0.032085 0.000000 0.002399 0.000000 0.016532 0.000000 0.000000 0.000000 0.026303 0.000000 0.000000 0.000000 Robinson, A.C. Schlessman, J.L. Heroux, A. Garcia-Moreno E., B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.000 94.280 90.000 31.167 60.487 38.124 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 Ca 2 40.078 CALCIUM ION 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 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 C10 H16 N2 O11 P2 402.188 THYMIDINE-3',5'-DIPHOSPHATE DNA 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 C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O 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 H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O 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 CA N 75 N N N 76 S C N 77 N C N 78 N O N 79 N C N 80 N C N 81 N C N 82 N O N 83 N N N 84 N O N 85 N H N 86 N H N 87 N H 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 N N 96 S C N 97 N C N 98 N O N 99 N C 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 H N 113 N H N 114 N N N 115 N C N 116 N C N 117 N O 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 N N 125 S C N 126 N C N 127 N O N 128 N C Y 129 N C Y 130 N N Y 131 N C Y 132 N C Y 133 N N N 134 N O 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 O 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 S C N 153 N C N 154 N C 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 H N 169 N H N 170 N N N 171 S C N 172 N C N 173 N O N 174 N C N 175 N C N 176 N C N 177 N C N 178 N O N 179 N H 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 H N 192 N N N 193 S C N 194 N C N 195 N O N 196 N C N 197 N C N 198 N C N 199 N C N 200 N N N 201 N O 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 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 N N 218 S C N 219 N C N 220 N O N 221 N C N 222 N C N 223 N S N 224 N C N 225 N O N 226 N H N 227 N H N 228 N H N 229 N H 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 N N 238 S C N 239 N C N 240 N O N 241 N C Y 242 N C Y 243 N C Y 244 N C Y 245 N C Y 246 N C Y 247 N C N 248 N O N 249 N H N 250 N H N 251 N H N 252 N H 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 N N 261 S C N 262 N C N 263 N O N 264 N C N 265 N C N 266 N C N 267 N O N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N N N 278 S C N 279 N C N 280 N O N 281 N C N 282 N O N 283 N O 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 H N 291 N P N 292 N O N 293 N O N 294 N O N 295 N P N 296 N O N 297 N O N 298 N O N 299 N O N 300 N C N 301 R C N 302 N O N 303 S C N 304 N O N 305 N C N 306 R C N 307 N N N 308 N C N 309 N O N 310 N N N 311 N C N 312 N O N 313 N C N 314 N C N 315 N C N 316 N H N 317 N H N 318 N H 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 H N 329 N H N 330 N H N 331 N H N 332 N N N 333 S C N 334 N C N 335 N O N 336 R C N 337 N O N 338 N C N 339 N O N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N N N 350 S C N 351 N C N 352 N O N 353 N C Y 354 N C Y 355 N C Y 356 N C Y 357 N N Y 358 N C Y 359 N C Y 360 N C Y 361 N C Y 362 N C N 363 N O N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N N