0.020117 0.000000 0.000000 0.000000 0.020117 0.000000 0.000000 0.000000 0.010940 0.00000 0.00000 0.00000 Kreusch, A. Spraggon, G. Lee, C.C. Klock, H. McMullan, D. Ng, K. Shin, T. Vincent, J. Warner, I. Ericson, C. Lesley, S.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 49.709 49.709 91.407 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 Fe 3 55.845 FE (III) 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 C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer 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 C3 H7 N O5 S 169.156 n CYSTEINESULFONIC ACID 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 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 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 FE N 89 N N N 90 S C N 91 N C N 92 N O N 93 N C N 94 N C N 95 N C N 96 N O N 97 N N N 98 N O 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 H N 109 N N N 110 S C N 111 N C N 112 N O N 113 N C N 114 N C N 115 N C N 116 N O 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 H N 125 N H N 126 N H N 127 N H N 128 N N N 129 N C N 130 N C N 131 N O N 132 N O N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N C N 139 N O N 140 N C N 141 N O N 142 N C N 143 N O N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N N N 153 S C N 154 N C N 155 N O N 156 N C Y 157 N C Y 158 N N Y 159 N C Y 160 N C Y 161 N N N 162 N O 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 H N 171 N H N 172 N H N 173 N O N 174 N H N 175 N H N 176 N N N 177 S C N 178 N C N 179 N O N 180 S C N 181 N C N 182 N C N 183 N C N 184 N O 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 H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N N N 199 S C N 200 N C N 201 N O N 202 N C N 203 N C N 204 N C N 205 N C N 206 N O 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 H N 218 N H N 219 N H N 220 N N N 221 S C N 222 N C N 223 N O N 224 N C N 225 N C N 226 N C N 227 N C N 228 N N N 229 N O N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N N N 246 S C N 247 N C N 248 N O N 249 N C N 250 N C N 251 N S N 252 N C N 253 N O N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N N N 266 R C N 267 N C N 268 N S N 269 N C N 270 N O N 271 N O N 272 N O N 273 N O N 274 N O N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N N N 283 S C N 284 N C N 285 N O N 286 N C Y 287 N C Y 288 N C Y 289 N C Y 290 N C Y 291 N C Y 292 N C N 293 N O N 294 N H N 295 N H N 296 N H 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 H N 305 N N N 306 S C N 307 N C N 308 N O N 309 N C N 310 N C N 311 N C N 312 N O 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 H N 322 N N N 323 S C N 324 N C N 325 N O N 326 N C N 327 N O N 328 N O N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N N N 337 S C N 338 N C N 339 N O N 340 R C N 341 N O N 342 N C N 343 N O N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N N