0.032165 0.000000 0.002007 0.000000 0.016629 0.000000 0.000000 0.000000 0.026233 0.00000 0.00000 0.00000 Caro, J.A. Schlessman, J.L. Garcia-Moreno, E.B. Heroux, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 93.57 90.00 31.090 60.137 38.194 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 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 109 6945 6950 10.1073/pnas.1200915109 22496593 Cavities determine the pressure unfolding of proteins. 2012 10.2210/pdb3meh/pdb pdb_00003meh 100 1 CCD 2010-01-25 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 1.1000 1.0 X25 NSLS 1.1000 SYNCHROTRON NSLS BEAMLINE X25 16101.383 Thermonuclease 3.1.31.1 Deletion UNP residues 126-131 G50F,V51N,I92A,P117G,H124L,S128A 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 402.188 THYMIDINE-3',5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 117 nat water Micrococcal nuclease, Staphylococcal nuclease no no ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG RGLAYAYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG RGLAYAYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ 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 562 Escherichia coli BL21(DE3) plasmid pET24a+ 1 2.21 44.42 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 software database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Version format compliance Atomic model Database references Atomic model Refinement description Database references Derived calculations Data collection Refinement description 1 0 2011-03-16 1 1 2011-07-13 1 2 2011-09-07 1 3 2012-05-23 1 4 2014-06-04 1 5 2017-11-08 1 6 2021-10-06 1 7 2023-09-06 _software.classification _software.contact_author _software.contact_author_email _software.date _software.language _software.location _software.name _software.type _software.version _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 Staph nuclease Delta+PHS CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS L25A AT CRYOGENIC TEMPERATURE Crystal structure of Staphylococcal nuclease variant Delta+PHS L38A at cryogenic temperature RCSB Y RCSB 2010-03-31 REL REL CA CALCIUM ION THP THYMIDINE-3',5'-DIPHOSPHATE HOH water 3BDC 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, T82A, I92A, Y113A, V114A and Y115A; all b-factors were reset to 20. PDB experimental model CA 151 2 CA CA 151 A THP 150 3 THP THP 150 A HOH 152 4 HOH HOH 152 A HOH 153 4 HOH HOH 153 A HOH 154 4 HOH HOH 154 A HOH 155 4 HOH HOH 155 A HOH 156 4 HOH HOH 156 A HOH 157 4 HOH HOH 157 A HOH 158 4 HOH HOH 158 A HOH 159 4 HOH HOH 159 A HOH 160 4 HOH HOH 160 A HOH 161 4 HOH HOH 161 A HOH 162 4 HOH HOH 162 A HOH 163 4 HOH HOH 163 A HOH 164 4 HOH HOH 164 A HOH 165 4 HOH HOH 165 A HOH 166 4 HOH HOH 166 A HOH 167 4 HOH HOH 167 A HOH 168 4 HOH HOH 168 A HOH 169 4 HOH HOH 169 A HOH 170 4 HOH HOH 170 A HOH 171 4 HOH HOH 171 A HOH 172 4 HOH HOH 172 A HOH 173 4 HOH HOH 173 A HOH 174 4 HOH HOH 174 A HOH 175 4 HOH HOH 175 A HOH 176 4 HOH HOH 176 A HOH 177 4 HOH HOH 177 A HOH 178 4 HOH HOH 178 A HOH 179 4 HOH HOH 179 A HOH 180 4 HOH HOH 180 A HOH 181 4 HOH HOH 181 A HOH 182 4 HOH HOH 182 A HOH 183 4 HOH HOH 183 A HOH 184 4 HOH HOH 184 A HOH 185 4 HOH HOH 185 A HOH 186 4 HOH HOH 186 A HOH 187 4 HOH HOH 187 A HOH 188 4 HOH HOH 188 A HOH 189 4 HOH HOH 189 A HOH 190 4 HOH HOH 190 A HOH 191 4 HOH HOH 191 A HOH 192 4 HOH HOH 192 A HOH 193 4 HOH HOH 193 A HOH 194 4 HOH HOH 194 A HOH 195 4 HOH HOH 195 A HOH 196 4 HOH HOH 196 A HOH 197 4 HOH HOH 197 A HOH 198 4 HOH HOH 198 A HOH 199 4 HOH HOH 199 A HOH 200 4 HOH HOH 200 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 203 4 HOH HOH 203 A HOH 204 4 HOH HOH 204 A HOH 205 4 HOH HOH 205 A HOH 206 4 HOH HOH 206 A HOH 207 4 HOH HOH 207 A HOH 208 4 HOH HOH 208 A HOH 209 4 HOH HOH 209 A HOH 210 4 HOH HOH 210 A HOH 211 4 HOH HOH 211 A HOH 212 4 HOH HOH 212 A HOH 213 4 HOH HOH 213 A HOH 