0.008762 0.000000 0.000000 0.000000 0.008762 0.000000 0.000000 0.000000 0.030684 0.00000 0.00000 0.00000 Peat, T.S. Newman, J. Waldo, G.S. Berendzen, J. Terwilliger, T.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 114.130 114.130 32.590 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE 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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE 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 UK Structure STRUE6 2005 0969-2126 6 1207 1214 10.1016/S0969-2126(98)00120-8 9753699 Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. 1998 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 110.0 1 IMAGE PLATE 1998-05 MARRESEARCH SINGLE CRYSTAL SINGLE WAVELENGTH M x-ray 1 0.9788 1.0 X8C NSLS 0.9788 SYNCHROTRON NSLS BEAMLINE X8C MSE HAS REPLACED MET, AS SELENO-METHIONINE WAS INCORPORATED INTO THE PROTEIN 15334.187 TRANSLATION INITIATION FACTOR 5A YES 1 man polymer 18.015 water 143 nat water no yes KWV(MSE)STKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKF TAQILSVSGDVIQL(MSE)D(MSE)RDYKTIEVP(MSE)KYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG KWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFTAQI LSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG 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 Pyrobaculum Escherichia Escherichia coli sample 13773 Pyrobaculum aerophilum 511693 Escherichia coli BL21 BL21 PET PET PET 1 3.53 60.0 A THREE WAVELENGTH DATA SET WAS USED TO FIND THE SELENIUM POSITIONS AND PHASE THE ELECTRON DENSITY MAPS. 7.5 PROTEIN WAS CRYSTALLIZED AT 8 DEGREES IN 50MM HEPES PH 7.5, 6-8% PEG 4000, 5MM BETA- MERCAPTOETHANOL, temperature 281K 281 repository Initial release Version format compliance Version format compliance 1 0 1998-11-04 1 1 2008-03-24 1 2 2011-07-13 Y BNL 1998-07-05 REL REL HOH water HOH 201 2 HOH HOH 201 A HOH 202 2 HOH HOH 202 A HOH 203 2 HOH HOH 203 A HOH 204 2 HOH HOH 204 A HOH 205 2 HOH HOH 205 A HOH 206 2 HOH HOH 206 A HOH 207 2 HOH HOH 207 A HOH 208 2 HOH HOH 208 A HOH 209 2 HOH HOH 209 A HOH 210 2 HOH HOH 210 A HOH 211 2 HOH HOH 211 A HOH 212 2 HOH HOH 212 A HOH 213 2 HOH HOH 213 A HOH 214 2 HOH HOH 214 A HOH 215 2 HOH HOH 215 A HOH 216 2 HOH HOH 216 A HOH 217 2 HOH HOH 217 A HOH 218 2 HOH HOH 218 A HOH 219 2 HOH HOH 219 A HOH 220 2 HOH HOH 220 A HOH 221 2 HOH HOH 