N 377 S C N 378 N C N 379 N O N 380 N C Y 381 N C Y 382 N C Y 383 N C Y 384 N C Y 385 N C Y 386 N C N 387 N O N 388 N O N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N N N 401 S C N 402 N C N 403 N O N 404 N C N 405 N C N 406 N C N 407 N O N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 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 sing 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 doub N 34 N sing 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 sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub 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 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 doub 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 sing N 74 N sing N 75 N sing N 76 N doub 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 doub 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 doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub 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 doub 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 Y 127 N sing Y 128 N doub Y 129 N doub N 130 N sing Y 131 N sing N 132 N sing Y 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 doub N 146 N sing 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 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 sing N 176 N sing N 177 N sing N 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 doub 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 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 sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N doub 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 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 doub N 231 N sing N 232 N sing N 233 N sing N 234 N sing Y 235 N doub Y 236 N sing Y 237 N sing N 238 N sing Y 239 N doub N 240 N sing Y 241 N doub N 242 N sing Y 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 doub 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 sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub 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 doub 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 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 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 sing N 307 N doub N 308 N sing N 309 N sing N 310 N sing N 311 N doub N 312 N sing N 313 N sing N 314 N doub 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 sing N 324 N sing N 325 N doub 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 sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N doub N 342 N sing N 343 N sing N 344 N sing N 345 N sing Y 346 N doub Y 347 N sing Y 348 N sing N 349 N sing Y 350 N doub Y 351 N sing Y 352 N sing N 353 N sing Y 354 N sing Y 355 N doub N 356 N sing Y 357 N doub N 358 N sing Y 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N doub N 370 N sing N 371 N sing N 372 N sing N 373 N sing Y 374 N doub Y 375 N sing Y 376 N sing N 377 N sing Y 378 N doub N 379 N sing Y 380 N doub N 381 N sing Y 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N doub 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 sing To be Published 0353 Crystal structure of Staphylococcal nuclease