 159 ARG 166 A PHE 167 n 160 PHE 167 A GLU 168 n 161 GLU 168 A GLY 169 n 162 GLY 169 A ASN 170 n 163 ASN 170 A VAL 171 n 164 VAL 171 A GLU 172 n 165 GLU 172 A ASP 173 n 166 ASP 173 A ARG 174 n 167 ARG 174 A LEU 175 n 168 LEU 175 A GLN 176 n 169 GLN 176 A LEU 177 n 170 LEU 177 A GLY 178 n 171 GLY 178 A GLN 179 n 172 GLN 179 A VAL 180 n 173 VAL 180 A TYR 181 n 174 TYR 181 A GLU 182 n 175 GLU 182 A ARG 183 n 176 ARG 183 A PHE 184 n 177 PHE 184 A LYS 185 n 178 LYS 185 A ALA 186 n 179 ALA 186 A GLY 187 n 180 GLY 187 A ASN 188 n 181 ASN 188 A PRO 189 n 182 PRO 189 A LEU 190 n 183 LEU 190 A GLY 191 n 184 GLY 191 A LEU 192 n 185 LEU 192 A VAL 193 n 186 VAL 193 A ASP 194 n 187 ASP 194 A THR 195 n 188 THR 195 A MET 196 n 189 MET 196 A VAL 197 n 190 VAL 197 A GLU 198 n 191 GLU 198 A LEU 199 n 192 LEU 199 A ARG 200 n 193 ARG 200 A HIS 201 n 194 HIS 201 A LEU 202 n 195 LEU 202 A HIS 203 n 196 HIS 203 A TYR 204 n 197 TYR 204 A GLU 205 n 198 GLU 205 A GLU 206 n 199 GLU 206 A ARG 207 n 200 ARG 207 A ILE 208 n 201 ILE 208 A ASN 209 n 202 ASN 209 A THR 210 n 203 THR 210 A THR 211 n 204 THR 211 A PHE 212 n 205 PHE 212 A ALA 213 n 206 ALA 213 A GLY 214 n 207 GLY 214 A VAL 215 n 208 VAL 215 A ARG 216 n 209 ARG 216 A PHE 217 n 210 PHE 217 A HIS 218 n 211 HIS 218 A ASN 219 n 212 ASN 219 A LEU 220 n 213 LEU 220 A SER 221 n 214 SER 221 A GLY 222 n 215 GLY 222 A GLN 223 n 216 GLN 223 A ALA 224 n 217 ALA 224 A GLN 225 n 218 GLN 225 A ARG 226 n 219 ARG 226 A LYS 227 n 220 LYS 227 A ILE 228 n 221 ILE 228 A GLU 229 n 222 GLU 229 A SER 230 n 223 SER 230 A PHE 231 n 224 PHE 231 A VAL 232 n 225 VAL 232 A TYR 233 n 226 TYR 233 A GLN 234 n 227 GLN 234 A LEU 235 n 228 LEU 235 A GLN 236 n 229 GLN 236 A ARG 237 n 230 ARG 237 A GLU 238 n 231 GLU 238 A author_defined_assembly 1 monomeric software_defined_assembly PISA 2 dimeric 2820 -1 24460 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 A N LYS 12 A N LYS 5 A O TYR 119 A O TYR 112 A O THR 118 A O THR 111 A N ALA 91 A N ALA 84 A O ILE 90 A O ILE 83 A N GLY 83 A N GLY 76 A O GLU 82 A O GLU 75 A N ILE 35 A N ILE 28 A N ILE 36 A N ILE 29 A O PHE 45 A O PHE 38 A N VAL 50 A N VAL 43 A O ALA 60 A O ALA 53 A N LEU 61 A N LEU 54 A O TYR 109 A O TYR 102 A O HIS 106 A O HIS 99 A N VAL 103 A N VAL 96 A N ALA 128 A N ALA 121 A O ILE 158 A O ILE 151 A N LEU 156 A N LEU 149 A O LYS 164 A O LYS 157 A N LEU 165 A N LEU 158 A O ALA 213 A O ALA 206 A O GLY 214 A O GLY 207 A N ARG 200 A N ARG 193 A O VAL 197 A O VAL 190 A N TYR 181 A N TYR 174 A O LYS 185 A O LYS 178 A N ILE 139 A N ILE 132 A N LEU 140 A N LEU 133 A O MET 151 A O MET 144 1 A GLN 9 64.90 109.72 protein_rep.param protein.top ks_5gp.param ks_5gp.top water_rep.param water.top ion.param ion.top dna-rna.param dna-rna.top 34.3 -4.75 0.00 7.15 2.98 0.00 1.77 BULK SOLVENT MODEL USED 0.244 0.006 0.194 0.194 2.10 33.01 1573 15505 10.1 92.2 RANDOM 200903.88 0.000000 1 RESTRAINED THROUGHOUT 0.0 MOLECULAR REPLACEMENT FLAT MODEL 70.5705 0.4 0.32 0.24 5.00 0.35 0.28 2.10 33.01 171 2132 92 0 1869 0.007 1.3 24.8 0.82 2.16 1.50 3.16 2.00 3.50 2.00 5.08 2.50 0.297 0.019 0.256 2.23 233 1771 6 11.6 72.6 12.4 2.10 50.0 3KYF 15600 1 data collection HKL-2000 phasing PHASES refinement CNS 1.2 data reduction HKL-2000 data scaling HKL-2000 Y Crystal structure of P4397 complexed with c-di-GMP 