N 354 S C N 355 N C N 356 N O N 357 N C Y 358 N C Y 359 N C Y 360 N C Y 361 N C Y 362 N C Y 363 N C N 364 N O N 365 N O 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 H N 377 N N N 378 S C N 379 N C N 380 N O N 381 N C N 382 N C N 383 N C N 384 N O 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 H N 392 N H N 393 N H N 394 N H N 395 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 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 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 sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing Y 153 N sing Y 154 N doub Y 155 N doub N 156 N sing Y 157 N sing N 158 N sing Y 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 doub 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 sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N doub 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 sing N 212 N sing N 213 N doub 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 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 doub N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N doub N 260 N sing N 261 N doub N 262 N doub 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 sing N 271 N sing N 272 N doub N 273 N sing N 274 N sing N 275 N sing N 276 N sing Y 277 N doub Y 278 N sing Y 279 N sing N 280 N sing Y 281 N doub N 282 N sing Y 283 N doub N 284 N sing Y 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 doub 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 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 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 N 351 N sing Y 352 N doub N 353 N sing Y 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 sing N 365 N doub 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 sing UK J.MOL.BIOL. JMOBAK 0070 0022-2836 330 309 321 10.1016/S0022-2836(03)00596-5 12823970 Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase 2003 10.2210/pdb1lm6/pdb pdb_00001lm6 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 2001-12-13 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 1.0 1.0 5.0.3 ALS 1.0 SYNCHROTRON ALS BEAMLINE 5.0.3 24230.684 peptide deformylase DEFB 3.5.1.88 1 man polymer 55.845 FE (III) ION 1 syn non-polymer 92.094 GLYCEROL 1 syn non-polymer 18.015 water 167 nat water no yes MGSDKIHHHHHHMSAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLR GGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEG(OCS)LSVDRNVPGYVVRH ARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE MGSDKIHHHHHHMSAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLR GGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVT VDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Streptococcus Escherichia sample 1313 Streptococcus pneumoniae 562 Escherichia coli plasmid pMH1 1 2.33 47.23 VAPOR DIFFUSION, SITTING DROP 8.0 PEG 8000, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_conn_type struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Non-polymer description Version format compliance Structure summary Data collection Database references Derived calculations Refinement description Data collection 1 0 2003-06-24 1 1 2007-10-16 1 2 2011-07-13 1 3 2014-11-12 1 4 2023-08-16 1 5 2023-11-15 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _chem_comp_atom.atom_id _chem_comp_bond.atom_id_2 1LM4 IS THE PDF STRUCTURE FROM STAPHYLOCOCCUS AUREUS 1LME IS THE PDF STRUCTURE FROM Thermotoga maritima RCSB Y RCSB 2002-04-30 REL FE FE (III) ION GOL GLYCEROL HOH water heterogen The modeled Fe(III) ion is a guess and has not been confirmed experimentally. THESE RESIDUES CORRESPOND TO THE FIRST SIX RESIDUES OF THIOREDOXIN FOLLOWED BY A HEXA-HIS PURIFICATION TAG. THE FULL LENGTH TAG SEQUENCE IS MGSDKIHHHHHH. 1LM4 PDB experimental model FE3 1 2 FE FE 204 A DRG 1 3 GOL GOL 301 A WAT 1 4 HOH HOH 302 A WAT 2 4 HOH HOH 303 A WAT 3 4 HOH HOH 304 A WAT 4 4 HOH HOH 305 A WAT 5 4 HOH HOH 306 A WAT 6 4 HOH HOH 307 A WAT 7 4 HOH HOH 308 A WAT 8 4 HOH HOH 309 A WAT 9 4 HOH HOH 310 A WAT 10 4 HOH HOH 311 A WAT 11 4 HOH HOH 312 A WAT 12 4 HOH HOH 313 A WAT 13 4 HOH HOH 314 A WAT 14 4 HOH HOH 315 A WAT 15 4 HOH HOH 316 A WAT 16 4 HOH HOH 317 A WAT 17 4 HOH HOH 318 A WAT 18 4 HOH HOH 319 A WAT 19 4 HOH HOH 320 A WAT 20 4 HOH HOH 321 A WAT 21 4 HOH HOH 322 A WAT 22 4 HOH HOH 323 A WAT 23 4 HOH HOH 324 A WAT 24 4 HOH HOH 325 A WAT 25 4 HOH HOH 326 A WAT 26 4 HOH HOH 327 A WAT 27 4 HOH HOH 328 A WAT 28 4 HOH HOH 329 A WAT 29 4 HOH HOH 330 A WAT 30 4 HOH HOH 331 A WAT 31 4 HOH HOH 332 A WAT 32 4 HOH HOH 333 A WAT 33 4 HOH HOH 334 A WAT 34 4 HOH HOH 335 A WAT 35 4 HOH HOH 336 A WAT 36 4 HOH HOH 337 A WAT 37 4 HOH HOH 338 A WAT 38 4 HOH HOH 339 A WAT 39 4 HOH HOH 340 A WAT 40 4 HOH HOH 341 A WAT 41 4 HOH HOH 342 A WAT 42 4 HOH HOH 343 A WAT 43 4 HOH HOH 344 A WAT 44 4 HOH HOH 345 A WAT 45 4 HOH HOH 346 A WAT 46 4 HOH HOH 347 A WAT 47 4 HOH HOH 348 A WAT 48 4 HOH HOH 349 A WAT 49 4 HOH HOH 350 A WAT 50 4 HOH HOH 351 A WAT 51 4 HOH HOH 352 A WAT 52 4 HOH HOH 353 A WAT 53 4 HOH HOH 354 A WAT 54 4 HOH HOH 355 A WAT 55 4 HOH HOH 356 A WAT 56 4 HOH HOH 357 A WAT 57 4 HOH HOH 358 A WAT 58 4 HOH HOH 359 A WAT 59 4 HOH HOH 360 A WAT 60 4 HOH HOH 361 A WAT 61 4 HOH HOH 362 A WAT 62 4 HOH HOH 363 A WAT 63 4 HOH HOH 364 A WAT 64 4 HOH HOH 365 A WAT 65 4 HOH HOH 366 A WAT 66 4 HOH HOH 367 A WAT 67 4 HOH HOH 368 A WAT 68 4 HOH HOH 369 A WAT 69 4 HOH HOH 370 A WAT 70 4 HOH HOH 371 A WAT 71 4 HOH HOH 372 A WAT 72 4 HOH HOH 373 A WAT 73 4 HOH HOH 374 A WAT 74 4 HOH HOH 375 A WAT 75 4 HOH HOH 376 A WAT 76 4 HOH HOH 377 A WAT 77 4 HOH HOH 378 A WAT 78 4 HOH HOH 379 A WAT 79 4 HOH HOH 380 A WAT 80 4 HOH HOH 381 A WAT 81 4 HOH HOH 382 A WAT 82 4 HOH HOH 383 A WAT 83 4 HOH HOH 384 A WAT 84 4 HOH HOH 385 A WAT 85 4 HOH HOH 386 A WAT 86 4 HOH HOH 387 A