0.032209 0.000000 0.001653 0.000000 0.016591 0.000000 0.000000 0.000000 0.026115 0.000000 0.000000 0.000000 Caro, J.A. Schlessman, J.L. Heroux, A. Garcia-Moreno E., B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.000 92.940 90.000 31.047 60.273 38.343 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 Cavity hydration in proteins 10.2210/pdb4k2l/pdb pdb_00004k2l 100 1 Meridionally-bent fused silica mirror with palladium and uncoated stripes verti cally-focusing at 6.6:1 demagnification PIXEL 2011-09-25 DECTRIS PILATUS 6M Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification SINGLE WAVELENGTH M x-ray 1 1.1000 1.0 X25 NSLS 1.1000 SYNCHROTRON NSLS BEAMLINE X25 16158.434 Thermonuclease 3.1.31.1 Nuclease A (UNP residues 83-231) G50P,V51N,I92Q,P117G,H124L,S128A,del(44-49) 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 402.188 THYMIDINE-3',5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 109 nat water TNase, Micrococcal nuclease, Staphylococcal nuclease no no ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG RGLAYQYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG RGLAYQYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ 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 nuc 1280 Staphylococcus aureus 469008 Escherichia coli BL21(DE3) plasmid pET24a+ 1 2.22 44.53 VAPOR DIFFUSION, HANGING DROP 8.0 22% 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 Data collection Database references Derived calculations Refinement description 1 0 2013-04-24 1 1 2023-09-20 _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 Crystal structure of Staphylococcal nuclease variant Delta+PHS at cryogenic temperature RCSB Y RCSB 2013-04-09 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 1 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 10 4 HOH HOH 310 A HOH 11 4 HOH HOH 311 A HOH 12 4 HOH HOH 312 A HOH 13 4 HOH HOH 313 A HOH 14 4 HOH HOH 314 A HOH 15 4 HOH HOH 315 A HOH 16 4 HOH HOH 316 A HOH 17 4 HOH HOH 317 A HOH 18 4 HOH HOH 318 A HOH 19 4 HOH HOH 319 A HOH 20 4 HOH HOH 320 A HOH 21 4 HOH HOH 321 A HOH 22 4 HOH HOH 322 A HOH 23 4 HOH HOH 323 A HOH 24 4 HOH HOH 324 A HOH 25 4 HOH HOH 325 A HOH 26 4 HOH HOH 326 A HOH 27 4 HOH HOH 327 A HOH 28 4 HOH HOH 328 A HOH 29 4 HOH HOH 329 A HOH 30 4 HOH HOH 330 A HOH 31 4 HOH HOH 331 A HOH 32 4 HOH HOH 332 A HOH 33 4 HOH HOH 333 A HOH 34 4 HOH HOH 334 A HOH 35 4 HOH HOH 335 A HOH 36 4 HOH HOH 336 A HOH 37 4 HOH HOH 337 A HOH 38 4 HOH HOH 338 A HOH 39 4 HOH HOH 339 A HOH 40 4 HOH HOH 340 A HOH 41 4 HOH HOH 341 A HOH 42 4 HOH HOH 342 A HOH 43 4 HOH HOH 343 A HOH 44 4 HOH HOH 344 A HOH 45 4 HOH HOH 345 A HOH 46 4 HOH HOH 346 A HOH 47 4 HOH HOH 347 A HOH 48 4 HOH HOH 348 A HOH 49 4 HOH HOH 349 A HOH 50 4 HOH HOH 350 A HOH 51 4 HOH HOH 351 A HOH 52 4 HOH HOH 352 A HOH 53 4 HOH HOH 353 A HOH 54 4 HOH HOH 354 A HOH 55 4 HOH HOH 355 A HOH 56 4 HOH HOH 356 A HOH 57 4 HOH HOH 357 A HOH 58 4 HOH HOH 358 A HOH 59 4 HOH HOH 359 A HOH 60 4 HOH HOH 360 A HOH 61 4 HOH HOH 361 A HOH 62 4 HOH HOH 362 A HOH 63 4 HOH HOH 363 A HOH 64 4 HOH HOH 364 A HOH 65 4 HOH HOH 365 A HOH 66 4 HOH HOH 366 A HOH 67 4 HOH HOH 367 A HOH 68 4 HOH HOH 368 A HOH 69 4 HOH HOH 369 A HOH 70 4 HOH HOH 370 A HOH 71 4 HOH HOH 371 A HOH 73 4 HOH HOH 372 A HOH 75 4 HOH HOH 373 A HOH 76 4 HOH HOH 374 A HOH 77 4 HOH HOH 375 A HOH 78 4 HOH HOH 376 A HOH 79 4 HOH HOH 377 A HOH 80 4 HOH HOH 378 A HOH 81 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 87 4 