0.025734 0.000000 0.000000 0.000000 0.025734 0.000000 0.000000 0.000000 0.004688 0.00000 0.00000 0.00000 Ipsaro, J.J. Haase, A.D. Hannon, G.J. Joshua-Tor, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 38.859 38.859 213.310 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 O4 W -2 247.838 TUNGSTATE(VI)ION non-polymer Zn 2 65.409 ZINC ION non-polymer 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 N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H 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 H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C 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 H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N N N 184 S C N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N C N 213 N N N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C N 235 N C N 236 N S N 237 N C N 238 N O N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N N N 251 S C N 252 N C N 253 N O N 254 N C Y 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C N 261 N O 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 H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N N N 274 S C N 275 N C N 276 N O N 277 N C N 278 N C N 279 N C N 280 N O N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N O N 296 N O N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N N N 305 S C N 306 N C N 307 N O N 308 R C N 309 N O N 310 N C N 311 N O N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N N N 322 S C N 323 N C N 324 N O N 325 N C Y 326 N C Y 327 N C Y 328 N C Y 329 N N Y 330 N C Y 331 N C Y 332 N C Y 333 N C Y 334 N C N 335 N O 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 H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N N N 349 S C N 350 N C N 351 N O N 352 N C Y 353 N C Y 354 N C Y 355 N C Y 356 N C Y 357 N C Y 358 N C N 359 N O N 360 N O N 361 N H N 362 N H N 363 N H 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 N N 373 S C N 374 N C N 375 N O N 376 N C N 377 N C N 378 N C N 379 N O 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 H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N W N 392 N O N 393 N O N 394 N O N 395 N O N 396 N ZN 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 sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub 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 doub N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 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 doub 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 sing 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 doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N 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 doub 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 sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub 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 sing N 241 N sing N 242 N sing N 243 N doub N 244 N sing N 245 N sing N 246 N sing N 247 N sing Y 248 N doub Y 249 N sing Y 250 N sing N 251 N sing Y 252 N doub N 253 N sing Y 254 N doub N 255 N sing Y 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 doub 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 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 doub 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 sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N doub N 313 N sing N 314 N sing N 315 