221 A HOH 222 2 HOH HOH 222 A HOH 223 2 HOH HOH 223 A HOH 224 2 HOH HOH 224 A HOH 225 2 HOH HOH 225 A HOH 226 2 HOH HOH 226 A HOH 227 2 HOH HOH 227 A HOH 228 2 HOH HOH 228 A HOH 229 2 HOH HOH 229 A HOH 230 2 HOH HOH 230 A HOH 231 2 HOH HOH 231 A HOH 232 2 HOH HOH 232 A HOH 233 2 HOH HOH 233 A HOH 234 2 HOH HOH 234 A HOH 235 2 HOH HOH 235 A HOH 236 2 HOH HOH 236 A HOH 237 2 HOH HOH 237 A HOH 238 2 HOH HOH 238 A HOH 239 2 HOH HOH 239 A HOH 240 2 HOH HOH 240 A HOH 241 2 HOH HOH 241 A HOH 242 2 HOH HOH 242 A HOH 243 2 HOH HOH 243 A HOH 244 2 HOH HOH 244 A HOH 245 2 HOH HOH 245 A HOH 246 2 HOH HOH 246 A HOH 247 2 HOH HOH 247 A HOH 248 2 HOH HOH 248 A HOH 249 2 HOH HOH 249 A HOH 250 2 HOH HOH 250 A HOH 251 2 HOH HOH 251 A HOH 252 2 HOH HOH 252 A HOH 253 2 HOH HOH 253 A HOH 254 2 HOH HOH 254 A HOH 255 2 HOH HOH 255 A HOH 256 2 HOH HOH 256 A HOH 257 2 HOH HOH 257 A HOH 258 2 HOH HOH 258 A HOH 259 2 HOH HOH 259 A HOH 260 2 HOH HOH 260 A HOH 261 2 HOH HOH 261 A HOH 262 2 HOH HOH 262 A HOH 263 2 HOH HOH 263 A HOH 264 2 HOH HOH 264 A HOH 265 2 HOH HOH 265 A HOH 266 2 HOH HOH 266 A HOH 267 2 HOH HOH 267 A HOH 268 2 HOH HOH 268 A HOH 269 2 HOH HOH 269 A HOH 270 2 HOH HOH 270 A HOH 271 2 HOH HOH 271 A HOH 272 2 HOH HOH 272 A HOH 273 2 HOH HOH 273 A HOH 274 2 HOH HOH 274 A HOH 275 2 HOH HOH 275 A HOH 276 2 HOH HOH 276 A HOH 277 2 HOH HOH 277 A HOH 278 2 HOH HOH 278 A HOH 279 2 HOH HOH 279 A HOH 280 2 HOH HOH 280 A HOH 281 2 HOH HOH 281 A HOH 282 2 HOH HOH 282 A HOH 283 2 HOH HOH 283 A HOH 284 2 HOH HOH 284 A HOH 285 2 HOH HOH 285 A HOH 286 2 HOH HOH 286 A HOH 287 2 HOH HOH 287 A HOH 288 2 HOH HOH 288 A HOH 289 2 HOH HOH 289 A HOH 290 2 HOH HOH 290 A HOH 291 2 HOH HOH 291 A HOH 292 2 HOH HOH 292 A HOH 293 2 HOH HOH 293 A HOH 294 2 HOH HOH 294 A HOH 295 2 HOH HOH 295 A HOH 296 2 HOH HOH 296 A HOH 297 2 HOH HOH 297 A HOH 298 2 HOH HOH 298 A HOH 299 2 HOH HOH 299 A HOH 300 2 HOH HOH 300 A HOH 301 2 HOH HOH 301 A HOH 302 2 HOH HOH 302 A HOH 303 2 HOH HOH 303 A HOH 304 2 HOH HOH 304 A HOH 305 2 HOH HOH 305 A HOH 306 2 HOH HOH 306 A HOH 307 2 HOH HOH 307 A HOH 308 2 HOH HOH 308 A HOH 309 2 HOH HOH 309 A HOH 310 2 HOH HOH 310 A HOH 311 2 HOH HOH 311 A HOH 312 2 HOH HOH 312 A HOH 313 2 HOH HOH 313 A HOH 314 2 HOH HOH 314 A HOH 315 2 HOH HOH 315 A HOH 316 2 HOH HOH 316 A HOH 317 2 HOH HOH 317 A HOH 318 2 HOH HOH 318 