variant Delta+PHS I72D at cryogenic temperature 10.2210/pdb4eqp/pdb pdb_00004eqp 100 1 Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification PIXEL 2012-03-30 DECTRIS PILATUS 6M Si(111) SINGLE WAVELENGTH M x-ray 1 1.10 1.0 X25 NSLS 1.10 SYNCHROTRON NSLS BEAMLINE X25 16145.393 Thermonuclease 3.1.31.1 Nuclease A (UNP residues 83-231) G50F/V51N/I72D/P117G/H124L/S128A/Del44-49 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 402.188 THYMIDINE-3',5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 121 nat water TNase, Micrococcal nuclease, Staphylococcal nuclease no no ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKDEVEFDKGQRTDKYG RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKDEVEFDKGQRTDKYG RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ 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 sample 1280 Staphylococcus aureus 469008 Escherichia coli BL21(DE3) plasmid pET24a+ 1 2.22 44.58 VAPOR DIFFUSION, HANGING DROP 8.0 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Structure summary Data collection Database references Derived calculations Refinement description 1 0 2012-05-02 1 1 2013-03-06 1 2 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2012-04-19 REL REL CA CALCIUM ION THP THYMIDINE-3',5'-DIPHOSPHATE HOH water 3BDC PDB ENTRY 3BDC PDB experimental model CA 1 2 CA CA 201 A THP 142 3 THP THP 202 A HOH 1 4 HOH HOH 301 A HOH 2 4 HOH HOH 302 A HOH 3 4 HOH HOH 303 A HOH 4 4 HOH HOH 304 A HOH 5 4 HOH HOH 305 A HOH 6 4 HOH HOH 306 A HOH 7 4 HOH HOH 307 A HOH 8 4 HOH HOH 308 A HOH 9 4 HOH HOH 309 A HOH 11 4 HOH HOH 310 A HOH 16 4 HOH HOH 311 A HOH 1 4 HOH HOH 312 A HOH 2 4 HOH HOH 313 A HOH 3 4 HOH HOH 314 A HOH 4 4 HOH HOH 315 A HOH 5 4 HOH HOH 316 A HOH 6 4 HOH HOH 317 A HOH 7 4 HOH HOH 318 A HOH 8 4 HOH HOH 319 A HOH 9 4 HOH HOH 320 A HOH 10 4 HOH HOH 321 A HOH 11 4 HOH HOH 322 A HOH 12 4 HOH HOH 323 A HOH 13 4 HOH HOH 324 A HOH 14 4 HOH HOH 325 A HOH 15 4 HOH HOH 326 A HOH 16 4 HOH HOH 327 A HOH 17 4 HOH HOH 328 A HOH 18 4 HOH HOH 329 A HOH 19 4 HOH HOH 330 A HOH 20 4 HOH HOH 331 A HOH 21 4 HOH HOH 332 A HOH 22 4 HOH HOH 333 A HOH 23 4 HOH HOH 334 A HOH 24 4 HOH HOH 335 A HOH 25 4 HOH HOH 336 A HOH 26 4 HOH HOH 337 A HOH 27 4 HOH HOH 338 A HOH 28 4 HOH HOH 339 A HOH 29 4 HOH HOH 340 A HOH 30 4 HOH HOH 341 A HOH 31 4 HOH HOH 342 A HOH 32 4 HOH HOH 343 A HOH 34 4 HOH HOH 344 A HOH 35 4 HOH HOH 345 A HOH 36 4 HOH HOH 346 A HOH 37 4 HOH HOH 347 A HOH 38 4 HOH HOH 348 A HOH 39 4 HOH HOH 349 A HOH 41 4 HOH HOH 350 A HOH 42 4 HOH HOH 351 A HOH 43 4 HOH HOH 352 A HOH 44 4 HOH HOH 353 A HOH 46 4 HOH HOH 354 A HOH 47 4 HOH HOH 355 A HOH 48 4 HOH HOH 356 A HOH 49 4 HOH HOH 357 A HOH 50 4 HOH HOH 358 A HOH 51 4 HOH HOH 359 A HOH 52 4 HOH HOH 360 A HOH 53 4 HOH HOH 361 A HOH 54 4 HOH HOH 362 A HOH 55 4 HOH HOH 363 A HOH 57 4 HOH HOH 364 A HOH 58 4 HOH HOH 365 A HOH 59 4 HOH HOH 366 A HOH 61 4 HOH HOH 367 A HOH 63 4 HOH HOH 368 A HOH 64 4 HOH HOH 369 A HOH 65 4 HOH HOH 370 A HOH 67 4 HOH HOH 371 A HOH 68 4 HOH HOH 372 A HOH 69 4 HOH HOH 373 A HOH 74 4 HOH HOH 374 A HOH 75 4 HOH HOH 375 A HOH 76 4 HOH HOH 376 A HOH 78 4 HOH HOH 377 A HOH 79 4 HOH HOH 378 A HOH 