0.011045 0.000000 0.007867 0.000000 0.027533 0.000000 0.000000 0.000000 0.016911 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 125.460 90.000 90.540 36.320 72.600 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 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 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer 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 To be published 0353 Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution 10.2210/pdb3ccg/pdb pdb_00003ccg 100 1 Flat mirror (vertical focusing) CCD 2008-02-01 MARMOSAIC 325 mm CCD Single crystal Si(111) bent (horizontal focusing) MAD M x-ray 1 0.91837 1.0 0.97922 1.0 0.97874 1.0 BL11-1 SSRL 0.91837, 0.97922, 0.97874 SYNCHROTRON SSRL BEAMLINE BL11-1 21759.070 HD superfamily hydrolase 1 man polymer 55.845 FE (III) ION 2 syn non-polymer 94.971 PHOSPHATE ION 1 syn non-polymer 18.015 water 198 nat water no yes G(MSE)WSYDKITDYL(MSE)NNLGEKRYKHSLGV(MSE)DTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICT NEGYELGDEDIRNSYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPN(MSE)SLLEKIIYIADYIEPGREFKGVDEL RKAADEDLNKALL(MSE)SFDNTIKFVIDKGGFLHHNTIEARNYLISRKG GMWSYDKITDYLMNNLGEKRYKHSLGVMDTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICTNEGYELGDEDIR NSYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPNMSLLEKIIYIADYIEPGREFKGVDELRKAADEDLNKALLMSF DNTIKFVIDKGGFLHHNTIEARNYLISRKG A 367850 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 Clostridium Clostridium acetobutylicum DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Escherichia sample NP_347894.1, CA_C1263 272562 Clostridium acetobutylicum ATCC 824 562 Escherichia coli HK100 Plasmid SpeedET 1 2.23 44.95 VAPOR DIFFUSION, SITTING DROP 5.9 NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software software struct_conn database_2 pdbx_struct_conn_angle struct_conn struct_conn_type struct_ref_seq_dif struct_site repository Initial release Advisory Version format compliance Refinement description Data collection Derived calculations Refinement description Database references Derived calculations 1 0 2008-03-11 1 1 2011-07-13 1 2 2017-10-25 1 3 2019-07-24 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _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_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _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 Y RCSB Y RCSB 2008-02-25 REL REL FE FE (III) ION PO4 PHOSPHATE ION HOH water THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. FE 1 2 FE FE 190 A FE 2 2 FE FE 191 A PO4 3 3 PO4 PO4 192 A HOH 4 4 HOH HOH 193 A HOH 5 4 HOH HOH 194 A HOH 6 4 HOH HOH 195 A HOH 7 4 HOH HOH 196 A HOH 