1 N N 2 N N 2 N N 2 N N 2 N N 3 N N A THR 16 A THR 9 HELX_P A SER 30 A SER 23 1 1 15 A PRO 66 A PRO 59 HELX_P A ASP 68 A ASP 61 5 2 3 A GLY 69 A GLY 62 HELX_P A ASN 75 A ASN 68 1 3 7 A LYS 131 A LYS 124 HELX_P A LEU 135 A LEU 128 5 4 5 A VAL 171 A VAL 164 HELX_P A LEU 175 A LEU 168 5 5 5 A GLU 206 A GLU 199 HELX_P A ILE 208 A ILE 201 5 6 3 A SER 221 A SER 214 HELX_P A GLU 238 A GLU 231 1 7 18 covale 1.600 one A 5GP 501 B P 5GP 1_555 A 5GP 502 C O3' 5GP 1_555 covale 1.601 one A 5GP 501 B O3' 5GP 1_555 A 5GP 502 C P 5GP 1_555 covale 1.598 one A 5GP 503 D P 5GP 1_555 A 5GP 504 E O3' 5GP 1_555 covale 1.600 one A 5GP 503 D O3' 5GP 1_555 A 5GP 504 E P 5GP 1_555 UNKNOWN FUNCTION c-di-GMP, PilZ domain, PP4397, VCA0042, UNKNOWN FUNCTION A ILE 65 A ILE 58 1 A PRO 66 A PRO 59 0.10 A ASN 188 A ASN 181 1 A PRO 189 A PRO 182 0.14 Q88EQ6_PSEPK UNP 1 8 Q88EQ6 PQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDG VRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRF EGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQRE 8 238 3KYF 8 238 Q88EQ6 A 1 1 231 6 4 8 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 12 A LYS 5 A LEU 14 A LEU 7 A VAL 117 A VAL 110 A HIS 120 A HIS 113 A VAL 88 A VAL 81 A CYS 94 A CYS 87 A PHE 79 A PHE 72 A HIS 85 A HIS 78 A LEU 34 A LEU 27 A PHE 38 A PHE 31 A ARG 44 A ARG 37 A SER 47 A SER 40 A VAL 49 A VAL 42 A ASP 53 A ASP 46 A THR 58 A THR 51 A ASP 62 A ASP 55 A HIS 106 A HIS 99 A GLY 111 A GLY 104 A LYS 99 A LYS 92 A VAL 103 A VAL 96 A ALA 128 A ALA 121 A ALA 129 A ALA 122 A MET 151 A MET 144 A ILE 158 A ILE 151 A GLY 162 A GLY 155 A GLU 168 A GLU 161 A THR 210 A THR 203 A HIS 218 A HIS 211 A LEU 192 A LEU 185 A GLU 205 A GLU 198 A VAL 180 A VAL 173 A ALA 186 A ALA 179 A ASP 137 A ASP 130 A LEU 140 A LEU 133 A MET 151 A MET 144 A ILE 158 A ILE 151 BINDING SITE FOR RESIDUE 5GP A 501 A 5GP 501 Software 10 BINDING SITE FOR RESIDUE 5GP A 502 A 5GP 502 Software 10 BINDING SITE FOR RESIDUE 5GP A 503 A 5GP 503 Software 16 BINDING SITE FOR RESIDUE 5GP A 504 A 5GP 504 Software 10 A ARG 123 A ARG 116 10 1_555 A ARG 127 A ARG 120 10 1_555 A HIS 201 A HIS 194 10 1_555 A HOH 271 F HOH 10 1_555 A HOH 274 F HOH 10 1_555 A HOH 288 F HOH 10 1_555 A HOH 325 F HOH 10 1_555 A 5GP 502 C 5GP 10 1_555 A 5GP 503 D 5GP 10 1_555 A 5GP 504 E 5GP 10 1_555 A PHE 84 A PHE 77 10 1_555 A GLY 87 A GLY 80 10 1_555 A GLN 121 A GLN 114 10 1_555 A ARG 122 A ARG 115 10 1_555 A ARG 123 A ARG 116 10 1_555 A HOH 300 F HOH 10 1_555 A HOH 319 F HOH 10 1_555 A HOH 322 F HOH 10 2_555 A 5GP 501 B 5GP 10 1_555 A 5GP 504 E 5GP 10 1_555 A ARG 127 A ARG 120 16 1_555 A ASP 157 A ASP 150 16 1_555 A SER 159 A SER 152 16 1_555 A THR 161 A THR 154 16 1_555 A GLY 162 A GLY 155 16 1_555 A CYS 163 A CYS 156 16 1_555 A LYS 164 A LYS 157 16 1_555 A ARG 200 A ARG 193 16 1_555 A HIS 201 A HIS 194 16 1_555 A GLY 214 A GLY 207 16 1_555 A VAL 215 A VAL 208 16 1_555 A ARG 216 A ARG 209 16 1_555 A HOH 271 F HOH 16 1_555 A HOH 394 F HOH 16 1_555 A 5GP 501 B 5GP 16 1_555 A 5GP 504 E 5GP 16 1_555 A ARG 122 A ARG 115 10 1_555 A ARG 123 A ARG 116 10 1_555 A ASN 124 A ASN 117 10 1_555 A ARG 127 A ARG 120 10 1_555 A HOH 250 F HOH 10 1_555 A HOH 272 F HOH 10 1_555 A HOH 379 F HOH 10 1_555 A 5GP 501 B 5GP 10 1_555 A 5GP 502 C 5GP 10 1_555 A 5GP 503 D 5GP 10 1_555 5 C 1 2 1