HOH HOH 385 A HOH 88 4 HOH HOH 386 A HOH 89 4 HOH HOH 387 A HOH 90 4 HOH HOH 388 A HOH 91 4 HOH HOH 389 A HOH 92 4 HOH HOH 390 A HOH 93 4 HOH HOH 391 A HOH 94 4 HOH HOH 392 A HOH 95 4 HOH HOH 393 A HOH 96 4 HOH HOH 394 A HOH 97 4 HOH HOH 395 A HOH 98 4 HOH HOH 396 A HOH 99 4 HOH HOH 397 A HOH 100 4 HOH HOH 398 A HOH 101 4 HOH HOH 399 A HOH 102 4 HOH HOH 400 A HOH 103 4 HOH HOH 401 A HOH 104 4 HOH HOH 402 A HOH 105 4 HOH HOH 403 A HOH 106 4 HOH HOH 404 A HOH 107 4 HOH HOH 405 A HOH 108 4 HOH HOH 406 A HOH 109 4 HOH HOH 407 A HOH 110 4 HOH HOH 408 A HOH 111 4 HOH HOH 409 A 2.500 2.500 32.320 32.320 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 ILE 72 n 66 ILE 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 GLN 92 n 86 GLN 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 2.5556 -0.4847 -0.1685 2.1329 0.3981 0.0894 -0.0802 0.0865 -0.2461 -0.0042 0.0988 0.0112 0.0109 0.0374 -0.0186 0.0945 0.0261 -0.0076 0.0775 -0.0129 0.1277 refined 13.6777 -3.1145 2.1498 X-RAY DIFFRACTION 3.4845 -0.3205 0.1192 1.7616 0.7155 1.0512 -0.1169 -0.2688 -0.0596 0.1874 0.0992 0.1089 0.1296 0.0987 0.0177 0.1060 0.0255 0.0100 0.0703 0.0332 0.0273 refined 10.3067 2.9714 9.5291 X-RAY DIFFRACTION 2.6912 -0.6968 0.0299 2.3299 0.3093 0.5028 -0.0492 0.1528 0.0966 -0.0685 0.0480 0.2316 0.0292 0.0055 0.0012 0.0574 -0.0065 -0.0105 0.0628 0.0336 0.0970 refined 6.5034 7.1931 1.7925 X-RAY DIFFRACTION 5.1936 0.4712 3.5620 5.8907 0.6596 4.4849 -0.3312 -0.4503 0.6627 0.4154 0.2081 0.6905 -0.2808 -0.2385 0.1231 0.1746 0.0690 0.0587 0.1436 -0.0690 0.2468 refined -0.5547 15.9852 13.9338 X-RAY DIFFRACTION A 7 A 38 X-RAY DIFFRACTION 1 A 39 A 80 X-RAY DIFFRACTION 2 A 81 A 128 X-RAY DIFFRACTION 3 A 129 A 141 X-RAY DIFFRACTION 4 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 82.3 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 87.6 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 76.9 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_555 150.6 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_555 126.3 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_555 103.8 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 96.1 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_555 145.4 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 89.7 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A HOH 304 D O HOH 1_555 76.5 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A HOH 304 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 304 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 304 D O HOH 1_555 76.9 A THP 202 C O5P THP 1_555 A CA 201 B CA CA 1_555 A HOH 304 D O HOH 1_555 76.6 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 A HOH 310 D O HOH 1_555 80.1 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 A HOH 310 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 310 D O HOH 1_555 65.3 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 A HOH 310 D O HOH 1_555 80.4 A THP 202 C O5P THP 1_555 A CA 201 B CA CA 1_555 A HOH 310 D O HOH 1_555 149.3 A HOH 304 D O HOH 1_555 A CA 201 B CA CA 1_555 A HOH 310 D O HOH 1_555 72.9 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 A TYR 54 69.06 -2.59 1 A ASN 118 -112.52 54.63 1 A ASN 138 58.20 -109.26 68.790 26.6664 14.530 -1.2400 0.0000 0.6500 -1.0500 0.0000 2.3600 0.9690 0.9550 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED 0.2139 0.1720 0.1743 0.1743 1.550 38.29 1051 20493 20493 5.1 99.49 0.2438 0.1888 1.000 0.300 