WAT 87 4 HOH HOH 388 A WAT 88 4 HOH HOH 389 A WAT 89 4 HOH HOH 390 A WAT 90 4 HOH HOH 391 A WAT 91 4 HOH HOH 392 A WAT 92 4 HOH HOH 393 A WAT 93 4 HOH HOH 394 A WAT 94 4 HOH HOH 395 A WAT 95 4 HOH HOH 396 A WAT 96 4 HOH HOH 397 A WAT 97 4 HOH HOH 398 A WAT 98 4 HOH HOH 399 A WAT 99 4 HOH HOH 400 A WAT 100 4 HOH HOH 401 A WAT 101 4 HOH HOH 402 A WAT 102 4 HOH HOH 403 A WAT 103 4 HOH HOH 404 A WAT 104 4 HOH HOH 405 A WAT 105 4 HOH HOH 406 A WAT 106 4 HOH HOH 407 A WAT 107 4 HOH HOH 408 A WAT 108 4 HOH HOH 409 A WAT 109 4 HOH HOH 410 A WAT 110 4 HOH HOH 411 A WAT 111 4 HOH HOH 412 A WAT 112 4 HOH HOH 413 A WAT 113 4 HOH HOH 414 A WAT 114 4 HOH HOH 415 A WAT 115 4 HOH HOH 416 A WAT 116 4 HOH HOH 417 A WAT 117 4 HOH HOH 418 A WAT 118 4 HOH HOH 419 A WAT 119 4 HOH HOH 420 A WAT 120 4 HOH HOH 421 A WAT 121 4 HOH HOH 422 A WAT 122 4 HOH HOH 423 A WAT 123 4 HOH HOH 424 A WAT 124 4 HOH HOH 425 A WAT 125 4 HOH HOH 426 A WAT 126 4 HOH HOH 427 A WAT 127 4 HOH HOH 428 A WAT 128 4 HOH HOH 429 A WAT 129 4 HOH HOH 430 A WAT 130 4 HOH HOH 431 A WAT 131 4 HOH HOH 432 A WAT 132 4 HOH HOH 433 A WAT 133 4 HOH HOH 434 A WAT 134 4 HOH HOH 435 A WAT 135 4 HOH HOH 436 A WAT 136 4 HOH HOH 437 A WAT 137 4 HOH HOH 438 A WAT 138 4 HOH HOH 439 A WAT 139 4 HOH HOH 440 A WAT 140 4 HOH HOH 441 A WAT 141 4 HOH HOH 442 A WAT 142 4 HOH HOH 443 A WAT 143 4 HOH HOH 444 A WAT 144 4 HOH HOH 445 A WAT 145 4 HOH HOH 446 A WAT 146 4 HOH HOH 447 A WAT 147 4 HOH HOH 448 A WAT 148 4 HOH HOH 449 A WAT 149 4 HOH HOH 450 A WAT 150 4 HOH HOH 451 A WAT 151 4 HOH HOH 452 A WAT 152 4 HOH HOH 453 A WAT 153 4 HOH HOH 454 A WAT 154 4 HOH HOH 455 A WAT 155 4 HOH HOH 456 A WAT 156 4 HOH HOH 457 A WAT 157 4 HOH HOH 458 A WAT 158 4 HOH HOH 459 A WAT 159 4 HOH HOH 460 A WAT 160 4 HOH HOH 461 A WAT 161 4 HOH HOH 462 A WAT 162 4 HOH HOH 463 A WAT 163 4 HOH HOH 464 A WAT 164 4 HOH HOH 465 A WAT 165 4 HOH HOH 466 A WAT 166 4 HOH HOH 467 A WAT 167 4 HOH HOH 468 A n 1 -11 A n 2 -10 A n 3 -9 A n 4 -8 A n 5 -7 A n 6 -6 A n 7 -5 A n 8 -4 A n 9 -3 A n 10 -2 A n 11 -1 A n 12 0 A MET 1 n 13 MET 1 A SER 2 n 14 SER 2 A ALA 3 n 15 ALA 3 A ILE 4 n 16 ILE 4 A ALA 5 n 17 GLU 5 A ARG 6 n 18 ARG 6 A ILE 7 n 19 ILE 7 A THR 8 n 20 THR 8 A LYS 9 n 21 LYS 9 A ALA 10 n 22 ALA 10 A ALA 11 n 23 ALA 11 A HIS 12 n 24 HIS 12 A LEU 13 n 25 LEU 13 A ILE 14 n 26 ILE 14 A ASP 15 n 27 ASP 15 A MET 16 n 28 MET 16 A ASN 17 n 29 ASN 17 A ASP 18 n 30 ASP 18 A ILE 19 n 31 ILE 19 A ILE 20 n 32 ILE 20 A ARG 21 n 33 ARG 21 A GLU 22 n 34 GLU 22 A GLY 23 n 35 GLY 23 A ASN 24 n 36 ASN 24 A PRO 25 n 37 PRO 25 A THR 26 n 38 THR 26 A LEU 27 n 39 LEU 27 A ARG 28 n 40 ARG 28 A THR 29 n 41 THR 29 A VAL 30 n 42 VAL 30 A ALA 31 n 43 ALA 31 A GLU 32 n 44 GLU 32 A GLU 33 n 45 GLU 33 A VAL 34 n 46 VAL 34 A THR 35 n 47 THR 35 A PHE 36 n 48 PHE 36 A PRO 37 n 49 PRO 37 A LEU 38 n 50 LEU 38 A SER 39 n 51 SER 39 A ASP 40 n 52 ASP 40 A GLN 41 