8 4 HOH HOH 197 A HOH 9 4 HOH HOH 198 A HOH 10 4 HOH HOH 199 A HOH 11 4 HOH HOH 200 A HOH 12 4 HOH HOH 201 A HOH 13 4 HOH HOH 202 A HOH 14 4 HOH HOH 203 A HOH 15 4 HOH HOH 204 A HOH 16 4 HOH HOH 205 A HOH 17 4 HOH HOH 206 A HOH 18 4 HOH HOH 207 A HOH 19 4 HOH HOH 208 A HOH 20 4 HOH HOH 209 A HOH 21 4 HOH HOH 210 A HOH 22 4 HOH HOH 211 A HOH 23 4 HOH HOH 212 A HOH 24 4 HOH HOH 213 A HOH 25 4 HOH HOH 214 A HOH 26 4 HOH HOH 215 A HOH 27 4 HOH HOH 216 A HOH 28 4 HOH HOH 217 A HOH 29 4 HOH HOH 218 A HOH 30 4 HOH HOH 219 A HOH 31 4 HOH HOH 220 A HOH 32 4 HOH HOH 221 A HOH 33 4 HOH HOH 222 A HOH 34 4 HOH HOH 223 A HOH 35 4 HOH HOH 224 A HOH 36 4 HOH HOH 225 A HOH 37 4 HOH HOH 226 A HOH 38 4 HOH HOH 227 A HOH 39 4 HOH HOH 228 A HOH 40 4 HOH HOH 229 A HOH 41 4 HOH HOH 230 A HOH 42 4 HOH HOH 231 A HOH 43 4 HOH HOH 232 A HOH 44 4 HOH HOH 233 A HOH 45 4 HOH HOH 234 A HOH 46 4 HOH HOH 235 A HOH 47 4 HOH HOH 236 A HOH 48 4 HOH HOH 237 A HOH 49 4 HOH HOH 238 A HOH 50 4 HOH HOH 239 A HOH 51 4 HOH HOH 240 A HOH 52 4 HOH HOH 241 A HOH 53 4 HOH HOH 242 A HOH 54 4 HOH HOH 243 A HOH 55 4 HOH HOH 244 A HOH 56 4 HOH HOH 245 A HOH 57 4 HOH HOH 246 A HOH 58 4 HOH HOH 247 A HOH 59 4 HOH HOH 248 A HOH 60 4 HOH HOH 249 A HOH 61 4 HOH HOH 250 A HOH 62 4 HOH HOH 251 A HOH 63 4 HOH HOH 252 A HOH 64 4 HOH HOH 253 A HOH 65 4 HOH HOH 254 A HOH 66 4 HOH HOH 255 A HOH 67 4 HOH HOH 256 A HOH 68 4 HOH HOH 257 A HOH 69 4 HOH HOH 258 A HOH 70 4 HOH HOH 259 A HOH 71 4 HOH HOH 260 A HOH 72 4 HOH HOH 261 A HOH 73 4 HOH HOH 262 A HOH 74 4 HOH HOH 263 A HOH 75 4 HOH HOH 264 A HOH 76 4 HOH HOH 265 A HOH 77 4 HOH HOH 266 A HOH 78 4 HOH HOH 267 A HOH 79 4 HOH HOH 268 A HOH 80 4 HOH HOH 269 A HOH 81 4 HOH HOH 270 A HOH 82 4 HOH HOH 271 A HOH 83 4 HOH HOH 272 A HOH 84 4 HOH HOH 273 A HOH 85 4 HOH HOH 274 A HOH 86 4 HOH HOH 275 A HOH 87 4 HOH HOH 276 A HOH 88 4 HOH HOH 277 A HOH 89 4 HOH HOH 278 A HOH 90 4 HOH HOH 279 A HOH 91 4 HOH HOH 280 A HOH 92 4 HOH HOH 281 A HOH 93 4 HOH HOH 282 A HOH 94 4 HOH HOH 283 A HOH 95 4 HOH HOH 284 A HOH 96 4 HOH HOH 285 A HOH 97 4 HOH HOH 286 A HOH 98 4 HOH HOH 287 A HOH 99 4 HOH HOH 288 A HOH 100 4 HOH HOH 289 A HOH 101 4 HOH HOH 290 A HOH 102 4 HOH HOH 291 A HOH 103 4 HOH HOH 292 A HOH 104 4 HOH HOH 293 A HOH 105 4 HOH HOH 294 A HOH 106 4 HOH HOH 295 A HOH 107 4 HOH HOH 296 A HOH 108 4 HOH HOH 297 A HOH 109 4 HOH HOH 298 A HOH 110 4 HOH HOH 299 A HOH 111 4 HOH HOH 300 A HOH 112 4 HOH HOH 301 A HOH 113 4 HOH HOH 302 A HOH 114 4 HOH HOH 303 A HOH 115 4 HOH HOH 304 A HOH 116 4 HOH HOH 305 A HOH 117 4 HOH HOH 306 A HOH 118 4 HOH HOH 307 A HOH 119 4 HOH HOH 308 A HOH 120 4 HOH HOH 309 A HOH 121 4 HOH HOH 310 A HOH 