80 4 HOH HOH 379 A HOH 82 4 HOH HOH 380 A HOH 83 4 HOH HOH 381 A HOH 84 4 HOH HOH 382 A HOH 85 4 HOH HOH 383 A HOH 86 4 HOH HOH 384 A HOH 88 4 HOH HOH 385 A HOH 89 4 HOH HOH 386 A HOH 90 4 HOH HOH 387 A HOH 91 4 HOH HOH 388 A HOH 92 4 HOH HOH 389 A HOH 95 4 HOH HOH 390 A HOH 96 4 HOH HOH 391 A HOH 97 4 HOH HOH 392 A HOH 98 4 HOH HOH 393 A HOH 100 4 HOH HOH 394 A HOH 101 4 HOH HOH 395 A HOH 103 4 HOH HOH 396 A HOH 104 4 HOH HOH 397 A HOH 105 4 HOH HOH 398 A HOH 106 4 HOH HOH 399 A HOH 109 4 HOH HOH 400 A HOH 111 4 HOH HOH 401 A HOH 112 4 HOH HOH 402 A HOH 113 4 HOH HOH 403 A HOH 114 4 HOH HOH 404 A HOH 116 4 HOH HOH 405 A HOH 118 4 HOH HOH 406 A HOH 119 4 HOH HOH 407 A HOH 121 4 HOH HOH 408 A HOH 122 4 HOH HOH 409 A HOH 123 4 HOH HOH 410 A HOH 124 4 HOH HOH 411 A HOH 125 4 HOH HOH 412 A HOH 143 4 HOH HOH 413 A HOH 145 4 HOH HOH 414 A HOH 146 4 HOH HOH 415 A HOH 1 4 HOH HOH 416 A HOH 2 4 HOH HOH 417 A HOH 3 4 HOH HOH 418 A HOH 4 4 HOH HOH 419 A HOH 5 4 HOH HOH 420 A HOH 1 4 HOH HOH 421 A 2.500 2.500 38.020 38.020 Phaser MODE: MR_AUTO n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A LEU 7 n 7 LEU 7 A HIS 8 n 8 HIS 8 A LYS 9 n 9 LYS 9 A GLU 10 n 10 GLU 10 A PRO 11 n 11 PRO 11 A ALA 12 n 12 ALA 12 A THR 13 n 13 THR 13 A LEU 14 n 14 LEU 14 A ILE 15 n 15 ILE 15 A LYS 16 n 16 LYS 16 A ALA 17 n 17 ALA 17 A ILE 18 n 18 ILE 18 A ASP 19 n 19 ASP 19 A GLY 20 n 20 GLY 20 A ASP 21 n 21 ASP 21 A THR 22 n 22 THR 22 A VAL 23 n 23 VAL 23 A LYS 24 n 24 LYS 24 A LEU 25 n 25 LEU 25 A MET 26 n 26 MET 26 A TYR 27 n 27 TYR 27 A LYS 28 n 28 LYS 28 A GLY 29 n 29 GLY 29 A GLN 30 n 30 GLN 30 A PRO 31 n 31 PRO 31 A MET 32 n 32 MET 32 A THR 33 n 33 THR 33 A PHE 34 n 34 PHE 34 A ARG 35 n 35 ARG 35 A LEU 36 n 36 LEU 36 A LEU 37 n 37 LEU 37 A LEU 38 n 38 LEU 38 A VAL 39 n 39 VAL 39 A ASP 40 n 40 ASP 40 A THR 41 n 41 THR 41 A PRO 42 n 42 PRO 42 A GLU 43 n 43 GLU 43 A PHE 50 n 44 PHE 50 A ASN 51 n 45 ASN 51 A GLU 52 n 46 GLU 52 A LYS 53 n 47 LYS 53 A TYR 54 n 48 TYR 54 A GLY 55 n 49 GLY 55 A PRO 56 n 50 PRO 56 A GLU 57 n 51 GLU 57 A ALA 58 n 52 ALA 58 A SER 59 n 53 SER 59 A ALA 60 n 54 ALA 60 A PHE 61 n 55 PHE 61 A THR 62 n 56 THR 62 A LYS 63 n 57 LYS 63 A LYS 64 n 58 LYS 64 A MET 65 n 59 MET 65 A VAL 66 n 60 VAL 66 A GLU 67 n 61 GLU 67 A ASN 68 n 62 ASN 68 A ALA 69 n 63 ALA 69 A LYS 70 n 64 LYS 70 A LYS 71 n 65 LYS 71 A ASP 72 n 66 ASP 72 A GLU 73 n 67 GLU 73 A VAL 74 n 68 VAL 74 A GLU 75 n 69 GLU 75 A PHE 76 n 70 PHE 76 A ASP 77 n 71 ASP 77 A LYS 78 n 72 LYS 78 A GLY 79 n 73 GLY 79 A GLN 80 n 74 GLN 80 A ARG 81 n 75 ARG 81 A THR 82 n 76 THR 82 A ASP 83 n 77 ASP 83 A LYS 84 n 78 LYS 84 A TYR 85 n 79 TYR 85 A GLY 86 n 80 GLY 86 A ARG 87 n 81 ARG 87 A GLY 88 n 82 GLY 88 A LEU 89 n 83 LEU 89 A ALA 90 n 84 ALA 90 A TYR 91 n 85 TYR 91 A ILE 92 n 86 ILE 92 A TYR 93 n 87 TYR 93 A ALA 94 n 88 ALA 94 A ASP 95 n 89 ASP 95 A GLY 96 n 90 GLY 96 A LYS 97 n 91 LYS 97 A MET 98 n 92 MET 98 A VAL 99 n 93 VAL 99 A ASN 100 n 94 ASN 100 A GLU 101 n 95 GLU 101 A ALA 102 n 96 ALA 102 A LEU 103 n 97 LEU 103 A VAL 104 n 98 VAL 104 A ARG 105 n 99 ARG 105 A GLN 106 n 100 GLN 106 A GLY 107 n 101 GLY 107 A LEU 108 n 102 LEU 108 A ALA 109 n 103 ALA 