n 53 GLN 41 A GLU 42 n 54 GLU 42 A ILE 43 n 55 ILE 43 A ILE 44 n 56 ILE 44 A LEU 45 n 57 LEU 45 A GLY 46 n 58 GLY 46 A GLU 47 n 59 GLU 47 A LYS 48 n 60 LYS 48 A MET 49 n 61 MET 49 A MET 50 n 62 MET 50 A GLN 51 n 63 GLN 51 A PHE 52 n 64 PHE 52 A LEU 53 n 65 LEU 53 A LYS 54 n 66 LYS 54 A HIS 55 n 67 HIS 55 A SER 56 n 68 SER 56 A GLN 57 n 69 GLN 57 A ASP 58 n 70 ASP 58 A PRO 59 n 71 PRO 59 A VAL 60 n 72 VAL 60 A MET 61 n 73 MET 61 A ALA 62 n 74 ALA 62 A GLU 63 n 75 GLU 63 A LYS 64 n 76 LYS 64 A MET 65 n 77 MET 65 A GLY 66 n 78 GLY 66 A LEU 67 n 79 LEU 67 A ARG 68 n 80 ARG 68 A GLY 69 n 81 GLY 69 A GLY 70 n 82 GLY 70 A VAL 71 n 83 VAL 71 A GLY 72 n 84 GLY 72 A LEU 73 n 85 LEU 73 A ALA 74 n 86 ALA 74 A ALA 75 n 87 ALA 75 A PRO 76 n 88 PRO 76 A GLN 77 n 89 GLN 77 A LEU 78 n 90 LEU 78 A ASP 79 n 91 ASP 79 A ILE 80 n 92 ILE 80 A SER 81 n 93 SER 81 A LYS 82 n 94 LYS 82 A ARG 83 n 95 ARG 83 A ILE 84 n 96 ILE 84 A ILE 85 n 97 ILE 85 A ALA 86 n 98 ALA 86 A VAL 87 n 99 VAL 87 A LEU 88 n 100 LEU 88 A VAL 89 n 101 VAL 89 A PRO 90 n 102 PRO 90 A ASN 91 n 103 ASN 91 A n 104 92 A n 105 93 A n 106 94 A n 107 95 A n 108 96 A n 109 97 A n 110 98 A n 111 99 A n 112 100 A n 113 101 A n 114 102 A TYR 103 n 115 TYR 103 A ASP 104 n 116 ASP 104 A LEU 105 n 117 LEU 105 A GLU 106 n 118 GLU 106 A ALA 107 n 119 ALA 107 A ILE 108 n 120 ILE 108 A MET 109 n 121 MET 109 A TYR 110 n 122 TYR 110 A ASN 111 n 123 ASN 111 A PRO 112 n 124 PRO 112 A LYS 113 n 125 LYS 113 A ILE 114 n 126 ILE 114 A VAL 115 n 127 VAL 115 A SER 116 n 128 SER 116 A HIS 117 n 129 HIS 117 A SER 118 n 130 SER 118 A VAL 119 n 131 VAL 119 A GLN 120 n 132 GLN 120 A ASP 121 n 133 ASP 121 A ALA 122 n 134 ALA 122 A ALA 123 n 135 ALA 123 A LEU 124 n 136 LEU 124 A GLY 125 n 137 GLY 125 A GLU 126 n 138 GLU 126 A GLY 127 n 139 GLY 127 A GLU 128 n 140 GLU 128 A GLY 129 n 141 GLY 129 A CYB 130 n 142 OCS 130 A LEU 131 n 143 LEU 131 A SER 132 n 144 SER 132 A VAL 133 n 145 VAL 133 A ASP 134 n 146 ASP 134 A ARG 135 n 147 ARG 135 A ASN 136 n 148 ASN 136 A VAL 137 n 149 VAL 137 A PRO 138 n 150 PRO 138 A GLY 139 n 151 GLY 139 A TYR 140 n 152 TYR 140 A VAL 141 n 153 VAL 141 A VAL 142 n 154 VAL 142 A ARG 143 n 155 ARG 143 A HIS 144 n 156 HIS 144 A ALA 145 n 157 ALA 145 A ARG 146 n 158 ARG 146 A VAL 147 n 159 VAL 147 A THR 148 n 160 THR 148 A VAL 149 n 161 VAL 149 A ASP 150 n 162 ASP 150 A TYR 151 n 163 TYR 151 A PHE 152 n 164 PHE 152 A ASP 153 n 165 ASP 153 A LYS 154 n 166 LYS 154 A ASP 155 n 167 ASP 155 A GLY 156 n 168 GLY 156 A GLU 157 n 169 GLU 157 A LYS 158 n 170 LYS 158 A HIS 159 n 171 HIS 159 A ARG 160 n 172 ARG 160 A ILE 161 n 173 ILE 161 A LYS 162 n 174 LYS 162 A LEU 163 n 175 LEU 163 A LYS 164 n 176 LYS 164 A GLY 165 n 177 GLY 165 A TYR 166 n 178 TYR 166 A ASN 167 n 179 ASN 167 A SER 168 n 180 SER 168 A ILE 169 n 181 ILE 169 A VAL 170 n 182 VAL 170 A VAL 171 n 183 VAL 171 A GLN 172 n 184 GLN 172 A