0.025044 0.014459 0.000000 0.000000 0.028918 0.000000 0.000000 0.000000 0.014391 0.00000 0.00000 0.00000 Kursula, P. Lehmann, F. Song, Y.H. Wilmanns, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 39.930 39.930 69.490 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 Cl -1 35.453 CHLORIDE 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 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 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 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 CL 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 O N 125 N H N 126 N H N 127 N N N 128 S C N 129 N C N 130 N O N 131 S C N 132 N C N 133 N C N 134 N C N 135 N O 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 H N 146 N H N 147 N H N 148 N H N 149 N N N 150 S C N 151 N C N 152 N O N 153 N C N 154 N C N 155 N C N 156 N C N 157 N O 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 H N 171 N N N 172 S C N 173 N C N 174 N O N 175 N C N 176 N C N 177 N C N 178 N C N 179 N N N 180 N O 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 H N 193 N H N 194 N H N 195 N H N 196 N N N 197 S C N 198 N C N 199 N O N 200 N C Y 201 N C Y 202 N C Y 203 N C Y 204 N C Y 205 N C Y 206 N C N 207 N O 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 N N 220 S C N 221 N C N 222 N O N 223 N C N 224 N C N 225 N C N 226 N O 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 N N 237 S C N 238 N C N 239 N O N 240 N C N 241 N O N 242 N O 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 R C N 255 N O N 256 N C N 257 N O 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 H N 266 N H N 267 N N N 268 S C N 269 N C N 270 N O N 271 N C Y 272 N C Y 273 N C Y 274 N C Y 275 N N Y 276 N C Y 277 N C Y 278 N C Y 279 N C Y 280 N C N 281 N O 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 H N 291 N H N 292 N H N 293 N H N 294 N N N 295 S C N 296 N C N 297 N O N 298 N C Y 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C Y 304 N C N 305 N O N 306 N O N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H 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 N N 319 S C N 320 N C N 321 N O N 322 N C N 323 N C N 324 N C N 325 N O 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 H N 333 N H N 334 N H N 335 N H N 336 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 sing N 123 N sing N 124 N doub N 125 N sing N 126 N sing 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 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 sing N 188 N sing N 189 N sing N 190 N doub N 191 N sing N 192 N sing N 193 N sing N 194 N sing Y 195 N doub Y 196 N sing Y 197 N sing N 198 N sing Y 199 N doub N 200 N sing Y 201 N doub N 202 N sing Y 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 doub 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 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 sing N 262 N sing N 263 N sing Y 264 N doub Y 265 N sing Y 266 N sing N 267 N sing Y 268 N doub Y 269 N sing Y 270 N sing N 271 N sing Y 272 N sing Y 273 N doub N 274 N sing Y 275 N doub N 276 N sing Y 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 