122 4 HOH HOH 311 A HOH 123 4 HOH HOH 312 A HOH 124 4 HOH HOH 313 A HOH 125 4 HOH HOH 314 A HOH 126 4 HOH HOH 315 A HOH 127 4 HOH HOH 316 A HOH 128 4 HOH HOH 317 A HOH 129 4 HOH HOH 318 A HOH 130 4 HOH HOH 319 A HOH 131 4 HOH HOH 320 A HOH 132 4 HOH HOH 321 A HOH 133 4 HOH HOH 322 A HOH 134 4 HOH HOH 323 A HOH 135 4 HOH HOH 324 A HOH 136 4 HOH HOH 325 A HOH 137 4 HOH HOH 326 A HOH 138 4 HOH HOH 327 A HOH 139 4 HOH HOH 328 A HOH 140 4 HOH HOH 329 A HOH 141 4 HOH HOH 330 A HOH 142 4 HOH HOH 331 A HOH 143 4 HOH HOH 332 A HOH 144 4 HOH HOH 333 A HOH 145 4 HOH HOH 334 A HOH 146 4 HOH HOH 335 A HOH 147 4 HOH HOH 336 A HOH 148 4 HOH HOH 337 A HOH 149 4 HOH HOH 338 A HOH 150 4 HOH HOH 339 A HOH 151 4 HOH HOH 340 A HOH 152 4 HOH HOH 341 A HOH 153 4 HOH HOH 342 A HOH 154 4 HOH HOH 343 A HOH 155 4 HOH HOH 344 A HOH 156 4 HOH HOH 345 A HOH 157 4 HOH HOH 346 A HOH 158 4 HOH HOH 347 A HOH 159 4 HOH HOH 348 A HOH 160 4 HOH HOH 349 A HOH 161 4 HOH HOH 350 A HOH 162 4 HOH HOH 351 A HOH 163 4 HOH HOH 352 A HOH 164 4 HOH HOH 353 A HOH 165 4 HOH HOH 354 A HOH 166 4 HOH HOH 355 A HOH 167 4 HOH HOH 356 A HOH 168 4 HOH HOH 357 A HOH 169 4 HOH HOH 358 A HOH 170 4 HOH HOH 359 A HOH 171 4 HOH HOH 360 A HOH 172 4 HOH HOH 361 A HOH 173 4 HOH HOH 362 A HOH 174 4 HOH HOH 363 A HOH 175 4 HOH HOH 364 A HOH 176 4 HOH HOH 365 A HOH 177 4 HOH HOH 366 A HOH 178 4 HOH HOH 367 A HOH 179 4 HOH HOH 368 A HOH 180 4 HOH HOH 369 A HOH 181 4 HOH HOH 370 A HOH 182 4 HOH HOH 371 A HOH 183 4 HOH HOH 372 A HOH 184 4 HOH HOH 373 A HOH 185 4 HOH HOH 374 A HOH 186 4 HOH HOH 375 A HOH 187 4 HOH HOH 376 A HOH 188 4 HOH HOH 377 A HOH 189 4 HOH HOH 378 A HOH 190 4 HOH HOH 379 A HOH 191 4 HOH HOH 380 A HOH 192 4 HOH HOH 381 A HOH 193 4 HOH HOH 382 A HOH 194 4 HOH HOH 383 A HOH 195 4 HOH HOH 384 A HOH 196 4 HOH HOH 385 A HOH 197 4 HOH HOH 386 A HOH 198 4 HOH HOH 387 A HOH 199 4 HOH HOH 388 A HOH 200 4 HOH HOH 389 A HOH 201 4 HOH HOH 390 A GLY 0 n 1 GLY 0 A MSE 1 n 2 MSE 1 A TRP 2 n 3 TRP 2 A SER 3 n 4 SER 3 A TYR 4 n 5 TYR 4 A ASP 5 n 6 ASP 5 A LYS 6 n 7 LYS 6 A ILE 7 n 8 ILE 7 A THR 8 n 9 THR 8 A ASP 9 n 10 ASP 9 A TYR 10 n 11 TYR 10 A LEU 11 n 12 LEU 11 A MSE 12 n 13 MSE 12 A ASN 13 n 14 ASN 13 A ASN 14 n 15 ASN 14 A LEU 15 n 16 LEU 15 A GLY 16 n 17 GLY 16 A GLU 17 n 18 GLU 17 A LYS 18 n 19 LYS 18 A ARG 19 n 20 ARG 19 A TYR 20 n 21 TYR 20 A LYS 21 n 22 LYS 21 A HIS 22 n 23 HIS 22 A SER 23 n 24 SER 23 A LEU 24 n 25 LEU 24 A GLY 25 n 26 GLY 25 A VAL 26 n 27 VAL 26 A MSE 27 n 28 MSE 27 A ASP 28 n 29 ASP 28 A THR 29 n 30 THR 29 A ALA 30 n 31 ALA 30 A VAL 31 n 32 VAL 31 A ARG 32 n 33 ARG 32 A LEU 33 n 34 LEU 33 A ALA 34 n 35 ALA 34 A GLY 35 n 36 GLY 35 A ILE 