0.017399 0.000000 0.001150 0.000000 0.024704 0.000000 0.000000 0.000000 0.020735 0.00000 0.00000 0.00000 Osipiuk, J. Maltseva, N. Dementieva, I. Clancy, S. Collart, F. Joachimiak, A. Midwest Center for Structural Genomics (MCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 93.78 90.00 57.476 40.479 48.333 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 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 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 Na 1 22.990 SODIUM ION non-polymer 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 US Proteins PSFGEY 0867 0887-3585 65 509 513 10.1002/prot.21054 16927377 Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif. 2006 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 2005-03-07 SBC-3 double crystal monochromator SINGLE WAVELENGTH M x-ray 1 0.97934 1.0 19-BM APS 0.97934 SYNCHROTRON APS BEAMLINE 19-BM 14234.623 hypothetical protein S4005 1 man polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 156 nat water no yes SNA(MSE)GLFDEVVGAFLKGDAGKYQAILSWVEEQGGIQVLLEKLQSGGLGAILSTWLSNQQRNQSVSGEQLESALGTN AVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVSAQANNDLLSAG(MSE)ELLKGKLFR SNAMGLFDEVVGAFLKGDAGKYQAILSWVEEQGGIQVLLEKLQSGGLGAILSTWLSNQQRNQSVSGEQLESALGTNAVSD LGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVSAQANNDLLSAGMELLKGKLFR A APC28208 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 Shigella Shigella flexneri 2457T Escherichia Escherichia coli sample yidB 198215 Shigella flexneri 2a 469008 Escherichia coli BL21(DE3) BL21(DE3) pMCSG7 1 2.0 37.5 VAPOR DIFFUSION, HANGING DROP 7.0 0.1 M Bis-Tris, 2 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 Midwest Center for Structural Genomics MCSG PSI, Protein Structure Initiative repository Initial release Version format compliance Source and taxonomy Version format compliance 1 0 2005-05-03 1 1 2008-04-30 1 2 2011-07-13 BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S).AUTHOR STATES THAT BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN. Y RCSB Y RCSB 2005-03-21 REL REL NA SODIUM ION HOH water NA 201 2 NA NA 201 A HOH 1 3 HOH HOH 202 A HOH 2 3 HOH HOH 203 A HOH 3 3 HOH HOH 204 A HOH 4 3 HOH HOH 205 A HOH 5 3 HOH HOH 206 A HOH 6 3 HOH HOH 207 A HOH 7 3 HOH HOH 208 A HOH 8 3 HOH HOH 209 A HOH 9 3 HOH HOH 210 A HOH 10 3 HOH HOH 211 A HOH 11 3 HOH HOH 212 A HOH 12 3 HOH HOH 213 A HOH 13 3 HOH HOH 214 A HOH 14 3 HOH HOH 215 A HOH 15 3 HOH HOH 216 A HOH 16 3 HOH HOH 217 A HOH 17 3 HOH HOH 218 A HOH 18 3 HOH