sing N 284 N sing N 285 N sing N 286 N sing N 287 N doub N 288 N sing N 289 N sing N 290 N sing N 291 N sing Y 292 N doub Y 293 N sing Y 294 N sing N 295 N sing Y 296 N doub N 297 N sing Y 298 N doub N 299 N sing Y 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 doub N 312 N sing 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 To be Published 0353 Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution 10.2210/pdb1oot/pdb pdb_00001oot 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 2003-03-01 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.8028 1.0 X13 EMBL/DESY, HAMBURG 0.8028 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 6581.299 Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region SH3 domain 1 man polymer 35.453 CHLORIDE ION 3 syn non-polymer 18.015 water 57 nat water no no GSSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV GSSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV 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 baker's yeast Saccharomyces Escherichia sample YFR024C 4932 Saccharomyces cerevisiae 562 Escherichia coli PDEST-17 1 1.98 37.27 VAPOR DIFFUSION 7.5 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K 295 chem_comp_atom chem_comp_bond database_2 diffrn_source pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2004-04-06 1 1 2008-04-29 1 2 2011-07-13 1 3 2023-08-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2003-03-04 REL REL CL CHLORIDE ION HOH water 1SEM PDB experimental model CL 111 2 CL CL 111 A CL 112 2 CL CL 112 A CL 113 2 CL CL 113 A HOH 1 3 HOH HOH 114 A HOH 2 3 HOH HOH 115 A HOH 3 3 HOH HOH 116 A HOH 4 3 HOH HOH 117 A HOH 8 3 HOH HOH 118 A HOH 15 3 HOH HOH 119 A HOH 16 3 HOH HOH 120 A HOH 19 3 HOH HOH 121 A HOH 21 3 HOH HOH 122 A HOH 24 3 HOH HOH 123 A HOH 26 3 HOH HOH 124 A HOH 28 3 HOH HOH 125 A HOH 29 3 HOH HOH 126 A HOH 30 3 HOH HOH 127 A HOH 32 3 HOH HOH 128 A HOH 34 3 HOH HOH 129 A HOH 47 3 HOH HOH 130 A HOH 51 3 HOH HOH 131 A HOH 52 3 HOH HOH 132 A HOH 54 3 HOH HOH 133 A HOH 55 3 HOH HOH 134 A HOH 56 3 HOH HOH 135 A HOH 57 3 HOH HOH 136 A HOH 59 3 HOH HOH 137 A HOH 60 3 HOH HOH 138 A HOH 61 3 HOH HOH 139 A HOH 64 3 HOH HOH 140 A HOH 65 3 HOH HOH 141 A HOH 66 3 HOH HOH 142 A HOH 67 3 HOH HOH 143 A HOH 68 3 HOH HOH 144 A HOH 69 3 HOH HOH 145 A HOH 70 3 HOH HOH 146 A HOH 71 3 HOH HOH 147 A HOH 74 3 HOH HOH 148 A HOH 76 3 HOH HOH 149 A HOH 77 3 HOH HOH 150 A HOH 79 3 HOH HOH 151 A HOH 81 3 HOH HOH 152 A HOH 84 3 HOH HOH 153 A HOH 85 3 HOH HOH 154 A HOH 86 3 HOH HOH 155 A HOH 87 3 HOH HOH 156 A HOH 88 3 HOH HOH 157 A HOH 89 3 HOH HOH 158 A HOH 91 3 HOH HOH 159 A HOH 94 3 HOH HOH 160 A HOH 95 3 HOH HOH 161 A HOH 96 3 HOH HOH 162 A HOH 97 3 HOH HOH 163 A HOH 98 3 HOH HOH 164 A HOH 99 3 HOH HOH 165 A HOH 100 3 HOH HOH 166 A HOH 104 3 HOH HOH 167 A HOH 105 3 HOH HOH 168 A HOH 106 3 HOH HOH 169 A HOH 107 3 HOH HOH 170 A n 1 -1 A n 2 0 A SER 1 n 3 SER 1 A PRO 2 n 4 PRO 2 A LYS 3 n 5 LYS 3 A ALA 4 n 6 ALA 4 A VAL 5 n 7 VAL 5 A ALA 6 n 8 ALA 6 A LEU 7 n 9 LEU 7 A TYR 8 n 10 TYR 8 A SER 9 n 11 SER 9 A PHE 10 n 12 PHE 10 A ALA 11 n 13 ALA 11 A GLY 12 n 