109 A LYS 110 n 104 LYS 110 A VAL 111 n 105 VAL 111 A ALA 112 n 106 ALA 112 A TYR 113 n 107 TYR 113 A VAL 114 n 108 VAL 114 A TYR 115 n 109 TYR 115 A LYS 116 n 110 LYS 116 A GLY 117 n 111 GLY 117 A ASN 118 n 112 ASN 118 A ASN 119 n 113 ASN 119 A THR 120 n 114 THR 120 A HIS 121 n 115 HIS 121 A GLU 122 n 116 GLU 122 A GLN 123 n 117 GLN 123 A LEU 124 n 118 LEU 124 A LEU 125 n 119 LEU 125 A ARG 126 n 120 ARG 126 A LYS 127 n 121 LYS 127 A ALA 128 n 122 ALA 128 A GLU 129 n 123 GLU 129 A ALA 130 n 124 ALA 130 A GLN 131 n 125 GLN 131 A ALA 132 n 126 ALA 132 A LYS 133 n 127 LYS 133 A LYS 134 n 128 LYS 134 A GLU 135 n 129 GLU 135 A LYS 136 n 130 LYS 136 A LEU 137 n 131 LEU 137 A ASN 138 n 132 ASN 138 A ILE 139 n 133 ILE 139 A TRP 140 n 134 TRP 140 A SER 141 n 135 SER 141 A n 136 142 A n 137 143 A n 138 144 A n 139 145 A n 140 146 A n 141 147 A n 142 148 A n 143 149 A 0.6566 -0.0111 -0.3871 2.7577 0.6405 0.3776 -0.0825 -0.0722 -0.0988 0.1110 0.0587 -0.0398 0.0675 0.0611 0.0238 0.0673 0.0125 -0.0047 0.0606 0.0042 0.0885 refined 12.7048 -42.1068 3.9920 X-RAY DIFFRACTION 1.2235 -0.4220 -0.1868 2.2498 0.0403 0.1154 -0.0278 -0.1331 0.0154 0.1586 0.0463 -0.1184 0.0290 0.0561 -0.0185 0.0409 0.0108 -0.0125 0.0560 0.0015 0.0382 refined 15.2053 -35.9186 5.7340 X-RAY DIFFRACTION 2.6772 1.7045 0.5810 6.7509 3.2019 3.2763 -0.0695 -0.3406 -0.2652 0.4590 0.0434 0.1424 0.2642 0.0252 0.0262 0.0995 0.0225 0.0260 0.0595 0.0511 0.0474 refined 8.4911 -39.7792 14.2235 X-RAY DIFFRACTION 3.3395 0.9156 -1.5779 6.7050 -3.9803 6.9900 -0.0036 0.2164 -0.0325 -0.1493 -0.0792 -0.0348 -0.1837 0.0737 0.0829 0.0481 -0.0105 -0.0126 0.0513 -0.0237 0.0345 refined 9.0309 -38.8260 -4.6917 X-RAY DIFFRACTION 1.8958 0.3935 0.3614 2.6511 0.2987 0.2715 -0.0221 0.0836 -0.1045 -0.0106 0.0343 -0.0270 0.0273 0.0192 -0.0121 0.0619 0.0034 -0.0047 0.0526 -0.0002 0.0470 refined 12.2377 -37.0776 -0.0005 X-RAY DIFFRACTION 2.0366 -0.3634 0.0678 2.1037 0.3824 0.7366 -0.0272 0.0404 0.0759 -0.0599 0.0198 0.1258 -0.0261 -0.0218 0.0074 0.0348 0.0019 -0.0047 0.0391 0.0039 0.0605 refined 3.4076 -28.4260 2.9228 X-RAY DIFFRACTION 12.6835 -1.1002 4.7185 4.9926 -1.5048 8.4282 -0.3124 -0.4567 0.3797 0.4956 0.2512 0.3411 -0.4120 -0.2884 0.0612 0.1094 0.0454 0.0450 0.0727 -0.0268 0.0725 refined -0.5566 -22.9542 14.8987 X-RAY DIFFRACTION A 7 A 24 X-RAY DIFFRACTION 1 A 25 A 53 X-RAY DIFFRACTION 2 A 54 A 71 X-RAY DIFFRACTION 3 A 72 A 80 X-RAY DIFFRACTION 4 A 81 A 97 X-RAY DIFFRACTION 5 A 98 A 130 X-RAY DIFFRACTION 6 A 131 A 141 X-RAY DIFFRACTION 7 author_and_software_defined_assembly PISA 1 monomeric A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A ASP 40 A OD1 ASP 40 1_555 83.3 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A THR 41 A O THR 41 1_555 88.0 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A THR 41 A O THR 41 1_555 77.8 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 152.7 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 123.7 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 101.4 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 94.8 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 69.6 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 