HOH 219 A HOH 19 3 HOH HOH 220 A HOH 20 3 HOH HOH 221 A HOH 21 3 HOH HOH 222 A HOH 22 3 HOH HOH 223 A HOH 23 3 HOH HOH 224 A HOH 24 3 HOH HOH 225 A HOH 25 3 HOH HOH 226 A HOH 26 3 HOH HOH 227 A HOH 27 3 HOH HOH 228 A HOH 28 3 HOH HOH 229 A HOH 29 3 HOH HOH 230 A HOH 30 3 HOH HOH 231 A HOH 31 3 HOH HOH 232 A HOH 32 3 HOH HOH 233 A HOH 33 3 HOH HOH 234 A HOH 34 3 HOH HOH 235 A HOH 35 3 HOH HOH 236 A HOH 36 3 HOH HOH 237 A HOH 37 3 HOH HOH 238 A HOH 38 3 HOH HOH 239 A HOH 39 3 HOH HOH 240 A HOH 40 3 HOH HOH 241 A HOH 41 3 HOH HOH 242 A HOH 42 3 HOH HOH 243 A HOH 43 3 HOH HOH 244 A HOH 44 3 HOH HOH 245 A HOH 45 3 HOH HOH 246 A HOH 46 3 HOH HOH 247 A HOH 47 3 HOH HOH 248 A HOH 48 3 HOH HOH 249 A HOH 49 3 HOH HOH 250 A HOH 50 3 HOH HOH 251 A HOH 51 3 HOH HOH 252 A HOH 52 3 HOH HOH 253 A HOH 53 3 HOH HOH 254 A HOH 54 3 HOH HOH 255 A HOH 55 3 HOH HOH 256 A HOH 56 3 HOH HOH 257 A HOH 57 3 HOH HOH 258 A HOH 58 3 HOH HOH 259 A HOH 59 3 HOH HOH 260 A HOH 60 3 HOH HOH 261 A HOH 61 3 HOH HOH 262 A HOH 62 3 HOH HOH 263 A HOH 63 3 HOH HOH 264 A HOH 64 3 HOH HOH 265 A HOH 65 3 HOH HOH 266 A HOH 66 3 HOH HOH 267 A HOH 67 3 HOH HOH 268 A HOH 68 3 HOH HOH 269 A HOH 69 3 HOH HOH 270 A HOH 70 3 HOH HOH 271 A HOH 71 3 HOH HOH 272 A HOH 72 3 HOH HOH 273 A HOH 73 3 HOH HOH 274 A HOH 74 3 HOH HOH 275 A HOH 75 3 HOH HOH 276 A HOH 76 3 HOH HOH 277 A HOH 77 3 HOH HOH 278 A HOH 78 3 HOH HOH 279 A HOH 79 3 HOH HOH 280 A HOH 80 3 HOH HOH 281 A HOH 81 3 HOH HOH 282 A HOH 82 3 HOH HOH 283 A HOH 83 3 HOH HOH 284 A HOH 84 3 HOH HOH 285 A HOH 85 3 HOH HOH 286 A HOH 86 3 HOH HOH 287 A HOH 87 3 HOH HOH 288 A HOH 88 3 HOH HOH 289 A HOH 89 3 HOH HOH 290 A HOH 90 3 HOH HOH 291 A HOH 91 3 HOH HOH 292 A HOH 92 3 HOH HOH 293 A HOH 93 3 HOH HOH 294 A HOH 94 3 HOH HOH 295 A HOH 95 3 HOH HOH 296 A HOH 96 3 HOH HOH 297 A HOH 97 3 HOH HOH 298 A HOH 98 3 HOH HOH 299 A HOH 99 3 HOH HOH 300 A HOH 100 3 HOH HOH 301 A HOH 101 3 HOH HOH 302 A HOH 102 3 HOH HOH 303 A HOH 103 3 HOH HOH 304 A HOH 104 3 HOH HOH 305 A HOH 105 3 HOH HOH 306 A HOH 106 3 HOH HOH 307 A HOH 107 3 HOH HOH 308 A HOH 108 3 HOH HOH 309 A HOH 109 3 HOH HOH 310 A HOH 110 3 HOH HOH 311 A HOH 111 3 HOH HOH 312 A HOH 112 3 HOH HOH 313 A HOH 113 3 HOH HOH 314 A HOH 114 3 HOH HOH 315 A HOH 115 3 HOH HOH 316 A HOH 116 3 HOH HOH 317 A HOH 117 3 HOH HOH 318 A HOH 118 3 HOH HOH 319 A HOH 119 3 HOH HOH 320 A HOH 120 3 HOH HOH 321 A HOH 121 3 HOH HOH 322 A HOH 122 3 HOH HOH 323 A HOH 123 3 HOH HOH 324 A HOH 124 3 HOH HOH 325 A HOH 125 3 HOH HOH 326 