14 GLY 12 A GLU 13 n 15 GLU 13 A GLU 14 n 16 GLU 14 A SER 15 n 17 SER 15 A GLY 16 n 18 GLY 16 A ASP 17 n 19 ASP 17 A LEU 18 n 20 LEU 18 A PRO 19 n 21 PRO 19 A PHE 20 n 22 PHE 20 A ARG 21 n 23 ARG 21 A LYS 22 n 24 LYS 22 A GLY 23 n 25 GLY 23 A ASP 24 n 26 ASP 24 A VAL 25 n 27 VAL 25 A ILE 26 n 28 ILE 26 A THR 27 n 29 THR 27 A ILE 28 n 30 ILE 28 A LEU 29 n 31 LEU 29 A LYS 30 n 32 LYS 30 A LYS 31 n 33 LYS 31 A SER 32 n 34 SER 32 A ASP 33 n 35 ASP 33 A SER 34 n 36 SER 34 A GLN 35 n 37 GLN 35 A ASN 36 n 38 ASN 36 A ASP 37 n 39 ASP 37 A TRP 38 n 40 TRP 38 A TRP 39 n 41 TRP 39 A THR 40 n 42 THR 40 A GLY 41 n 43 GLY 41 A ARG 42 n 44 ARG 42 A VAL 43 n 45 VAL 43 A ASN 44 n 46 ASN 44 A GLY 45 n 47 GLY 45 A ARG 46 n 48 ARG 46 A GLU 47 n 49 GLU 47 A GLY 48 n 50 GLY 48 A ILE 49 n 51 ILE 49 A PHE 50 n 52 PHE 50 A PRO 51 n 53 PRO 51 A ALA 52 n 54 ALA 52 A ASN 53 n 55 ASN 53 A TYR 54 n 56 TYR 54 A VAL 55 n 57 VAL 55 A GLU 56 n 58 GLU 56 A LEU 57 n 59 LEU 57 A VAL 58 n 60 VAL 58 A author_defined_assembly 1 monomeric 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 GLY 48 A O GLY 50 A N GLY 41 A N GLY 43 A O THR 40 A O THR 42 A N LYS 30 A N LYS 32 A O ILE 26 A O ILE 28 A N ALA 4 A N ALA 6 A N VAL 5 A N VAL 7 A O GLU 56 A O GLU 58 1 A GLY -1 A GLY 1 1 Y 1 A SER 0 A SER 2 1 Y 15.044 1.17 0.58 0.00 1.17 0.00 -1.75 0.979 0.969 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT 0.17046 0.13207 0.13397 0.13397 1.39 20.00 656 13120 13120 5.0 97.76 1.018 0.038 RANDOM 1 ISOTROPIC, AT LATE STAGES OF REFINEMENT ANISOTROPIC THROUGHOUT 0.0 MOLECULAR REPLACEMENT 0.053 0.052 0.80 0.80 1.40 1SEM Engh & Huber BABINET MODEL WITH MASK 1.39 20.00 60 578 3 0 515 0.020 0.021 536 0.003 0.020 474 1.842 1.936 739 0.879 3.000 1112 5.179 5.000 71 0.114 0.200 76 0.011 0.020 635 0.002 0.020 117 0.190 0.200 79 0.246 0.200 576 0.090 0.200 336 0.129 0.200 26 0.212 0.200 7 0.366 0.200 42 0.258 0.200 18 2.991 4.000 330 4.075 5.000 542 3.992 4.000 206 5.918 5.000 197 2.246 2.000 536 7.140 2.000 63 5.126 2.000 515 0.313 0.264 1.426 45 841 841 20 92 21.65 1.38 30 1OOT 13185 13185 -3 0.056 1 15.0 5.5 97.0 1.38 1.44 2.7 1398 0.414 3.1 88.1 refinement REFMAC 5.1.27 data reduction XDS data scaling XDS phasing AMoRE Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution 1 N N 2 N N 2 N N 2 N N 3 N N STRUCTURAL GENOMICS SH3 DOMAIN, STURCTURAL GENOMICS, STRUCTURAL GENOMICS YFJ4_YEAST UNP 1 314 P43603 TSSPKAVALYSFAGEESGDLPFRKGDVITILKKSDSQNDWWTGRVNGREGIFPANYVELV 314 373 1OOT -1 58 P43603 A 1 1 60 1 THR cloning artifact GLY -1 1OOT A P43603 UNP 314 1 5 anti-parallel anti-parallel anti-parallel anti-parallel A ARG 46 A ARG 48 A PRO 51 A PRO 53 A TRP 38 A TRP 40 A VAL 43 A VAL 45 A VAL 25 A VAL 27 A LYS 30 A LYS 32 A LYS 3 A LYS 5 A ALA 6 A ALA 8 A VAL 55 A VAL 57 A LEU 57 A LEU 59 BINDING SITE FOR RESIDUE CL A 111 A CL 111 Software 4 BINDING SITE FOR RESIDUE CL A 112 A CL 112 Software 1 BINDING SITE FOR RESIDUE CL A 113 A CL 113 Software 1 A LYS 22 A LYS 24 4 3_664 A ARG 46 A ARG 48 4 1_555 A GLU 47 A GLU 49 4 1_555 A HOH 129 E HOH 4 1_555 A ALA 11 A ALA 13 1 1_555 A GLN 35 A GLN 37 1 1_555 152 P 31 2 1