A HOH 319 2 HOH HOH 319 A HOH 320 2 HOH HOH 320 A HOH 321 2 HOH HOH 321 A HOH 322 2 HOH HOH 322 A HOH 323 2 HOH HOH 323 A HOH 324 2 HOH HOH 324 A HOH 325 2 HOH HOH 325 A HOH 326 2 HOH HOH 326 A HOH 327 2 HOH HOH 327 A HOH 328 2 HOH HOH 328 A HOH 329 2 HOH HOH 329 A HOH 330 2 HOH HOH 330 A HOH 331 2 HOH HOH 331 A HOH 332 2 HOH HOH 332 A HOH 333 2 HOH HOH 333 A HOH 334 2 HOH HOH 334 A HOH 335 2 HOH HOH 335 A HOH 336 2 HOH HOH 336 A HOH 337 2 HOH HOH 337 A HOH 338 2 HOH HOH 338 A HOH 339 2 HOH HOH 339 A HOH 340 2 HOH HOH 340 A HOH 341 2 HOH HOH 341 A HOH 342 2 HOH HOH 342 A HOH 343 2 HOH HOH 343 A LYS 4 n 1 LYS 4 A TRP 5 n 2 TRP 5 A VAL 6 n 3 VAL 6 A MSE 7 n 4 MSE 7 A SER 8 n 5 SER 8 A THR 9 n 6 THR 9 A LYS 10 n 7 LYS 10 A TYR 11 n 8 TYR 11 A VAL 12 n 9 VAL 12 A GLU 13 n 10 GLU 13 A ALA 14 n 11 ALA 14 A GLY 15 n 12 GLY 15 A GLU 16 n 13 GLU 16 A LEU 17 n 14 LEU 17 A LYS 18 n 15 LYS 18 A GLU 19 n 16 GLU 19 A GLY 20 n 17 GLY 20 A SER 21 n 18 SER 21 A TYR 22 n 19 TYR 22 A VAL 23 n 20 VAL 23 A VAL 24 n 21 VAL 24 A ILE 25 n 22 ILE 25 A ASP 26 n 23 ASP 26 A GLY 27 n 24 GLY 27 A GLU 28 n 25 GLU 28 A PRO 29 n 26 PRO 29 A CYS 30 n 27 CYS 30 A ARG 31 n 28 ARG 31 A VAL 32 n 29 VAL 32 A VAL 33 n 30 VAL 33 A GLU 34 n 31 GLU 34 A ILE 35 n 32 ILE 35 A GLU 36 n 33 GLU 36 A LYS 37 n 34 LYS 37 A SER 38 n 35 SER 38 A LYS 39 n 36 LYS 39 A THR 40 n 37 THR 40 A GLY 41 n 38 GLY 41 A LYS 42 n 39 LYS 42 A HIS 43 n 40 HIS 43 A GLY 44 n 41 GLY 44 A SER 45 n 42 SER 45 A ALA 46 n 43 ALA 46 A LYS 47 n 44 LYS 47 A ALA 48 n 45 ALA 48 A ARG 49 n 46 ARG 49 A ILE 50 n 47 ILE 50 A VAL 51 n 48 VAL 51 A ALA 52 n 49 ALA 52 A VAL 53 n 50 VAL 53 A GLY 54 n 51 GLY 54 A VAL 55 n 52 VAL 55 A PHE 56 n 53 PHE 56 A ASP 57 n 54 ASP 57 A GLY 58 n 55 GLY 58 A GLY 59 n 56 GLY 59 A LYS 60 n 57 LYS 60 A ARG 61 n 58 ARG 61 A THR 62 n 59 THR 62 A LEU 63 n 60 LEU 63 A SER 64 n 61 SER 64 A LEU 65 n 62 LEU 65 A PRO 66 n 63 PRO 66 A VAL 67 n 64 VAL 67 A ASP 68 n 65 ASP 68 A ALA 69 n 66 ALA 69 A GLN 70 n 67 GLN 70 A VAL 71 n 68 VAL 71 A GLU 72 n 69 GLU 72 A VAL 73 n 70 VAL 73 A PRO 74 n 71 PRO 74 A ILE 75 n 72 ILE 75 A ILE 76 n 73 ILE 76 A GLU 77 n 74 GLU 77 A LYS 78 n 75 LYS 78 A PHE 79 n 76 PHE 79 A THR 80 n 77 THR 80 A ALA 81 n 78 ALA 81 A GLN 82 n 79 GLN 82 A ILE 83 n 80 ILE 83 A LEU 84 n 81 LEU 84 A SER 85 n 82 SER 85 A VAL 86 n 83 VAL 86 A SER 87 