A HOH 126 3 HOH HOH 327 A HOH 127 3 HOH HOH 328 A HOH 128 3 HOH HOH 329 A HOH 129 3 HOH HOH 330 A HOH 130 3 HOH HOH 331 A HOH 131 3 HOH HOH 332 A HOH 132 3 HOH HOH 333 A HOH 133 3 HOH HOH 334 A HOH 134 3 HOH HOH 335 A HOH 135 3 HOH HOH 336 A HOH 136 3 HOH HOH 337 A HOH 137 3 HOH HOH 338 A HOH 138 3 HOH HOH 339 A HOH 139 3 HOH HOH 340 A HOH 140 3 HOH HOH 341 A HOH 141 3 HOH HOH 342 A HOH 142 3 HOH HOH 343 A HOH 143 3 HOH HOH 344 A HOH 144 3 HOH HOH 345 A HOH 145 3 HOH HOH 346 A HOH 146 3 HOH HOH 347 A HOH 147 3 HOH HOH 348 A HOH 148 3 HOH HOH 349 A HOH 149 3 HOH HOH 350 A HOH 150 3 HOH HOH 351 A HOH 151 3 HOH HOH 352 A HOH 152 3 HOH HOH 353 A HOH 153 3 HOH HOH 354 A HOH 154 3 HOH HOH 355 A HOH 155 3 HOH HOH 356 A HOH 156 3 HOH HOH 357 A n 1 -2 A n 2 -1 A n 3 0 A n 4 1 A n 5 2 A LEU 3 n 6 LEU 3 A PHE 4 n 7 PHE 4 A ASP 5 n 8 ASP 5 A GLU 6 n 9 GLU 6 A VAL 7 n 10 VAL 7 A VAL 8 n 11 VAL 8 A GLY 9 n 12 GLY 9 A ALA 10 n 13 ALA 10 A PHE 11 n 14 PHE 11 A LEU 12 n 15 LEU 12 A LYS 13 n 16 LYS 13 A GLY 14 n 17 GLY 14 A ASP 15 n 18 ASP 15 A ALA 16 n 19 ALA 16 A GLY 17 n 20 GLY 17 A LYS 18 n 21 LYS 18 A TYR 19 n 22 TYR 19 A GLN 20 n 23 GLN 20 A ALA 21 n 24 ALA 21 A ILE 22 n 25 ILE 22 A LEU 23 n 26 LEU 23 A SER 24 n 27 SER 24 A TRP 25 n 28 TRP 25 A VAL 26 n 29 VAL 26 A GLU 27 n 30 GLU 27 A GLU 28 n 31 GLU 28 A GLN 29 n 32 GLN 29 A GLY 30 n 33 GLY 30 A GLY 31 n 34 GLY 31 A ILE 32 n 35 ILE 32 A GLN 33 n 36 GLN 33 A VAL 34 n 37 VAL 34 A LEU 35 n 38 LEU 35 A LEU 36 n 39 LEU 36 A GLU 37 n 40 GLU 37 A LYS 38 n 41 LYS 38 A LEU 39 n 42 LEU 39 A GLN 40 n 43 GLN 40 A SER 41 n 44 SER 41 A GLY 42 n 45 GLY 42 A GLY 43 n 46 GLY 43 A LEU 44 n 47 LEU 44 A GLY 45 n 48 GLY 45 A ALA 46 n 49 ALA 46 A ILE 47 n 50 ILE 47 A LEU 48 n 51 LEU 48 A SER 49 n 52 SER 49 A THR 50 n 53 THR 50 A TRP 51 n 54 TRP 51 A LEU 52 n 55 LEU 52 A SER 53 n 56 SER 53 A ASN 54 n 57 ASN 54 A GLN 55 n 58 GLN 55 A GLN 56 n 59 GLN 56 A ARG 57 n 60 ARG 57 A ASN 58 n 61 ASN 58 A GLN 59 n 62 GLN 59 A SER 60 n 63 SER 60 A VAL 61 n 64 VAL 61 A SER 62 n 65 SER 62 A GLY 63 n 66 GLY 63 A GLU 64 n 67 GLU 64 A GLN 65 n 68 GLN 65 A LEU 66 n 69 LEU 66 A GLU 67 n 70 GLU 67 A SER 68 n 71 SER 68 A ALA 69 n 72 ALA 69 A LEU 70 n 73 LEU 70 A GLY 71 n 74 GLY 71 A THR 72 n 75 THR 72 A ASN 73 n 76 ASN 73 A ALA 74 n 77 ALA 74 A VAL 75 n 78 VAL 75 A SER 76 n 79 SER 76 A ASP 77 n 80 ASP 77 A LEU 78 n 81 LEU 78 A GLY 79 n 82 GLY 79 A GLN 80 n 83 GLN 80 A LYS 81 n 84 LYS 81 A LEU 82 n 85 LEU 82 A GLY 83 n 86 GLY 83 A VAL 84 n 87 VAL 84 A ASP 