N sing N 316 N sing Y 317 N doub Y 318 N sing Y 319 N sing N 320 N sing Y 321 N doub Y 322 N sing Y 323 N sing N 324 N sing Y 325 N sing Y 326 N doub N 327 N sing Y 328 N doub N 329 N sing Y 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 doub N 341 N sing N 342 N sing N 343 N sing N 344 N sing Y 345 N doub Y 346 N sing Y 347 N sing N 348 N sing Y 349 N doub N 350 N sing Y 351 N doub N 352 N sing Y 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N doub N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 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 doub N 377 N doub N 378 N sing N 379 N sing UK Nature NATUAS 0006 0028-0836 491 279 283 10.1038/nature11502 23064227 The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. 2012 10.2210/pdb4ggk/pdb pdb_00004ggk 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2012-04-14 ADSC QUANTUM 315 Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror SINGLE WAVELENGTH M x-ray 1 1.2716 1.0 1.2983 1.0 X29A NSLS 1.2716, 1.2983 SYNCHROTRON NSLS BEAMLINE X29A 22342.830 Mitochondrial cardiolipin hydrolase 3.1.4.- Cytoplasmic domain, UNP residues 31-221 1 man polymer 65.409 ZINC ION 1 syn non-polymer 247.838 TUNGSTATE(VI)ION 1 syn non-polymer 18.015 water 35 nat water Choline phosphatase 6, Mitochondrial phospholipase, MitoPLD, Phosphatidylcholine-hydrolyzing phospholipase D6, Phospholipase D6, PLD 6 no no MLAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQL LHQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDT EYVRLFLEEFERIWEEFDPTKYSFFPQKHRGHLVPR MLAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQL LHQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDT EYVRLFLEEFERIWEEFDPTKYSFFPQKHRGHLVPR 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 mouse sample Pld6 10090 Mus musculus 7108 Spodoptera frugiperda Sf9 baculovirus pFL 1 1.80 31.74 VAPOR DIFFUSION, HANGING DROP 6.5 50 mM Bis-Tris, pH 6.5, 18% PEG-3350, 2% tascimate, pH 6.0, 1:100 m/m ratio protein:chymotrypsin, 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 Data collection Database references Derived calculations Refinement description 1 0 2012-10-10 1 1 2012-12-12 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_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_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_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_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 Nuc (dsDNAse) Crystal structure of Nuc (dsDNAse) in complex with tungstate RCSB Y RCSB 2012-08-06 REL REL ZN ZINC ION WO4 TUNGSTATE(VI)ION HOH water 1BYR PDB entry 1BYR PDB experimental model ZN 210 2 ZN ZN 301 A WO4 211 3 WO4 WO4 302 A HOH 1 4 HOH HOH 401 A HOH 2 4 HOH HOH 402 A HOH 3 4 HOH HOH 403 A HOH 4 4 HOH HOH 404 A HOH 5 4 HOH HOH 405 A HOH 6 4 HOH HOH 406 A HOH 7 4 HOH HOH 407 A HOH 8 4 HOH HOH 408 A HOH 9 4 HOH HOH 409 A HOH 10 4 HOH HOH 410 A HOH 11 4 HOH HOH 411 A HOH 12 4 HOH HOH 412 A HOH 13 4 HOH HOH 413 A HOH 14 4 HOH HOH 414 A HOH 15 4 HOH HOH 415 A HOH 16 4 HOH HOH 416 A HOH 17 4 HOH HOH 417 A HOH 18 4 HOH HOH 418 A HOH 19 4 HOH HOH 419 A HOH 20 4 HOH HOH 420 A HOH 21 4 HOH HOH 421 A HOH 22 4 HOH HOH 422 A HOH 23 4 HOH HOH 423 A HOH 24 4 HOH HOH 424 A HOH 25 4 HOH HOH 425 A HOH 26 4 HOH HOH 426 A HOH 27 4 HOH HOH 427 A HOH 28 4 HOH HOH 428 A HOH 29 4 HOH HOH 429 A HOH 30 4 HOH HOH 430 A HOH 31 4 HOH HOH 431 A HOH 