146.6 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 91.2 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 76.6 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 137.6 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 137.2 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 79.2 A THP 202 C O5P THP 1_555 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 75.3 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 80.6 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 138.7 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 64.0 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 80.7 A THP 202 C O5P THP 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 149.2 A HOH 334 D O HOH 1_555 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 74.1 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 A O LYS 97 A O LYS 91 A N ALA 94 A N ALA 88 A O TYR 91 A O TYR 85 A N GLU 75 A N GLU 69 A O VAL 74 A O VAL 68 A N GLU 10 A N GLU 10 A N THR 13 A N THR 13 A O MET 26 A O MET 26 A N VAL 23 A N VAL 23 A O PHE 34 A O PHE 34 A N ARG 35 A N ARG 35 A O GLY 88 A O GLY 82 A N ASP 40 A N ASP 40 A O LYS 110 A O LYS 104 1 A ALA 1 A ALA 1 1 Y 1 A THR 2 A THR 2 1 Y 1 A SER 3 A SER 3 1 Y 1 A THR 4 A THR 4 1 Y 1 A LYS 5 A LYS 5 1 Y 1 A LYS 6 A LYS 6 1 Y 1 A GLU 142 A GLU 136 1 Y 1 A ASP 143 A ASP 137 1 Y 1 A ASN 144 A ASN 138 1 Y 1 A ALA 145 A ALA 139 1 Y 1 A ASP 146 A ASP 140 1 Y 1 A SER 147 A SER 141 1 Y 1 A GLY 148 A GLY 142 1 Y 1 A GLN 149 A GLN 143 1 Y 1 -3.12 0.50 120.30 117.18 A A A NE CZ NH2 ARG ARG ARG 126 126 126 N 1 A TYR 54 72.85 -5.25 1 A ASN 138 54.94 -109.64 56.790 17.4924 7.140 0.0400 0.0000 0.0100 0.0600 0.0000 -0.1000 0.9670 0.9630 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED 0.1884 0.1730 0.1738 0.1738 1.350 38.02 1561 30958 30957 5.0 100.0 0.2086 0.1840 1.000 0.330 0.9054 1.2400 0.0270 0.0539 0.0534 RANDOM 1 THROUGHOUT 0.0 MOLECULAR REPLACEMENT 0.0540 0.0530 0.8000 0.8000 1.4000 PDB ENTRY 3BDC MAXIMUM LIKELIHOOD MASK 1.350 38.02 121 1180 26 0 1033 0.017 0.022 1165 1.832 2.004 1589 6.769 5.000 155 33.784 25.098 51 13.962 15.000 238 8.589 15.000 5 0.128 0.200 174 0.016 0.021 855 1.315 1.500 681 2.098 2.000 1109 3.367 3.000 484 4.680 4.500 466 0.3160 0.2320 1.386 107 2149 2256 20 100.0 1.350 50.0 4EQP 30978 30978 0 0 0.054 1.9 1 16.7 6.3 100.0 0.171 1.350 1.370 1522 0.979 1 5.3 100.0 0.162 1.370 1.400 1547 1.099 1 5.9 100.0 0.144 1.400 1.430 1553 1.391 1 6.4 100.0 0.133 1.430 1.450 1523 1.507 1 6.3 100.0 0.119 1.450 1.490 1563 1.341 1 6.0 100.0 0.107 1.490 1.520 1538 1.312 1 6.4 100.0 0.102 1.520 1.560 1540 1.464 1 6.1 100.0 0.087 1.560 1.600 1539 1.320 1 6.5 100.0 0.078 1.600 1.650 1556 1.262 1 6.4 100.0 0.073 1.650 1.700 1529 1.325 1 6.1 100.0 0.066 1.700 1.760 1544 1.324 1 6.5 100.0 0.062 1.760 1.830 1572 1.566 1 6.2 100.0 0.061 1.830 1.920 1518 1.875 1 6.6 100.0 0.056 1.920 2.020 1564 2.089 1 6.5 100.0 0.050 2.020 2.140 1533 2.208 1 6.3 100.0 0.052 2.140 2.310 1553 2.529 1 6.5 100.0 0.050 2.310 2.540 1570 2.651 1 6.7 100.0 0.048 2.540 2.910 1546 2.718 1 6.5 100.0 0.048 2.910 3.660 1560 3.325 1 6.5 99.9 0.053 3.660 50.000 1608 