85 n 88 ASP 85 A THR 86 n 89 THR 86 A SER 87 n 90 SER 87 A THR 88 n 91 THR 88 A ALA 89 n 92 ALA 89 A SER 90 n 93 SER 90 A SER 91 n 94 SER 91 A LEU 92 n 95 LEU 92 A LEU 93 n 96 LEU 93 A ALA 94 n 97 ALA 94 A GLU 95 n 98 GLU 95 A GLN 96 n 99 GLN 96 A LEU 97 n 100 LEU 97 A PRO 98 n 101 PRO 98 A LYS 99 n 102 LYS 99 A ILE 100 n 103 ILE 100 A ILE 101 n 104 ILE 101 A ASP 102 n 105 ASP 102 A ALA 103 n 106 ALA 103 A LEU 104 n 107 LEU 104 A SER 105 n 108 SER 105 A PRO 106 n 109 PRO 106 A GLN 107 n 110 GLN 107 A GLY 108 n 111 GLY 108 A GLU 109 n 112 GLU 109 A VAL 110 n 113 VAL 110 A n 114 111 A n 115 112 A GLN 113 n 116 GLN 113 A ALA 114 n 117 ALA 114 A ASN 115 n 118 ASN 115 A ASN 116 n 119 ASN 116 A ASP 117 n 120 ASP 117 A LEU 118 n 121 LEU 118 A LEU 119 n 122 LEU 119 A SER 120 n 123 SER 120 A ALA 121 n 124 ALA 121 A GLY 122 n 125 GLY 122 A MSE 123 n 126 MSE 123 A GLU 124 n 127 GLU 124 A LEU 125 n 128 LEU 125 A LEU 126 n 129 LEU 126 A LYS 127 n 130 LYS 127 A GLY 128 n 131 GLY 128 A LYS 129 n 132 LYS 129 A LEU 130 n 133 LEU 130 A PHE 131 n 134 PHE 131 A n 135 132 A author_defined_assembly 1 monomeric A ASP 77 A OD1 ASP 80 1_555 A NA 201 B NA NA 1_555 A SER 76 B A OG SER 79 1_555 111.0 A ASP 77 A OD1 ASP 80 1_555 A NA 201 B NA NA 1_555 A ASN 73 B A OD1 ASN 76 1_555 103.2 A SER 76 B A OG SER 79 1_555 A NA 201 B NA NA 1_555 A ASN 73 B A OD1 ASN 76 1_555 87.7 A ASP 77 A OD1 ASP 80 1_555 A NA 201 B NA NA 1_555 A GLN 80 A A OE1 GLN 83 1_555 103.8 A SER 76 B A OG SER 79 1_555 A NA 201 B NA NA 1_555 A GLN 80 A A OE1 GLN 83 1_555 85.3 A ASN 73 B A OD1 ASN 76 1_555 A NA 201 B NA NA 1_555 A GLN 80 A A OE1 GLN 83 1_555 152.8 A ASP 77 A OD1 ASP 80 1_555 A NA 201 B NA NA 1_555 A HOH 303 C O HOH 1_555 148.3 A SER 76 B A OG SER 79 1_555 A NA 201 B NA NA 1_555 A HOH 303 C O HOH 1_555 90.7 A ASN 73 B A OD1 ASN 76 1_555 A NA 201 B NA NA 1_555 A HOH 303 C O HOH 1_555 53.2 A GLN 80 A A OE1 GLN 83 1_555 A NA 201 B NA NA 1_555 A HOH 303 C O HOH 1_555 100.6 A MSE 123 SELENOMETHIONINE A MSE 126 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 1 A HOH 274 C HOH 1 A HOH 311 C HOH 1 A HOH 319 C HOH 1 A HOH 339 C HOH 1 A SER -2 A SER 1 1 Y 1 A ASN -1 A ASN 2 1 Y 1 A ALA 0 A ALA 3 1 Y 1 A MSE 1 A MSE 4 1 Y 1 A GLY 2 A GLY 5 1 Y 1 A SER 111 A SER 114 1 Y 1 A ALA 112 A ALA 115 1 Y 1 A ARG 132 A ARG 135 1 Y 22.941 0.62 0.00 -0.18 0.57 0.00 -1.21 0.969 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET. 0.2079 0.1617 0.1643 0.1643 1.45 40.00 1739 17111 17111 86.50 2.090 0.037 RANDOM 1 0 