n 84 SER 87 A GLY 88 n 85 GLY 88 A ASP 89 n 86 ASP 89 A VAL 90 n 87 VAL 90 A ILE 91 n 88 ILE 91 A GLN 92 n 89 GLN 92 A LEU 93 n 90 LEU 93 A MSE 94 n 91 MSE 94 A ASP 95 n 92 ASP 95 A MSE 96 n 93 MSE 96 A ARG 97 n 94 ARG 97 A ASP 98 n 95 ASP 98 A TYR 99 n 96 TYR 99 A LYS 100 n 97 LYS 100 A THR 101 n 98 THR 101 A ILE 102 n 99 ILE 102 A GLU 103 n 100 GLU 103 A VAL 104 n 101 VAL 104 A PRO 105 n 102 PRO 105 A MSE 106 n 103 MSE 106 A LYS 107 n 104 LYS 107 A TYR 108 n 105 TYR 108 A VAL 109 n 106 VAL 109 A GLU 110 n 107 GLU 110 A GLU 111 n 108 GLU 111 A GLU 112 n 109 GLU 112 A ALA 113 n 110 ALA 113 A LYS 114 n 111 LYS 114 A GLY 115 n 112 GLY 115 A ARG 116 n 113 ARG 116 A LEU 117 n 114 LEU 117 A ALA 118 n 115 ALA 118 A PRO 119 n 116 PRO 119 A GLY 120 n 117 GLY 120 A ALA 121 n 118 ALA 121 A GLU 122 n 119 GLU 122 A VAL 123 n 120 VAL 123 A GLU 124 n 121 GLU 124 A VAL 125 n 122 VAL 125 A TRP 126 n 123 TRP 126 A GLN 127 n 124 GLN 127 A ILE 128 n 125 ILE 128 A LEU 129 n 126 LEU 129 A ASP 130 n 127 ASP 130 A ARG 131 n 128 ARG 131 A TYR 132 n 129 TYR 132 A LYS 133 n 130 LYS 133 A ILE 134 n 131 ILE 134 A ILE 135 n 132 ILE 135 A ARG 136 n 133 ARG 136 A VAL 137 n 134 VAL 137 A LYS 138 n 135 LYS 138 A GLY 139 n 136 GLY 139 A author_defined_assembly 4 tetrameric A MSE 7 SELENOMETHIONINE A MSE 4 MET A MSE 94 SELENOMETHIONINE A MSE 91 MET A MSE 96 SELENOMETHIONINE A MSE 93 MET A MSE 106 SELENOMETHIONINE A MSE 103 MET 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 4_665 y+1,-x+1,z crystal symmetry operation 114.1300000000 114.1300000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 3_645 -y+1,x-1,z crystal symmetry operation 114.1300000000 -114.1300000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_755 -x+2,-y,z crystal symmetry operation 228.2600000000 0.0000000000 0.0000000000 A O LYS 10 A O LYS 7 A N VAL 73 A N VAL 70 A O VAL 23 A O VAL 20 A N CYS 30 A N CYS 27 A O ARG 31 A O ARG 28 A N VAL 53 A N VAL 50 A O ALA 48 A O ALA 45 A N LEU 65 A N LEU 62 A O GLU 77 A O GLU 74 A N GLN 127 A N GLN 124 A O GLU 124 A O GLU 121 A N ARG 136 A N ARG 133 A O ILE 91 A O ILE 88 A N VAL 104 A N VAL 101 1 A VAL 6 -133.29 -63.00 1 A TYR 108 -98.90 34.55 1 A LEU 129 58.44 -125.16 1 A LYS 138 115.28 -92.59 PROTEIN_REP.PARAM PROTEIN.TOP WATER_REP.PARAM WATER.TOP 24.30 3.20000 0.00000 0.00000 3.20000 0.00000 -6.40000 