36 n 37 ILE 36 A TYR 37 n 38 TYR 37 A ASN 38 n 39 ASN 38 A GLU 39 n 40 GLU 39 A ASP 40 n 41 ASP 40 A THR 41 n 42 THR 41 A GLU 42 n 43 GLU 42 A LYS 43 n 44 LYS 43 A ALA 44 n 45 ALA 44 A ARG 45 n 46 ARG 45 A ILE 46 n 47 ILE 46 A ALA 47 n 48 ALA 47 A GLY 48 n 49 GLY 48 A LEU 49 n 50 LEU 49 A VAL 50 n 51 VAL 50 A HIS 51 n 52 HIS 51 A ASP 52 n 53 ASP 52 A CYS 53 n 54 CYS 53 A ALA 54 n 55 ALA 54 A LYS 55 n 56 LYS 55 A LYS 56 n 57 LYS 56 A LEU 57 n 58 LEU 57 A PRO 58 n 59 PRO 58 A GLY 59 n 60 GLY 59 A GLU 60 n 61 GLU 60 A LYS 61 n 62 LYS 61 A ILE 62 n 63 ILE 62 A ILE 63 n 64 ILE 63 A GLU 64 n 65 GLU 64 A ILE 65 n 66 ILE 65 A CYS 66 n 67 CYS 66 A THR 67 n 68 THR 67 A ASN 68 n 69 ASN 68 A GLU 69 n 70 GLU 69 A GLY 70 n 71 GLY 70 A TYR 71 n 72 TYR 71 A GLU 72 n 73 GLU 72 A LEU 73 n 74 LEU 73 A GLY 74 n 75 GLY 74 A ASP 75 n 76 ASP 75 A GLU 76 n 77 GLU 76 A ASP 77 n 78 ASP 77 A ILE 78 n 79 ILE 78 A ARG 79 n 80 ARG 79 A ASN 80 n 81 ASN 80 A SER 81 n 82 SER 81 A TYR 82 n 83 TYR 82 A LEU 83 n 84 LEU 83 A LEU 84 n 85 LEU 84 A HIS 85 n 86 HIS 85 A GLY 86 n 87 GLY 86 A LEU 87 n 88 LEU 87 A ALA 88 n 89 ALA 88 A GLY 89 n 90 GLY 89 A ARG 90 n 91 ARG 90 A ILE 91 n 92 ILE 91 A LEU 92 n 93 LEU 92 A ALA 93 n 94 ALA 93 A LYS 94 n 95 LYS 94 A LYS 95 n 96 LYS 95 A VAL 96 n 97 VAL 96 A ILE 97 n 98 ILE 97 A GLY 98 n 99 GLY 98 A ILE 99 n 100 ILE 99 A ASP 100 n 101 ASP 100 A ASP 101 n 102 ASP 101 A GLU 102 n 103 GLU 102 A ASP 103 n 104 ASP 103 A VAL 104 n 105 VAL 104 A LEU 105 n 106 LEU 105 A ASN 106 n 107 ASN 106 A ALA 107 n 108 ALA 107 A ILE 108 n 109 ILE 108 A GLU 109 n 110 GLU 109 A PHE 110 n 111 PHE 110 A HIS 111 n 112 HIS 111 A THR 112 n 113 THR 112 A THR 113 n 114 THR 113 A GLY 114 n 115 GLY 114 A ARG 115 n 116 ARG 115 A PRO 116 n 117 PRO 116 A ASN 117 n 118 ASN 117 A MSE 118 n 119 MSE 118 A SER 119 n 120 SER 119 A LEU 120 n 121 LEU 120 A LEU 121 n 122 LEU 121 A GLU 122 n 123 GLU 122 A LYS 123 n 124 LYS 123 A ILE 124 n 125 ILE 124 A ILE 125 n 126 ILE 125 A TYR 126 n 127 TYR 126 A ILE 127 n 128 ILE 127 A ALA 128 n 129 ALA 128 A ASP 129 n 130 ASP 129 A TYR 130 n 131 TYR 130 A ILE 131 n 132 ILE 131 A GLU 132 n 133 GLU 132 A PRO 133 n 134 PRO 133 A GLY 134 n 135 GLY 134 A ARG 135 n 136 ARG 135 A GLU 136 n 137 GLU 136 A PHE 137 n 138 PHE 137 A LYS 138 n 139 LYS 138 A GLY 139 n 140 GLY 139 A VAL 140 n 141 VAL 140 A ASP 141 n 142 ASP 141 A GLU 142 n 143 GLU 142 A LEU 143 n 144 LEU 143 A ARG 144 n 145 ARG 144 A LYS 145 n 146 LYS 145 A ALA 146 n 147 ALA 146 A ALA 147 n 148 ALA 147 A ASP 148 n 149 ASP 148 A GLU 149 n 150 GLU 149 A ASP 150 n 151 ASP 150 A LEU 151 n 152 LEU 151 A ASN 152 n 153 ASN 152 A LYS 153 n 154 LYS 153 A ALA 154 