214 4 HOH HOH 214 A HOH 215 4 HOH HOH 215 A HOH 216 4 HOH HOH 216 A HOH 217 4 HOH HOH 217 A HOH 218 4 HOH HOH 218 A HOH 219 4 HOH HOH 219 A HOH 220 4 HOH HOH 220 A HOH 221 4 HOH HOH 221 A HOH 222 4 HOH HOH 222 A HOH 223 4 HOH HOH 223 A HOH 224 4 HOH HOH 224 A HOH 225 4 HOH HOH 225 A HOH 226 4 HOH HOH 226 A HOH 227 4 HOH HOH 227 A HOH 228 4 HOH HOH 228 A HOH 229 4 HOH HOH 229 A HOH 230 4 HOH HOH 230 A HOH 231 4 HOH HOH 231 A HOH 232 4 HOH HOH 232 A HOH 233 4 HOH HOH 233 A HOH 234 4 HOH HOH 234 A HOH 235 4 HOH HOH 235 A HOH 236 4 HOH HOH 236 A HOH 237 4 HOH HOH 237 A HOH 238 4 HOH HOH 238 A HOH 239 4 HOH HOH 239 A HOH 240 4 HOH HOH 240 A HOH 241 4 HOH HOH 241 A HOH 242 4 HOH HOH 242 A HOH 243 4 HOH HOH 243 A HOH 244 4 HOH HOH 244 A HOH 245 4 HOH HOH 245 A HOH 246 4 HOH HOH 246 A HOH 247 4 HOH HOH 247 A HOH 248 4 HOH HOH 248 A HOH 249 4 HOH HOH 249 A HOH 250 4 HOH HOH 250 A HOH 251 4 HOH HOH 251 A HOH 252 4 HOH HOH 252 A HOH 253 4 HOH HOH 253 A HOH 254 4 HOH HOH 254 A HOH 255 4 HOH HOH 255 A HOH 256 4 HOH HOH 256 A HOH 257 4 HOH HOH 257 A HOH 258 4 HOH HOH 258 A HOH 259 4 HOH HOH 259 A HOH 260 4 HOH HOH 260 A HOH 261 4 HOH HOH 261 A HOH 262 4 HOH HOH 262 A HOH 263 4 HOH HOH 263 A HOH 264 4 HOH HOH 264 A HOH 265 4 HOH HOH 265 A HOH 266 4 HOH HOH 266 A HOH 267 4 HOH HOH 267 A HOH 268 4 HOH HOH 268 A 36.820 2.500 2.500 31.030 31.030 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 ALA 92 n 86 ALA 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 author_and_software_defined_assembly PISA 1 monomeric A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A ASP 40 A OD1 ASP 40 1_555 82.0 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A THR 41 A O THR 41 1_555 87.3 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 A THR 41 A O THR 41 1_555 76.8 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 152.9 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 123.8 A THR 41 A O THR 41 1_555 A CA 151 B CA CA 1_555 A GLU 43 A OE2 GLU 43 1_555 105.2 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A THP 150 C O6P THP 1_555 95.0 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 A THP 150 C O6P THP 1_555 69.0 A THR 41 A O THR 41 1_555 A CA 151 B CA CA 1_555 A THP 150 C O6P THP 1_555 145.0 A GLU 43 A OE2 GLU 43 1_555 A CA 151 B CA CA 1_555 A THP 150 C O6P THP 1_555 88.4 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 76.3 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 137.8 A THR 41 A O THR 41 1_555 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 136.6 A GLU 43 A OE2 GLU 43 1_555 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 78.2 A THP 150 C O6P THP 1_555 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 77.2 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 80.9 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 139.3 A THR 41 A O THR 41 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 65.8 A GLU 43 A OE2 GLU 43 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 82.6 A THP 150 C O6P THP 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 149.1 A HOH 155 D O HOH 1_555 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 72.0 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 93 A O TYR 87 A N GLU 73 A N GLU 67 A O VAL 74 A O VAL 68 A N GLU 10 A N GLU 10 A N LYS 16 A N LYS 16 A O LYS 24 A O LYS 24 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 14.26 2.00 110.40 124.66 A A A CB CA C ASN ASN ASN 118 118 118 C C N 1 A A CB CG ASN ASN 118 118 -0.146 0.023 1.506 1.360 C C N 1 A ILE 18 -119.65 -71.16 1 A TYR 54 68.12 -2.95 1 A ASN 138 52.39 -105.74 55.24 24.749 12.44 -1.200 0.000 0.610 -1.790 0.000 3.070 0.967 0.946 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY 0.234 0.186 0.1863 0.191 1.500 31.030 2233 22510 22299 10.000 99.060 0.245 0.200 1.00 0.00 0.826 1.593 0.060 0.084 0.091 RANDOM 