0.8645 2.5080 0.0520 0.0787 0.0847 RANDOM 1 THROUGHOUT 0.0 0 MOLECULAR REPLACEMENT 0.0790 0.0850 0.8000 0.8000 1.2000 PDB ENTRY 3BDC MAXIMUM LIKELIHOOD MASK 1.550 38.29 109 1169 26 0 1034 0.019 0.020 1142 1.913 2.000 1550 6.267 5.000 147 33.018 25.098 51 14.660 15.000 230 8.220 15.000 5 0.147 0.200 168 0.012 0.021 835 0.2800 0.2130 1.588 63 1327 1390 1390 20 95.08 31.7 1.550 50.0 4K2L 20512 20512 0 0 0.054 2.292 1 18.5 6.1 99.7 0.191 1.550 1.580 8.4 999 1.078 1 4.8 98.2 0.176 1.580 1.610 1013 1.093 1 5.1 99.8 0.160 1.610 1.640 1035 1.187 1 5.8 100.0 0.149 1.640 1.670 1018 1.198 1 6.3 100.0 0.131 1.670 1.710 1012 1.337 1 6.0 100.0 0.122 1.710 1.750 1038 1.366 1 6.4 100.0 0.106 1.750 1.790 1011 1.502 1 6.5 100.0 0.096 1.790 1.840 1053 1.759 1 6.2 100.0 0.088 1.840 1.890 988 1.812 1 6.3 100.0 0.077 1.890 1.950 1030 2.041 1 6.4 100.0 0.074 1.950 2.020 1031 2.316 1 6.1 100.0 0.069 2.020 2.100 1025 2.633 1 6.6 100.0 0.063 2.100 2.200 1033 2.828 1 6.4 99.9 0.059 2.200 2.320 1019 2.822 1 6.3 100.0 0.057 2.320 2.460 1030 3.089 1 6.3 99.9 0.052 2.460 2.650 1033 2.957 1 6.4 100.0 0.051 2.650 2.920 1021 3.179 1 6.2 99.9 0.050 2.920 3.340 1036 3.443 1 6.2 99.7 0.048 3.340 4.210 1035 3.651 1 6.0 98.9 0.051 4.210 50.000 1052 3.881 1 6.0 98.6 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 Mon Jun 27 09:33:44 2011 (svn ) http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 2.3.0 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 I92Q 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 2.846 A ASP 21 A OD2 ASP 21 1_555 A CA 201 B CA CA 1_555 metalc 2.678 A ASP 40 A OD1 ASP 40 1_555 A CA 201 B CA CA 1_555 metalc 2.797 A THR 41 A O THR 41 1_555 A CA 201 B CA CA 1_555 metalc 3.062 A GLU 43 A OE2 GLU 43 1_555 A CA 201 B CA CA 1_555 metalc 3.104 A CA 201 B CA CA 1_555 A THP 202 C O5P THP 1_555 metalc 2.852 A CA 201 B CA CA 1_555 A HOH 304 D O HOH 1_555 metalc 2.939 A CA 201 B CA CA 1_555 A HOH 310 D O HOH 1_555 HYDROLASE Staphylococcal nuclease, hyperstable variant, pdtp, cavity, pressure, HYDROLASE NUC_STAAU UNP 1 83 P00644 ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ 83 231 4K2L 1 149 P00644 A 1 1 143 1 THR deletion 4K2L A P00644 UNP 126 1 LYS deletion 4K2L A P00644 UNP 127 1 HIS deletion 4K2L A P00644 UNP 128 1 PRO deletion 4K2L A P00644 UNP 129 1 LYS deletion 4K2L A P00644 UNP 130 1 LYS deletion 4K2L A P00644 UNP 131 1 GLY engineered mutation PHE 50 4K2L A P00644 UNP 132 44 1 VAL engineered mutation ASN 51 4K2L A P00644 UNP 133 45 1 ILE engineered mutation GLN 92 4K2L A P00644 UNP 174 86 1 PRO engineered mutation GLY 117 4K2L A P00644 UNP 199 111 1 HIS engineered mutation LEU 124 4K2L A P00644 UNP 206 118 1 SER engineered mutation ALA 128 4K2L 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 ILE 72 A ILE 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 20 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 304 D HOH 7 1_555 A HOH 310 D HOH 7 1_555 A ARG 35 A ARG 35 20 1_555 A ASP 40 A ASP 40 20 1_555 A LYS 84 A LYS 78 20 1_555 A TYR 85 A TYR 79 20 1_555 A ARG 87 A ARG 81 20 1_555 A TYR 113 A TYR 107 20 1_555 A TYR 115 A TYR 109 20 1_555 A LYS 127 A LYS 121 20 1_655 A CA 201 B CA 20 1_555 A HOH 301 D HOH 20 1_555 A HOH 304 D HOH 20 1_555 A HOH 326 D HOH 20 1_555 A HOH 335 D HOH 20 1_555 A HOH 338 D HOH 20 1_555 A HOH 341 D HOH 20 1_555 A HOH 343 D HOH 20 1_555 A HOH 361 D HOH 20 1_555 A HOH 367 D HOH 20 1_555 A HOH 392 D HOH 20 1_555 A HOH 394 D HOH 20 1_555 4 P 1 21 1