n 155 ALA 154 A LEU 155 n 156 LEU 155 A LEU 156 n 157 LEU 156 A MSE 157 n 158 MSE 157 A SER 158 n 159 SER 158 A PHE 159 n 160 PHE 159 A ASP 160 n 161 ASP 160 A ASN 161 n 162 ASN 161 A THR 162 n 163 THR 162 A ILE 163 n 164 ILE 163 A LYS 164 n 165 LYS 164 A PHE 165 n 166 PHE 165 A VAL 166 n 167 VAL 166 A ILE 167 n 168 ILE 167 A ASP 168 n 169 ASP 168 A LYS 169 n 170 LYS 169 A GLY 170 n 171 GLY 170 A GLY 171 n 172 GLY 171 A PHE 172 n 173 PHE 172 A LEU 173 n 174 LEU 173 A HIS 174 n 175 HIS 174 A HIS 175 n 176 HIS 175 A ASN 176 n 177 ASN 176 A THR 177 n 178 THR 177 A ILE 178 n 179 ILE 178 A GLU 179 n 180 GLU 179 A ALA 180 n 181 ALA 180 A ARG 181 n 182 ARG 181 A ASN 182 n 183 ASN 182 A TYR 183 n 184 TYR 183 A LEU 184 n 185 LEU 184 A ILE 185 n 186 ILE 185 A SER 186 n 187 SER 186 A ARG 187 n 188 ARG 187 A LYS 188 n 189 LYS 188 A n 190 189 A 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 refined 0.0000 0.0000 0.0000 X-RAY DIFFRACTION A 0 A 1 A 188 A 189 X-RAY DIFFRACTION 1 software_defined_assembly PISA 2 dimeric 1390 -7.2 17530 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 A HIS 51 A NE2 HIS 52 1_555 97.5 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 A ASP 52 A OD2 ASP 53 1_555 90.1 A HIS 51 A NE2 HIS 52 1_555 A FE 191 C FE FE 1_555 A ASP 52 A OD2 ASP 53 1_555 82.6 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 A ASP 129 A OD1 ASP 130 1_555 77.5 A HIS 51 A NE2 HIS 52 1_555 A FE 191 C FE FE 1_555 A ASP 129 A OD1 ASP 130 1_555 96.6 A ASP 52 A OD2 ASP 53 1_555 A FE 191 C FE FE 1_555 A ASP 129 A OD1 ASP 130 1_555 167.4 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 A PO4 192 D O4 PO4 1_555 82.2 A HIS 51 A NE2 HIS 52 1_555 A FE 191 C FE FE 1_555 A PO4 192 D O4 PO4 1_555 173.4 A ASP 52 A OD2 ASP 53 1_555 A FE 191 C FE FE 1_555 A PO4 192 D O4 PO4 1_555 90.8 A ASP 129 A OD1 ASP 130 1_555 A FE 191 C FE FE 1_555 A PO4 192 D O4 PO4 1_555 89.8 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 175.0 A HIS 51 A NE2 HIS 52 1_555 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 83.9 A ASP 52 A OD2 ASP 53 1_555 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 94.8 A ASP 129 A OD1 ASP 130 1_555 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 97.7 A PO4 192 D O4 PO4 1_555 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 97.0 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 A HIS 85 A NE2 HIS 86 1_555 86.7 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 A HIS 111 A NE2 HIS 112 1_555 90.7 A HIS 85 A NE2 HIS 86 1_555 A FE 190 B FE FE 1_555 A HIS 111 A NE2 HIS 112 1_555 93.6 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 A PO4 192 D O1 PO4 1_555 92.2 