HIS 173 n 185 HIS 173 A GLU 174 n 186 GLU 174 A ILE 175 n 187 ILE 175 A ASP 176 n 188 ASP 176 A HIS 177 n 189 HIS 177 A ILE 178 n 190 ILE 178 A ASN 179 n 191 ASN 179 A GLY 180 n 192 GLY 180 A ILE 181 n 193 ILE 181 A MET 182 n 194 MET 182 A PHE 183 n 195 PHE 183 A TYR 184 n 196 TYR 184 A ASP 185 n 197 ASP 185 A ARG 186 n 198 ARG 186 A ILE 187 n 199 ILE 187 A ASN 188 n 200 ASN 188 A GLU 189 n 201 GLU 189 A LYS 190 n 202 LYS 190 A ASP 191 n 203 ASP 191 A PRO 192 n 204 PRO 192 A PHE 193 n 205 PHE 193 A ALA 194 n 206 ALA 194 A VAL 195 n 207 VAL 195 A ALA 196 n 208 LYS 196 A ASP 197 n 209 ASP 197 A GLY 198 n 210 GLY 198 A LEU 199 n 211 LEU 199 A LEU 200 n 212 LEU 200 A ILE 201 n 213 ILE 201 A LEU 202 n 214 LEU 202 A n 215 203 A author_defined_assembly 1 monomeric A OCS 130 A SG OCS 142 1_555 A FE 204 B FE FE 1_555 A HIS 173 A NE2 HIS 185 1_555 112.5 A OCS 130 A SG OCS 142 1_555 A FE 204 B FE FE 1_555 A HIS 177 A NE2 HIS 189 1_555 111.0 A HIS 173 A NE2 HIS 185 1_555 A FE 204 B FE FE 1_555 A HIS 177 A NE2 HIS 189 1_555 113.8 A OCS 130 A SG OCS 142 1_555 A FE 204 B FE FE 1_555 A HOH 369 D O HOH 1_555 130.3 A HIS 173 A NE2 HIS 185 1_555 A FE 204 B FE FE 1_555 A HOH 369 D O HOH 1_555 89.8 A HIS 177 A NE2 HIS 189 1_555 A FE 204 B FE FE 1_555 A HOH 369 D O HOH 1_555 97.7 A OCS 130 CYSTEINESULFONIC ACID A OCS 142 CYS 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 N LEU 73 A N LEU 85 A O ALA 86 A O ALA 98 A N VAL 89 A N VAL 101 A O LEU 105 A O LEU 117 A N TYR 110 A N TYR 122 A O PHE 152 A O PHE 164 A N VAL 149 A N VAL 161 A O ILE 161 A O ILE 173 A O ARG 143 A O ARG 155 A N ALA 122 A N ALA 134 A N ALA 123 A N ALA 135 A O LEU 202 A O LEU 214 1 A CG GLU 5 A CG GLU 17 1 Y 1 A CD GLU 5 A CD GLU 17 1 Y 1 A OE1 GLU 5 A OE1 GLU 17 1 Y 1 A OE2 GLU 5 A OE2 GLU 17 1 Y 1 A CG LYS 196 A CG LYS 208 1 Y 1 A CD LYS 196 A CD LYS 208 1 Y 1 A CE LYS 196 A CE LYS 208 1 Y 1 A NZ LYS 196 A NZ LYS 208 1 Y 1 A MET -11 A MET 1 1 Y 1 A GLY -10 A GLY 2 1 Y 1 A SER -9 A SER 3 1 Y 1 A ASP -8 A ASP 4 1 Y 1 A LYS -7 A LYS 5 1 Y 1 A ILE -6 A ILE 6 1 Y 1 A HIS -5 A HIS 7 1 Y 1 A HIS -4 A HIS 8 1 Y 1 A HIS -3 A HIS 9 1 Y 1 A HIS -2 A HIS 10 1 Y 1 A HIS -1 A HIS 11 1 Y 1 A HIS 0 A HIS 12 1 Y 1 A ILE 92 A ILE 104 1 Y 1 A VAL 93 A VAL 105 1 Y 1 A GLU 94 A GLU 106 1 Y 1 A GLU 95 A GLU 107 1 Y 1 A GLY 96 A GLY 108 1 Y 1 A GLU 97 A GLU 109 1 Y 1 A THR 98 A THR 110 1 Y 1 A PRO 99 A PRO 111 1 Y 1 A GLN 100 A GLN 112 1 Y 1 A GLU 101 A GLU 113 1 Y 1 A ALA 102 A ALA 114 1 Y 1 A GLU 203 A GLU 215 1 Y 1 A GLU 22 -39.60 152.74 1 A ARG 135 156.73 -179.52 1 A LYS 190 -55.21 -72.67 PROTEIN_REP_NEW.PARAM PROTEIN_NEW.TOP WATER_REP.PARAM WATER.TOP ION.PARAM ION.TOP GLYCEROL_NEW.PARAM GLYCEROL.TOP 29.6 5.40 0.00 0.00 5.40 0.00 -10.79 0.256 0.008 0.208 0.208 1.75 33.65 1119 22277 5.0 99.5 RANDOM 2045273.26 0.000000 1 RESTRAINED THROUGHOUT MOLECULAR REPLACEMENT 1LM4 FLAT MODEL 51.1237 