32 4 HOH HOH 432 A HOH 33 4 HOH HOH 433 A HOH 34 4 HOH HOH 434 A HOH 35 4 HOH HOH 435 A n 1 30 A n 2 31 A n 3 32 A n 4 33 A n 5 34 A n 6 35 A PRO 36 n 7 PRO 36 A ARG 37 n 8 ARG 37 A ARG 38 n 9 ARG 38 A GLU 39 n 10 GLU 39 A VAL 40 n 11 VAL 40 A LEU 41 n 12 LEU 41 A PHE 42 n 13 PHE 42 A PHE 43 n 14 PHE 43 A PRO 44 n 15 PRO 44 A SER 45 n 16 SER 45 A GLN 46 n 17 GLN 46 A VAL 47 n 18 VAL 47 A THR 48 n 19 THR 48 A CYS 49 n 20 CYS 49 A THR 50 n 21 THR 50 A GLU 51 n 22 GLU 51 A ALA 52 n 23 ALA 52 A LEU 53 n 24 LEU 53 A LEU 54 n 25 LEU 54 A GLN 55 n 26 GLN 55 A ALA 56 n 27 ALA 56 A PRO 57 n 28 PRO 57 A GLY 58 n 29 GLY 58 A n 30 59 A n 31 60 A n 32 61 A n 33 62 A n 34 63 A n 35 64 A n 36 65 A CYS 66 n 37 CYS 66 A PRO 67 n 38 PRO 67 A CYS 68 n 39 CYS 68 A SER 69 n 40 SER 69 A LEU 70 n 41 LEU 70 A PRO 71 n 42 PRO 71 A HIS 72 n 43 HIS 72 A SER 73 n 44 SER 73 A GLU 74 n 45 GLU 74 A SER 75 n 46 SER 75 A SER 76 n 47 SER 76 A LEU 77 n 48 LEU 77 A SER 78 n 49 SER 78 A ARG 79 n 50 ARG 79 A LEU 80 n 51 LEU 80 A LEU 81 n 52 LEU 81 A ARG 82 n 53 ARG 82 A ALA 83 n 54 ALA 83 A LEU 84 n 55 LEU 84 A LEU 85 n 56 LEU 85 A ALA 86 n 57 ALA 86 A ALA 87 n 58 ALA 87 A ARG 88 n 59 ARG 88 A SER 89 n 60 SER 89 A SER 90 n 61 SER 90 A LEU 91 n 62 LEU 91 A GLU 92 n 63 GLU 92 A LEU 93 n 64 LEU 93 A CYS 94 n 65 CYS 94 A LEU 95 n 66 LEU 95 A PHE 96 n 67 PHE 96 A ALA 97 n 68 ALA 97 A PHE 98 n 69 PHE 98 A SER 99 n 70 SER 99 A SER 100 n 71 SER 100 A PRO 101 n 72 PRO 101 A GLN 102 n 73 GLN 102 A LEU 103 n 74 LEU 103 A GLY 104 n 75 GLY 104 A ARG 105 n 76 ARG 105 A ALA 106 n 77 ALA 106 A VAL 107 n 78 VAL 107 A GLN 108 n 79 GLN 108 A LEU 109 n 80 LEU 109 A LEU 110 n 81 LEU 110 A HIS 111 n 82 HIS 111 A GLN 112 n 83 GLN 112 A ARG 113 n 84 ARG 113 A GLY 114 n 85 GLY 114 A VAL 115 n 86 VAL 115 A ARG 116 n 87 ARG 116 A VAL 117 n 88 VAL 117 A ARG 118 n 89 ARG 118 A VAL 119 n 90 VAL 119 A ILE 120 n 91 ILE 120 A THR 121 n 92 THR 121 A ASP 122 n 93 ASP 122 A CYS 123 n 94 CYS 123 A ASP 124 n 95 ASP 124 A TYR 125 n 96 TYR 125 A MET 126 n 97 MET 126 A n 98 127 A n 99 128 A n 100 129 A GLY 130 n 101 GLY 130 A SER 131 n 102 SER 131 A GLN 132 n 103 GLN 132 A ILE 133 n 104 ILE 133 A GLY 134 n 105 GLY 134 A LEU 135 n 106 LEU 135 A LEU 136 n 107 LEU 136 A ARG 137 n 108 ARG 137 A LYS 138 n 109 LYS 138 A ALA 139 n 110 ALA 139 A GLY 140 n 111 GLY 140 A ILE 141 n 112 ILE 141 A GLN 142 n 113 GLN 142 A VAL 143 n 114 VAL 143 A ARG 144 n 115 ARG 144 A HIS 145 n 116 HIS 145 A ASP 146 n 117 ASP 146 A GLN 147 n 118 GLN 147 A ASP 148 n 119 ASP 148 A LEU 149 n 120 LEU 149 A GLY 150 n 121 GLY 150 A TYR 151 n 122 TYR 151 A MET 152 n 123 MET 152 A HIS 153 n 124 HIS 153 A HIS 154 n 125 HIS 154 A LYS 155 n 126 LYS 155 A PHE 156 n 127 PHE 156 A ALA 157 n 128 ALA 157 A ILE 158 n 129 ILE 158 A VAL 159 n 130 VAL 159 A ASP 160 n 131 ASP 160 A LYS 161 n 132 LYS 161 A LYS 162 n 133 LYS 162 A VAL 163 n 134 VAL 163 A LEU 164 n 135 LEU 164 A ILE 165 n 136 ILE 165 A THR 166 n 137 THR 166 A GLY 167 n 138 GLY 167 A SER 168 n 139 SER 168 A LEU 169 n 140 LEU 169 A ASN 170 n 141 ASN 170 A TRP 171 n 142 TRP 171 A THR 172 n 143 THR 172 A THR 173 n 144 THR 173 A GLN 174 n 145 GLN 174 A ALA 175 n 146 ALA 175 A ILE 176 n 147 ILE 176 A GLN 177 n 148 GLN 177 A ASN 178 n 149 ASN 178 A ASN 179 n 150 ASN 179 A ARG 180 n 151 ARG 180 A GLU 181 n 152 GLU 181 A ASN 182 n 153 ASN 182 A VAL 183 n 154 VAL 183 A