A HIS 85 A NE2 HIS 86 1_555 A FE 190 B FE FE 1_555 A PO4 192 D O1 PO4 1_555 93.1 A HIS 111 A NE2 HIS 112 1_555 A FE 190 B FE FE 1_555 A PO4 192 D O1 PO4 1_555 172.9 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 A HOH 195 E O HOH 1_555 89.0 A HIS 85 A NE2 HIS 86 1_555 A FE 190 B FE FE 1_555 A HOH 195 E O HOH 1_555 175.6 A HIS 111 A NE2 HIS 112 1_555 A FE 190 B FE FE 1_555 A HOH 195 E O HOH 1_555 87.5 A PO4 192 D O1 PO4 1_555 A FE 190 B FE FE 1_555 A HOH 195 E O HOH 1_555 86.1 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 176.6 A HIS 85 A NE2 HIS 86 1_555 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 94.4 A HIS 111 A NE2 HIS 112 1_555 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 92.4 A PO4 192 D O1 PO4 1_555 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 84.5 A HOH 195 E O HOH 1_555 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 89.8 A MSE 1 SELENOMETHIONINE A MSE 2 MET A MSE 12 SELENOMETHIONINE A MSE 13 MET A MSE 27 SELENOMETHIONINE A MSE 28 MET A MSE 118 SELENOMETHIONINE A MSE 119 MET A MSE 157 SELENOMETHIONINE A MSE 158 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A CD GLU 17 A CD GLU 18 1 Y 1 A OE1 GLU 17 A OE1 GLU 18 1 Y 1 A OE2 GLU 17 A OE2 GLU 18 1 Y 1 A CD LYS 18 A CD LYS 19 1 Y 1 A CE LYS 18 A CE LYS 19 1 Y 1 A NZ LYS 18 A NZ LYS 19 1 Y 1 A CD LYS 21 A CD LYS 22 1 Y 1 A CE LYS 21 A CE LYS 22 1 Y 1 A NZ LYS 21 A NZ LYS 22 1 Y 1 A CG GLU 72 A CG GLU 73 1 Y 1 A CD GLU 72 A CD GLU 73 1 Y 1 A OE1 GLU 72 A OE1 GLU 73 1 Y 1 A OE2 GLU 72 A OE2 GLU 73 1 Y 1 A CD GLU 76 A CD GLU 77 1 Y 1 A OE1 GLU 76 A OE1 GLU 77 1 Y 1 A OE2 GLU 76 A OE2 GLU 77 1 Y 1 A CG ASN 80 A CG ASN 81 1 Y 1 A OD1 ASN 80 A OD1 ASN 81 1 Y 1 A ND2 ASN 80 A ND2 ASN 81 1 Y 1 A N LEU 84 A N LEU 85 1 Y 1 A CD GLU 102 A CD GLU 103 1 Y 1 A OE1 GLU 102 A OE1 GLU 103 1 Y 1 A OE2 GLU 102 A OE2 GLU 103 1 Y 1 A CE LYS 138 A CE LYS 139 1 Y 1 A NZ LYS 138 A NZ LYS 139 1 Y 1 A CG ASP 141 A CG ASP 142 1 Y 1 A OD1 ASP 141 A OD1 ASP 142 1 Y 1 A OD2 ASP 141 A OD2 ASP 142 1 Y 1 A CE LYS 145 A CE LYS 146 1 Y 1 A NZ LYS 145 A NZ LYS 146 1 Y 1 A NZ LYS 153 A NZ LYS 154 1 Y 1 A CZ ARG 187 A CZ ARG 188 1 Y 1 A NH1 ARG 187 A NH1 ARG 188 1 Y 1 A NH2 ARG 187 A NH2 ARG 188 1 Y 1 A GLY 189 A GLY 190 1 Y 1 A A OH OE2 TYR GLU 4 42 1.83 B 1 A A O O HOH HOH 201 261 1.89 1 A A OE2 O GLU HOH 64 201 2.03 A 1 A A O O HOH HOH 201 245 2.17 1 A A CG CD1 TYR TYR 82 82 -0.086 0.013 1.387 1.301 B B N 1 A A O3 O PO4 HOH 192 201 2.03 1_555 4_555 1 A ASN 80 -115.85 74.65 15.356 -0.750 0.000 -1.000 0.290 0.000 -0.700 0.964 0.945 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. IRON HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE BASED ON AN X-RAY FLUORESCENCE SCAN FOR METAL, ANOMALOUS DIFFERENCE FOURIERS, AND COORDINATION GEOMETRY. 