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.084 0.091 0.800 0.800 1.400 3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, T82A, I92A, Y113A, V114A and Y115A; all b-factors were reset to 20. MAXIMUM LIKELIHOOD MASK 1.500 31.030 117 1173 26 0 1030 0.018 0.022 1162 1.834 1.998 1583 6.554 5.000 154 31.423 25.192 52 16.525 15.000 232 9.939 15.000 5 0.146 0.200 172 0.014 0.021 859 1.642 1.500 681 2.439 2.000 1105 3.439 3.000 481 4.976 4.500 465 0.268 0.258 1.539 147 1412 1559 20 93.630 30.0 1.500 60.000 3MEH 22523 22523 0 0 0.060 1.929 1 15.200 12.200 99.000 0.397 1.50 1.53 1042 0.787 1 8.90 92.50 0.378 1.53 1.55 1103 0.790 1 9.60 95.50 0.334 1.55 1.58 1087 0.820 1 10.40 98.70 0.290 1.58 1.62 1135 0.854 1 11.00 99.80 0.258 1.62 1.65 1139 0.930 1 11.70 99.70 0.228 1.65 1.69 1121 0.912 1 12.40 100.00 0.207 1.69 1.73 1158 0.966 1 12.80 99.90 0.177 1.73 1.78 1104 1.098 1 13.20 100.00 0.145 1.78 1.83 1169 1.262 1 13.10 100.00 0.131 1.83 1.89 1102 1.465 1 13.30 100.00 0.109 1.89 1.96 1131 1.688 1 13.10 100.00 0.098 1.96 2.04 1143 1.981 1 13.20 100.00 0.084 2.04 2.13 1131 2.247 1 13.10 100.00 0.075 2.13 2.24 1138 2.577 1 13.10 99.90 0.074 2.24 2.38 1132 2.878 1 13.00 99.80 0.067 2.38 2.56 1144 3.123 1 12.90 100.00 0.060 2.56 2.82 1147 3.370 1 12.60 99.70 0.052 2.82 3.23 1140 3.455 1 12.00 99.90 0.045 3.23 4.07 1139 3.494 1 12.10 99.90 0.039 4.07 60.00 1118 2.845 1 11.80 94.60 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO package data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK package phasing Randy J. Read cimr-phaser@lists.cam.ac.uk Tue Jul 1 14:16:50 2008 http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 2.1.3 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 help@deposit.rcsb.org Jan. 22, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.100 data collection CBASS data reduction HKL-2000 Crystal structure of Staphylococcal nuclease variant Delta+PHS I92A at cryogenic temperature 1 N N 2 N N 3 N N 4 N N A TYR 54 A TYR 48 HELX_P A ASN 68 A ASN 62 1 1 15 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 2.811 A ASP 21 A OD2 ASP 21 1_555 A CA 151 B CA CA 1_555 metalc 2.666 A ASP 40 A OD1 ASP 40 1_555 A CA 151 B CA CA 1_555 metalc 2.859 A THR 41 A O THR 41 1_555 A CA 151 B CA CA 1_555 metalc 2.971 A GLU 43 A OE2 GLU 43 1_555 A CA 151 B CA CA 1_555 metalc 3.088 A THP 150 C O6P THP 1_555 A CA 151 B CA CA 1_555 metalc 2.822 A CA 151 B CA CA 1_555 A HOH 155 D O HOH 1_555 metalc 2.838 A CA 151 B CA CA 1_555 A HOH 158 D O HOH 1_555 HYDROLASE hyperstable variant, hydrolase, pdtp, cavity, pressure NUC_STAAU UNP 1 83 P00644 ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ 83 231 3MEH 1 149 P00644 A 1 1 143 1 THR deletion 3MEH A P00644 UNP 126 1 LYS deletion 3MEH A P00644 UNP 127 1 HIS deletion 3MEH A P00644 UNP 128 1 PRO deletion 3MEH A P00644 UNP 129 1 LYS deletion 3MEH A P00644 UNP 130 1 LYS deletion 3MEH A P00644 UNP 131 1 GLY engineered mutation PHE 50 3MEH A P00644 UNP 132 44 1 VAL engineered mutation ASN 51 3MEH A P00644 UNP 133 45 1 ILE engineered mutation ALA 92 3MEH A P00644 UNP 174 86 1 PRO engineered mutation GLY 117 3MEH A P00644 UNP 199 111 1 HIS engineered mutation LEU 124 3MEH A P00644 UNP 206 118 1 SER engineered mutation ALA 128 3MEH 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 151 A CA 151 Software 7 BINDING SITE FOR RESIDUE THP A 150 A THP 150 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 150 C THP 7 1_555 A HOH 155 D HOH 7 1_555 A HOH 158 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 LEU 89 A LEU 83 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 151 B CA 20 1_555 A HOH 152 D HOH 20 1_555 A HOH 155 D HOH 20 1_555 A HOH 169 D HOH 20 1_555 A HOH 172 D HOH 20 1_555 A HOH 176 D HOH 20 1_555 A HOH 187 D HOH 20 1_555 A HOH 190 D HOH 20 1_555 A HOH 193 D HOH 20 1_555 A HOH 195 D HOH 20 1_555 A HOH 215 D HOH 20 1_555 4 P 1 21 1