LEU 184 n 155 LEU 184 A ILE 185 n 156 ILE 185 A MET 186 n 157 MET 186 A GLU 187 n 158 GLU 187 A ASP 188 n 159 ASP 188 A THR 189 n 160 THR 189 A GLU 190 n 161 GLU 190 A TYR 191 n 162 TYR 191 A VAL 192 n 163 VAL 192 A ARG 193 n 164 ARG 193 A LEU 194 n 165 LEU 194 A PHE 195 n 166 PHE 195 A LEU 196 n 167 LEU 196 A GLU 197 n 168 GLU 197 A GLU 198 n 169 GLU 198 A PHE 199 n 170 PHE 199 A GLU 200 n 171 GLU 200 A ARG 201 n 172 ARG 201 A ILE 202 n 173 ILE 202 A TRP 203 n 174 TRP 203 A GLU 204 n 175 GLU 204 A GLU 205 n 176 GLU 205 A PHE 206 n 177 PHE 206 A ASP 207 n 178 ASP 207 A PRO 208 n 179 PRO 208 A THR 209 n 180 THR 209 A n 181 210 A n 182 211 A n 183 212 A n 184 213 A n 185 214 A n 186 215 A n 187 216 A n 188 217 A n 189 218 A n 190 219 A n 191 220 A n 192 221 A n 193 222 A n 194 223 A n 195 224 A n 196 225 A 5.2756 -1.1767 -0.1849 2.6755 -0.4657 3.4310 0.0673 0.4078 -0.2012 -0.2536 -0.0997 -0.0417 -0.1366 0.0669 0.0324 0.0484 -0.0124 -0.0006 0.0696 -0.0277 0.0300 refined -10.3089 -15.4007 -12.2358 X-RAY DIFFRACTION A 36 A 302 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 2 dimeric 3180 -17 14370 A CYS 49 A SG CYS 20 1_555 A ZN 301 B ZN ZN 1_555 A CYS 66 A SG CYS 37 1_555 119.3 A CYS 49 A SG CYS 20 1_555 A ZN 301 B ZN ZN 1_555 A CYS 68 A SG CYS 39 1_555 105.2 A CYS 66 A SG CYS 37 1_555 A ZN 301 B ZN ZN 1_555 A CYS 68 A SG CYS 39 1_555 111.5 A CYS 49 A SG CYS 20 1_555 A ZN 301 B ZN ZN 1_555 A HIS 72 A NE2 HIS 43 1_555 106.6 A CYS 66 A SG CYS 37 1_555 A ZN 301 B ZN ZN 1_555 A HIS 72 A NE2 HIS 43 1_555 102.3 A CYS 68 A SG CYS 39 1_555 A ZN 301 B ZN ZN 1_555 A HIS 72 A NE2 HIS 43 1_555 111.8 A HIS 153 A NE2 HIS 124 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O1 WO4 1_555 67.7 A HIS 153 A NE2 HIS 124 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O2 WO4 1_555 161.9 A WO4 302 C O1 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O2 WO4 1_555 107.2 A HIS 153 A NE2 HIS 124 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O3 WO4 1_555 59.7 A WO4 302 C O1 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O3 WO4 1_555 111.2 A WO4 302 C O2 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O3 WO4 1_555 109.6 A HIS 153 A NE2 HIS 124 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O4 WO4 1_555 87.7 A WO4 302 C O1 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O4 WO4 1_555 109.1 A WO4 302 C O2 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O4 WO4 1_555 110.2 A WO4 302 C O3 WO4 1_555 A WO4 302 C W WO4 1_555 A WO4 302 C O4 WO4 1_555 109.7 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 A N LEU 41 A N LEU 12 A O VAL 183 A O VAL 154 A O MET 186 A O MET 157 A N LEU 164 A N LEU 135 A O ILE 165 A O ILE 136 A N ALA 157 A N ALA 128 A O PHE 156 A O PHE 127 A N CYS 94 A N CYS 65 A N LEU 93 A N LEU 64 A O ILE 120 A O ILE 91 A N VAL 119 A N VAL 90 A O ARG 144 A O ARG 115 1 A WO4 302 C WO4 1 A MET 30 A MET 1 1 Y 1 A LEU 31 A LEU 2 1 Y 1 A ALA 32 A ALA 3 1 Y 1 A GLY 33 A GLY 4 1 Y 1 A ARG 34 A ARG 5 1 Y 1 A ARG 35 A ARG 6 1 Y 1 A LEU 59 A LEU 30 1 Y 1 A PRO 60 A PRO 31 1 Y 1 A PRO 61 A PRO 32 1 Y 1 A GLY 62 A GLY 33 1 Y 1 A PRO 63 A PRO 34 1 Y 1 A SER 64 A SER 35 1 Y 1 A GLY 65 A GLY 36 1 Y 1 A ALA 127 A ALA 98 1 Y 1 A LEU 128 A LEU 99 1 Y 1 A ASN 129 A ASN 100 1 Y 1 A LYS 210 A LYS 181 1 Y 1 A TYR 211 A TYR 182 1 Y 1 A SER 212 A SER 183 1 Y 1 A PHE 213 A PHE 184 1 Y 1 A PHE 