0.352357 0.27 0.21 5.0 0.22 0.17 1.75 33.65 167 1667 7 0 1493 0.014 1.7 24.4 1.66 0.325 0.024 0.269 1.86 177 3484 6 4.8 98.1 22.7 1.75 35.0 1LM6 22277 2.0 0.048 1 20.6 8 99.5 1.75 1.85 3661 0.241 1 98.1 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement CNS 1.0 Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae 1 N N 2 N N 3 N N 4 N N The biological unit is a monomer A SER 2 A SER 14 HELX_P A THR 8 A THR 20 1 1 7 A ASP 15 A ASP 27 HELX_P A ILE 19 A ILE 31 5 2 5 A ASN 24 A ASN 36 HELX_P A THR 29 A THR 41 5 3 6 A SER 39 A SER 51 HELX_P A GLN 57 A GLN 69 1 4 19 A ASP 58 A ASP 70 HELX_P A GLY 66 A GLY 78 1 5 9 A PRO 76 A PRO 88 HELX_P A ASP 79 A ASP 91 5 6 4 A LYS 164 A LYS 176 HELX_P A ASN 179 A ASN 191 1 7 16 A MET 182 A MET 194 HELX_P A ILE 187 A ILE 199 5 8 6 covale 1.328 both A GLY 129 A C GLY 141 1_555 A OCS 130 A N OCS 142 1_555 covale 1.335 both A OCS 130 A C OCS 142 1_555 A LEU 131 A N LEU 143 1_555 metalc 2.518 A OCS 130 A SG OCS 142 1_555 A FE 204 B FE FE 1_555 metalc 2.428 A HIS 173 A NE2 HIS 185 1_555 A FE 204 B FE FE 1_555 metalc 1.900 A HIS 177 A NE2 HIS 189 1_555 A FE 204 B FE FE 1_555 metalc 2.433 A FE 204 B FE FE 1_555 A HOH 369 D O HOH 1_555 HYDROLASE PDF, Metalloenzyme, peptide deformylase, HYDROLASE A PHE 36 A PHE 48 1 A PRO 37 A PRO 49 1.02 DEF_STRPN UNP 1 1 Q9F2F0 MSAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDI SKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHR IKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE 1 203 1LM6 1 203 Q9F2F0 A 1 13 215 1 SEE REMARK 999 MET -11 1LM6 A Q9F2F0 UNP 1 1 SEE REMARK 999 GLY -10 1LM6 A Q9F2F0 UNP 2 1 SEE REMARK 999 SER -9 1LM6 A Q9F2F0 UNP 3 1 SEE REMARK 999 ASP -8 1LM6 A Q9F2F0 UNP 4 1 SEE REMARK 999 LYS -7 1LM6 A Q9F2F0 UNP 5 1 SEE REMARK 999 ILE -6 1LM6 A Q9F2F0 UNP 6 1 SEE REMARK 999 HIS -5 1LM6 A Q9F2F0 UNP 7 1 SEE REMARK 999 HIS -4 1LM6 A Q9F2F0 UNP 8 1 SEE REMARK 999 HIS -3 1LM6 A Q9F2F0 UNP 9 1 SEE REMARK 999 HIS -2 1LM6 A Q9F2F0 UNP 10 1 SEE REMARK 999 HIS -1 1LM6 A Q9F2F0 UNP 11 1 SEE REMARK 999 HIS 0 1LM6 A Q9F2F0 UNP 12 1 CYS modified residue OCS 130 1LM6 A Q9F2F0 UNP 130 142 5 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel A GLY 72 A GLY 84 A ALA 74 A ALA 86 A ILE 84 A ILE 96 A VAL 89 A VAL 101 A LEU 105 A LEU 117 A HIS 117 A HIS 129 A VAL 147 A VAL 159 A PHE 152 A PHE 164 A LYS 158 A LYS 170 A LEU 163 A LEU 175 A ARG 143 A ARG 155 A HIS 144 A HIS 156 A ASP 121 A ASP 133 A LEU 124 A LEU 136 A LEU 199 A LEU 211 A LEU 202 A LEU 214 BINDING SITE FOR RESIDUE FE A 204 A FE 204 Software 5 BINDING SITE FOR RESIDUE GOL A 301 A GOL 301 Software 5 A GLN 77 A GLN 89 5 1_555 A OCS 130 A OCS 142 5 1_555 A HIS 173 A HIS 185 5 1_555 A HIS 177 A HIS 189 5 1_555 A HOH 369 D HOH 5 1_555 A GLU 128 A GLU 140 5 1_555 A GLY 129 A GLY 141 5 1_555 A TYR 166 A TYR 178 5 1_555 A HIS 173 A HIS 185 5 1_555 A HOH 409 D HOH 5 1_555 78 P 43