4.069 1 6.5 100.0 data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK program phasing Randy J. Read cimr-phaser@lists.cam.ac.uk Tue Aug 24 18:17:37 2010 http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 2.2.1 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data collection CBASS data reduction HKL-2000 Crystal structure of Staphylococcal nuclease variant Delta+PHS I72D at cryogenic temperature 1 N N 2 N N 3 N N 4 N N A TYR 54 A TYR 48 HELX_P A ALA 69 A ALA 63 1 1 16 A VAL 99 A VAL 93 HELX_P A GLN 106 A GLN 100 1 2 8 A HIS 121 A HIS 115 HELX_P A GLU 135 A GLU 129 1 3 15 A LEU 137 A LEU 131 HELX_P A SER 141 A SER 135 5 4 5 metalc 2.817 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 metalc 2.741 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 metalc 2.882 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 metalc 3.017 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 metalc 3.121 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 metalc 2.809 A CA 201 B CA CA 1_555 A HOH 334 D O HOH 1_555 metalc 2.883 A CA 201 B CA CA 1_555 A HOH 341 D O HOH 1_555 HYDROLASE Staphylococcal nuclease, hyperstable, pdTp, ionizable group, HYDROLASE NUC_STAAU UNP 1 83 P00644 ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ 83 231 4EQP 1 149 P00644 A 1 1 143 1 THR deletion 4EQP A P00644 UNP 126 1 LYS deletion 4EQP A P00644 UNP 127 1 HIS deletion 4EQP A P00644 UNP 128 1 PRO deletion 4EQP A P00644 UNP 129 1 LYS deletion 4EQP A P00644 UNP 130 1 LYS deletion 4EQP A P00644 UNP 131 1 GLY engineered mutation PHE 50 4EQP A P00644 UNP 132 44 1 VAL engineered mutation ASN 51 4EQP A P00644 UNP 133 45 1 ILE engineered mutation ASP 72 4EQP A P00644 UNP 154 66 1 PRO engineered mutation GLY 117 4EQP A P00644 UNP 199 111 1 HIS engineered mutation LEU 124 4EQP A P00644 UNP 206 118 1 SER engineered mutation ALA 128 4EQP A P00644 UNP 210 122 7 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel A LYS 97 A LYS 91 A MET 98 A MET 92 A GLY 88 A GLY 82 A ALA 94 A ALA 88 A ASP 72 A ASP 66 A GLU 75 A GLU 69 A LYS 9 A LYS 9 A ALA 17 A ALA 17 A THR 22 A THR 22 A TYR 27 A TYR 27 A GLN 30 A GLN 30 A LEU 36 A LEU 36 A GLY 88 A GLY 82 A ALA 94 A ALA 88 A VAL 39 A VAL 39 A ASP 40 A ASP 40 A LYS 110 A LYS 104 A VAL 111 A VAL 105 BINDING SITE FOR RESIDUE CA A 201 A CA 201 Software 7 BINDING SITE FOR RESIDUE THP A 202 A THP 202 Software 23 A ASP 21 A ASP 21 7 1_555 A ASP 40 A ASP 40 7 1_555 A THR 41 A THR 41 7 1_555 A GLU 43 A GLU 43 7 1_555 A THP 202 C THP 7 1_555 A HOH 334 D HOH 7 1_555 A HOH 341 D HOH 7 1_555 A ARG 35 A ARG 35 23 1_555 A ASP 40 A ASP 40 23 1_555 A LYS 84 A LYS 78 23 1_555 A TYR 85 A TYR 79 23 1_555 A ARG 87 A ARG 81 23 1_555 A LEU 89 A LEU 83 23 1_555 A TYR 113 A TYR 107 23 1_555 A TYR 115 A TYR 109 23 1_555 A LYS 127 A LYS 121 23 1_655 A CA 201 B CA 23 1_555 A HOH 308 D HOH 23 1_555 A HOH 312 D HOH 23 1_555 A HOH 315 D HOH 23 1_555 A HOH 323 D HOH 23 1_555 A HOH 332 D HOH 23 1_555 A HOH 334 D HOH 23 1_555 A HOH 335 D HOH 23 1_555 A HOH 348 D HOH 23 1_555 A HOH 349 D HOH 23 1_555 A HOH 359 D HOH 23 1_555 A HOH 365 D HOH 23 1_555 A HOH 371 D HOH 23 1_555 A HOH 379 D HOH 23 1_555 4 P 1 21 1