5. PHOSPHATE IS MODELED BASED ON ELECTRON DENSITY AND PROPOSED FUNCTION. 0.217 0.180 0.182 1.500 25.872 1560 30979 5.000 99.560 1.381 0.053 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MAD 0.079 0.082 0.800 0.800 1.200 MAXIMUM LIKELIHOOD WITH PHASES MASK 1.500 25.872 198 1677 7 0 1472 0.017 0.022 1639 0.001 0.020 1103 1.563 1.965 2227 1.065 3.000 2694 3.972 5.000 214 33.877 24.156 77 11.479 15.000 295 13.723 15.000 11 0.078 0.200 241 0.007 0.020 1897 0.002 0.020 341 1.826 3.000 1012 0.527 3.000 417 2.848 5.000 1634 4.390 8.000 627 6.330 11.000 593 0.284 0.231 1.539 109 2152 2261 20 98.560 17.062 1.50 25.872 3CCG 30979 -3.00 0.038 1 11.530 98.300 0.362 1.50 1.55 2.1 10409 5469 1 96.70 0.271 1.55 1.62 2.7 12822 6692 1 97.80 0.199 1.62 1.69 3.6 10764 5622 1 98.30 0.158 1.69 1.78 4.5 11514 6010 1 98.70 0.116 1.78 1.89 6.4 11230 5863 1 98.80 0.074 1.89 2.04 9.4 11789 6153 1 99.00 0.047 2.04 2.24 14.4 11229 5835 1 99.00 0.036 2.24 2.56 18.4 11466 5953 1 99.00 0.028 2.56 3.23 23.6 11670 6030 1 98.60 0.022 3.23 25.872 30.1 11506 5914 1 97.10 refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program 5.4.0067 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing George Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html XSCALE package data extraction PDB sw-help@rcsb.rutgers.edu July 2, 2007 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 3.000 data collection MAR345 CCD data reduction XDS phasing SHELXD phasing autoSHARP Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution 1 N N 2 N N 2 N N 3 N N 4 N N A SER 3 A SER 4 HELX_P A ASN 38 A ASN 39 1 1 36 A ASP 40 A ASP 41 HELX_P A HIS 51 A HIS 52 1 2 12 A PRO 58 A PRO 59 HELX_P A GLU 69 A GLU 70 1 3 12 A GLY 74 A GLY 75 HELX_P A ARG 79 A ARG 80 1 4 6 A LEU 84 A LEU 85 HELX_P A VAL 96 A VAL 97 1 5 13 A ASP 101 A ASP 102 HELX_P A PHE 110 A PHE 111 1 6 10 A SER 119 A SER 120 HELX_P A GLU 132 A GLU 133 1 7 14 A GLY 139 A GLY 140 HELX_P A ASP 150 A ASP 151 1 8 12 A ASP 150 A ASP 151 HELX_P A GLY 170 A GLY 171 1 9 21 A HIS 174 A HIS 175 HELX_P A LYS 188 A LYS 189 1 10 15 covale 1.330 both A GLY 0 A C GLY 1 1_555 A MSE 1 A N MSE 2 1_555 covale 1.328 both A MSE 1 A C MSE 2 1_555 A TRP 2 A N TRP 3 1_555 covale 1.327 both A A LEU 11 A C LEU 12 1_555 A MSE 12 A N MSE 13 1_555 covale 1.327 both B A LEU 11 A C LEU 12 1_555 A MSE 12 A N MSE 13 1_555 covale 1.327 both A A A MSE 12 A C MSE 13 1_555 A ASN 13 A N ASN 14 1_555 covale 1.327 both B B A MSE 12 A C MSE 13 1_555 A ASN 13 A N ASN 14 1_555 covale 1.320 both A VAL 