0 SAD 0.106 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 1.45 40.00 156 1096 1 0 939 0.017 0.022 1024 1.427 1.976 1386 4.030 5.000 125 40.405 28.235 51 14.390 15.000 202 14.281 15.000 1 0.098 0.200 170 0.006 0.020 741 0.225 0.200 495 0.300 0.200 728 0.147 0.200 107 0.190 0.200 60 0.172 0.200 21 1.440 1.500 639 2.166 2.000 1034 3.084 3.000 396 4.393 4.500 352 1.958 3.000 1035 5.690 3.000 157 3.849 3.000 1015 0.29 0.183 1.488 41 414 414 20 28.59 1.45 40 1Z67 17111 17111 0 0 0.04 1 39.2 4.1 86.5 0.33 1.45 1.48 2.14 291 1 1.6 26.5 refinement REFMAC 5.2.0005 data reduction HKL-2000 data scaling SCALEPACK phasing SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE hypothetical protein S4005 Structure of Homeodomain-like Protein of Unknown Function S4005 from Shigella flexneri 1 N N 2 N N 3 N N A LEU 3 A LEU 6 HELX_P A GLY 14 A GLY 17 1 1 12 A GLY 17 A GLY 20 HELX_P A GLN 29 A GLN 32 1 2 13 A GLY 31 A GLY 34 HELX_P A GLY 42 A GLY 45 1 3 12 A LEU 44 A LEU 47 HELX_P A SER 53 A SER 56 1 4 10 A SER 62 A SER 65 HELX_P A GLY 71 A GLY 74 1 5 10 A GLY 71 A GLY 74 HELX_P A GLY 83 A GLY 86 1 6 13 A ASP 85 A ASP 88 HELX_P A LEU 104 A LEU 107 1 7 20 A ASP 117 A ASP 120 HELX_P A PHE 131 A PHE 134 1 8 15 covale 1.328 A GLY 122 A C GLY 125 1_555 A MSE 123 A N MSE 126 1_555 covale 1.342 A MSE 123 A C MSE 126 1_555 A GLU 124 A N GLU 127 1_555 metalc 2.450 A NA 201 B NA NA 1_555 A ASP 77 A OD1 ASP 80 1_555 metalc 2.553 B A NA 201 B NA NA 1_555 A SER 76 A OG SER 79 1_555 metalc 2.585 B A NA 201 B NA NA 1_555 A ASN 73 A OD1 ASN 76 1_555 metalc 2.851 A A GLN 80 A OE1 GLN 83 1_555 A NA 201 B NA NA 1_555 metalc 2.682 A NA 201 B NA NA 1_555 A HOH 303 C O HOH 1_555 Structural Genomics, Unknown Function structural genomics, hypothetical protein, Shigella flexneri, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, Unknown Function Q83IZ7_SHIFL UNP 1 1 Q83IZ7 MGLFDEVVGAFLKGDAGKYQAILSWVEEQGGIQVLLEKLQSGGLGAILSTWLSNQQRNQSVSGEQLESALGTNAVSDLGQ KLGVDTSTASSLLAEQLPKIIDALSPQGEVSAQANNDLLSAGMELLKGKLFR 1 132 1Z67 1 132 Q83IZ7 A 1 4 135 1 CLONING ARTIFACT SER -2 1Z67 A Q83IZ7 UNP 1 1 CLONING ARTIFACT ASN -1 1Z67 A Q83IZ7 UNP 2 1 CLONING ARTIFACT ALA 0 1Z67 A Q83IZ7 UNP 3 1 MET MODIFIED RESIDUE MSE 1 1Z67 A Q83IZ7 UNP 1 4 1 MET MODIFIED RESIDUE MSE 123 1Z67 A Q83IZ7 UNP 123 126 BINDING SITE FOR RESIDUE NA A 201 Software 6 A GLN 33 A GLN 36 6 4_546 A ASN 73 A ASN 76 6 1_555 A SER 76 A SER 79 6 1_555 A ASP 77 A ASP 80 6 1_555 A GLN 80 A GLN 83 6 1_555 A HOH 303 C HOH 6 1_555 5 C 1 2 1