ALTHOUGH AN ANOMALOUS PARAMETER FILE SHOULD HAVE BEEN USED IN REFINEMENT (SE ATOMS IN STRUCTURE), THIS WAS NOT DONE. DATA CUTOFF HIGH (ABS(F)) : 1392611.86 DATA CUTOFF LOW (ABS(F)) : 0.00 0.2360000 0.007 0.2140000 0.2140000 1.75 50.00 1052 21532 4.900 99.7 RANDOM 1 RESTRAINED THROUGHOUT 0.000 MAD COMBINATION 110.6 0.37 0.23 0.21 5.00 0.15 0.13 1.75 50.00 143 1176 0 0 1033 0.005 1.30 25.50 0.70 0.64 1.500 1.13 2.000 0.41 2.000 0.73 2.500 0.2780000 0.022 0.2530000 1.83 153 2507 8 5.80 99.90 17.10 1.750 50.000 1BKB 21532 0.000 0.0620000 0.0540000 1 8.0000 7.800 99.8 0.2670000 1.75 1.83 3.300 0.2300000 7.50 99.8 refinement CNS 0.3 phasing SOLVE data reduction DENZO data reduction MOSFLM data scaling CCP4 phasing CNS 0.3 TRANSLATION INITIATION FACTOR 5A INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM 1 N N 2 N N A ALA 14 A ALA 11 HELX_P A GLU 16 A GLU 13 5 1 3 A GLU 111 A GLU 108 HELX_P A ARG 116 A ARG 113 1 2 6 covale 1.330 A MSE 7 A N MSE 4 1_555 A VAL 6 A C VAL 3 1_555 covale 1.326 A MSE 7 A C MSE 4 1_555 A SER 8 A N SER 5 1_555 covale 1.331 A MSE 94 A N MSE 91 1_555 A LEU 93 A C LEU 90 1_555 covale 1.329 A MSE 94 A C MSE 91 1_555 A ASP 95 A N ASP 92 1_555 covale 1.332 A MSE 96 A N MSE 93 1_555 A ASP 95 A C ASP 92 1_555 covale 1.328 A MSE 96 A C MSE 93 1_555 A ARG 97 A N ARG 94 1_555 covale 1.330 A MSE 106 A N MSE 103 1_555 A PRO 105 A C PRO 102 1_555 covale 1.332 A MSE 106 A C MSE 103 1_555 A LYS 107 A N LYS 104 1_555 TRANSLATION TRANSLATION INITIATION FACTOR, TRANSLATION IF5A_PYRAE UNP 1 1 P56635 KWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFTAQI LSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG 1 136 1BKB 4 139 P56635 A 1 1 136 1 MET CONFLICT MSE 7 1BKB A P56635 UNP 4 4 1 MET CONFLICT MSE 94 1BKB A P56635 UNP 91 91 1 MET CONFLICT MSE 96 1BKB A P56635 UNP 93 93 1 MET CONFLICT MSE 106 1BKB A P56635 UNP 103 103 2 4 3 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 10 A LYS 7 A GLU 13 A GLU 10 A GLN 70 A GLN 67 A VAL 73 A VAL 70 A TYR 22 A TYR 19 A ILE 25 A ILE 22 A GLU 28 A GLU 25 A SER 38 A SER 35 A LYS 47 A LYS 44 A GLY 54 A GLY 51 A LYS 60 A LYS 57 A PRO 66 A PRO 63 A GLU 77 A GLU 74 A GLN 82 A GLN 79 A GLU 122 A GLU 119 A ILE 128 A ILE 125 A ARG 131 A ARG 128 A VAL 137 A VAL 134 A ILE 91 A ILE 88 A LEU 93 A LEU 90 A ILE 102 A ILE 99 A VAL 104 A VAL 101 79 I 4