214 A PHE 185 1 Y 1 A PRO 215 A PRO 186 1 Y 1 A GLN 216 A GLN 187 1 Y 1 A LYS 217 A LYS 188 1 Y 1 A HIS 218 A HIS 189 1 Y 1 A ARG 219 A ARG 190 1 Y 1 A GLY 220 A GLY 191 1 Y 1 A HIS 221 A HIS 192 1 Y 1 A LEU 222 A LEU 193 1 Y 1 A VAL 223 A VAL 194 1 Y 1 A PRO 224 A PRO 195 1 Y 1 A ARG 225 A ARG 196 1 Y 1 A HIS 72 -102.09 53.85 1 A SER 89 -145.62 -41.45 41.182 -0.16 0.00 0.00 -0.16 0.00 0.31 0.939 0.928 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.25123 0.20938 0.21144 0.21144 2.10 38.27 514 9676 9676 5.0 99.43 11.951 0.146 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.254 0.202 0.80 0.80 1.40 PDB entry 1BYR MAXIMUM LIKELIHOOD MASK 2.10 38.27 35 1357 6 0 1316 0.013 0.021 1352 0.001 0.020 941 1.382 1.967 1818 0.884 3.003 2268 6.462 5.000 161 42.316 22.923 65 14.372 15.000 238 16.486 15.000 14 0.076 0.200 207 0.005 0.020 1465 0.001 0.020 284 0.551 1.500 535 0.132 1.500 219 0.998 2.000 857 1.695 3.000 317 2.779 4.500 292 0.294 0.226 2.157 35 565 642 20 93.46 2.10 40.0 4GGK 10188 0.0 -3.0 1 18.3 5.8 99.5 2.10 2.23 5.6 2879 1 5.8 98.1 data collection CBASS phasing PHASER refinement REFMAC 5.5.0072 data reduction XDS data scaling SCALA Crystal structure of Zucchini from mouse (mZuc / PLD6 / MitoPLD) bound to tungstate 1 N N 2 N N 3 N N 4 N N A SER 75 A SER 46 HELX_P A ALA 86 A ALA 57 1 1 12 A SER 100 A SER 71 HELX_P A ARG 113 A ARG 84 1 2 14 A SER 131 A SER 102 HELX_P A ALA 139 A ALA 110 1 3 9 A THR 172 A THR 143 HELX_P A ASN 179 A ASN 150 1 4 8 A ASP 188 A ASP 159 HELX_P A PHE 206 A PHE 177 1 5 19 metalc 2.292 A CYS 49 A SG CYS 20 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.329 A CYS 66 A SG CYS 37 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.349 A CYS 68 A SG CYS 39 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.093 A HIS 72 A NE2 HIS 43 1_555 A ZN 301 B ZN ZN 1_555 metalc 3.034 A HIS 153 A NE2 HIS 124 1_555 A WO4 302 C W WO4 1_555 HYDROLASE piRNA pathway, protein-RNA interactions, piRNA biogenesis, RNA interference, RNAi, HKD motif CCCH zinc finger, nuclease, nucleic acid binding, outer mitochondrial membrane, HYDROLASE A PHE 43 A PHE 14 1 A PRO 44 A PRO 15 11.29 PLD6_MOUSE UNP 1 31 Q5SWZ9 LAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQLL HQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDTE YVRLFLEEFERIWEEFDPTKYSFFPQKHRGH 31 221 4GGK 31 221 Q5SWZ9 A 1 2 192 1 expression tag MET 30 4GGK A Q5SWZ9 UNP 1 1 expression tag LEU 222 4GGK A Q5SWZ9 UNP 193 1 expression tag VAL 223 4GGK A Q5SWZ9 UNP 194 1 expression tag PRO 224 4GGK A Q5SWZ9 UNP 195 1 expression tag ARG 225 4GGK A Q5SWZ9 UNP 196 7 anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel A ARG 38 A ARG 9 A PHE 43 A PHE 14 A GLU 181 A GLU 152 A MET 186 A MET 157 A VAL 163 A VAL 134 A GLY 167 A GLY 138 A LYS 155 A LYS 126 A VAL 159 A VAL 130 A SER 90 A SER 61 A LEU 95 A LEU 66 A ARG 116 A ARG 87 A THR 121 A THR 92 A GLN 142 A GLN 113 A HIS 145 A HIS 116 BINDING SITE FOR RESIDUE ZN A 301 A ZN 301 Software 4 BINDING SITE FOR RESIDUE WO4 A 302 A WO4 302 Software 8 A CYS 49 A CYS 20 4 1_555 A CYS 66 A CYS 37 4 1_555 A CYS 68 A CYS 39 4 1_555 A HIS 72 A HIS 43 4 1_555 A PHE 96 A PHE 67 8 1_555 A PHE 96 A PHE 67 8 7_555 A HIS 153 A HIS 124 8 1_555 A HIS 153 A HIS 124 8 7_555 A LYS 155 A LYS 126 8 7_555 A LYS 155 A LYS 126 8 1_555 A ASN 170 A ASN 141 8 7_555 A ASN 170 A ASN 141 8 1_555 96 P 43 21 2