26 A C VAL 27 1_555 A MSE 27 A N MSE 28 1_555 covale 1.325 both A MSE 27 A C MSE 28 1_555 A ASP 28 A N ASP 29 1_555 covale 1.317 both A ASN 117 A C ASN 118 1_555 A MSE 118 A N MSE 119 1_555 covale 1.322 both A MSE 118 A C MSE 119 1_555 A SER 119 A N SER 120 1_555 covale 1.328 both A A LEU 156 A C LEU 157 1_555 A MSE 157 A N MSE 158 1_555 covale 1.340 both B A LEU 156 A C LEU 157 1_555 A MSE 157 A N MSE 158 1_555 covale 1.333 both A A MSE 157 A C MSE 158 1_555 A SER 158 A N SER 159 1_555 covale 1.329 both B A MSE 157 A C MSE 158 1_555 A SER 158 A N SER 159 1_555 metalc 2.272 A HIS 22 A NE2 HIS 23 1_555 A FE 191 C FE FE 1_555 metalc 2.524 A HIS 51 A NE2 HIS 52 1_555 A FE 191 C FE FE 1_555 metalc 2.173 A ASP 52 A OD1 ASP 53 1_555 A FE 190 B FE FE 1_555 metalc 2.482 A ASP 52 A OD2 ASP 53 1_555 A FE 191 C FE FE 1_555 metalc 2.195 A HIS 85 A NE2 HIS 86 1_555 A FE 190 B FE FE 1_555 metalc 2.205 A HIS 111 A NE2 HIS 112 1_555 A FE 190 B FE FE 1_555 metalc 2.162 A ASP 129 A OD1 ASP 130 1_555 A FE 191 C FE FE 1_555 metalc 2.176 A FE 190 B FE FE 1_555 A PO4 192 D O1 PO4 1_555 metalc 2.046 A FE 190 B FE FE 1_555 A HOH 195 E O HOH 1_555 metalc 2.096 A FE 190 B FE FE 1_555 A HOH 199 E O HOH 1_555 metalc 2.358 A FE 191 C FE FE 1_555 A PO4 192 D O4 PO4 1_555 metalc 1.711 A FE 191 C FE FE 1_555 A HOH 195 E O HOH 1_555 HYDROLASE NP_347894.1, predicted HD superfamily hydrolase involved in NAD metabolism, HD domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, HYDROLASE Q97JL1_CLOAB UNP 1 1 Q97JL1 MWSYDKITDYLMNNLGEKRYKHSLGVMDTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICTNEGYELGDEDIRN SYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPNMSLLEKIIYIADYIEPGREFKGVDELRKAADEDLNKALLMSFD NTIKFVIDKGGFLHHNTIEARNYLISRKG 1 189 3CCG 1 189 Q97JL1 A 1 2 190 1 expression tag GLY 0 3CCG A Q97JL1 UNP 1 BINDING SITE FOR RESIDUE FE A 190 A FE 190 Software 5 BINDING SITE FOR RESIDUE FE A 191 A FE 191 Software 5 BINDING SITE FOR RESIDUE PO4 A 192 A PO4 192 Software 15 A ASP 52 A ASP 53 5 1_555 A HIS 85 A HIS 86 5 1_555 A HIS 111 A HIS 112 5 1_555 A HOH 195 E HOH 5 1_555 A HOH 199 E HOH 5 1_555 A HIS 22 A HIS 23 5 1_555 A HIS 51 A HIS 52 5 1_555 A ASP 52 A ASP 53 5 1_555 A ASP 129 A ASP 130 5 1_555 A HOH 195 E HOH 5 1_555 A ARG 19 A ARG 20 15 1_555 A HIS 22 A HIS 23 15 1_555 A ASP 52 A ASP 53 15 1_555 A LYS 55 A LYS 56 15 1_555 A GLU 60 A GLU 61 15 4_555 A GLU 64 A GLU 65 15 4_555 A HIS 85 A HIS 86 15 1_555 A ASP 129 A ASP 130 15 1_555 A ARG 135 A ARG 136 15 1_555 A HOH 195 E HOH 15 1_555 A HOH 199 E HOH 15 1_555 A HOH 201 E HOH 15 4_555 A HOH 246 E HOH 15 4_555 A HOH 250 E HOH 15 1_555 A HOH 261 E HOH 15 4_555 5 C 1 2 1