0.015113 0.000000 0.006499 0.000000 0.020653 0.000000 0.000000 0.000000 0.024401 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 113.27 90.00 66.170 48.420 44.610 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 Ca 2 40.078 CALCIUM ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL 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 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 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 putative calcium-regulated periplasmic protein of unknown function (NP_809836.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.40 A resolution 10.2210/pdb3db7/pdb pdb_00003db7 100 1 Flat mirror (vertical focusing) CCD 2008-03-04 MARMOSAIC 325 mm CCD Single crystal Si(111) bent monochromator (horizontal focusing) MAD M x-ray 1 0.91837 1.0 0.97947 1.0 0.97891 1.0 BL11-1 SSRL 0.91837,0.97947,0.97891 SYNCHROTRON SSRL BEAMLINE BL11-1 14790.481 putative calcium-regulated periplasmic protein 1 man polymer 40.078 CALCIUM ION 3 syn non-polymer 62.068 1,2-ETHANEDIOL 2 syn non-polymer 18.015 water 194 nat water no yes GADDDKPIQVTQ(MSE)PQLAQQFIKQHFSDSKVALAK(MSE)ESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSV PVAIIPAAIQKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN GADDDKPIQVTQMPQLAQQFIKQHFSDSKVALAKMESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSVPVAIIPAA IQKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN A 389981 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 sample NP_809836.1, BT_0923 818 Bacteroides thetaiotaomicron 562 Escherichia coli HK100 Plasmid SpeedET 1 2.22 44.58 VAPOR DIFFUSION, SITTING DROP 7.3 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7., NANODROP, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative pdbx_struct_assembly_auth_evidence software pdbx_struct_special_symmetry software struct_conn database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Advisory Version format compliance Author supporting evidence Refinement description Data collection Derived calculations Refinement description Database references Derived calculations 1 0 2008-10-28 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_alt_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.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_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 2008-05-30 REL REL CA CALCIUM ION EDO 1,2-ETHANEDIOL HOH water THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 20-145 OF THE FULL LENGTH PROTEIN. CA 1 2 CA CA 1 A CA 2 2 CA CA 2 A CA 3 2 CA CA 3 A EDO 4 3 EDO EDO 4 A EDO 5 3 EDO EDO 5 A HOH 6 4 HOH HOH 146 A HOH 7 4 HOH HOH 147 A HOH 8 4 HOH HOH 148 A HOH 9 4 HOH HOH 149 A HOH 10 4 HOH HOH 150 A HOH 11 4 HOH HOH 151 A HOH 12 4 HOH HOH 152 A HOH 13 4 HOH HOH 153 A HOH 14 4 HOH HOH 154 A HOH 15 4 HOH HOH 155 A HOH 16 4 HOH HOH 156 A HOH 17 4 HOH HOH 157 A HOH 18 4 HOH HOH 158 A HOH 19 4 HOH HOH 159 A HOH 20 4 HOH HOH 160 A HOH 21 4 HOH HOH 161 A HOH 22 4 HOH HOH 162 A HOH 23 4 HOH HOH 163 A HOH 24 4 HOH HOH 164 A HOH 25 4 HOH HOH 165 A HOH 26 4 HOH HOH 166 A HOH 27 4 HOH HOH 167 A HOH 28 4 HOH HOH 168 A HOH 29 4 HOH HOH 169 A HOH 30 4 HOH HOH 170 A HOH 31 4 HOH HOH 171 A HOH 32 4 HOH HOH 172 A HOH 33 4 HOH HOH 173 A HOH 34 4 HOH HOH 174 A HOH 35 4 HOH HOH 175 A HOH 36 4 HOH HOH 176 A HOH 37 4 HOH HOH 177 A HOH 38 4 HOH HOH 178 A HOH 39 4 HOH HOH 179 A HOH 40 4 HOH HOH 180 A HOH 41 4 HOH HOH 181 A HOH 42 4 HOH HOH 182 A HOH 43 4 HOH HOH 183 A HOH 44 4 HOH HOH 184 A HOH 45 4 HOH HOH 185 A HOH 46 4 HOH HOH 186 A HOH 47 4 HOH HOH 187 A HOH 48 4 HOH HOH 188 A HOH 49 4 HOH HOH 189 A HOH 50 4 HOH HOH 190 A HOH 51 4 HOH HOH 191 A HOH 52 4 HOH HOH 192 A HOH 53 4 HOH HOH 193 A HOH 54 4 HOH HOH 194 A HOH 55 4 HOH HOH 195 A HOH 56 4 HOH HOH 196 A HOH 57 4 HOH HOH 197 A HOH 58 4 HOH HOH 198 A HOH 59 4 HOH HOH 199 A HOH 60 4 HOH HOH 200 A HOH 61 4 HOH HOH 201 A HOH 62 4 HOH HOH 202 A HOH 63 4 HOH HOH 203 A HOH 64 4 HOH HOH 204 A HOH 65 4 HOH HOH 205 A HOH 66 4 HOH HOH 206 A HOH 67 4 HOH HOH 207 A HOH 68 4 HOH HOH 208 A HOH 69 4 HOH HOH 209 A HOH 70 4 HOH HOH 210 A HOH 71 4 HOH HOH 211 A HOH 72 4 HOH HOH 212 A HOH 73 4 HOH HOH 213 A HOH 74 4 HOH HOH 214 A HOH 75 4 HOH HOH 215 A HOH 76 4 HOH HOH 216 A HOH 77 4 HOH HOH 217 A HOH 78 4 HOH HOH 218 A HOH 79 4 HOH HOH 219 A HOH 80 4 HOH HOH 220 A HOH 81 4 HOH HOH 221 A HOH 82 4 HOH HOH 222 A HOH 83 4 HOH HOH 223 A HOH 84 4 HOH HOH 224 A HOH 85 4 HOH HOH 225 A HOH 86 4 HOH HOH 226 A HOH 87 4 HOH HOH 227 A HOH 88 4 HOH HOH 228 A HOH 89 4 HOH HOH 229 A HOH 90 4 HOH HOH 230 A HOH 91 4 HOH HOH 231 A HOH 92 4 HOH HOH 232 A HOH 93 4 HOH HOH 233 A HOH 94 4 HOH HOH 234 A HOH 95 4 HOH HOH 235 A HOH 96 4 HOH HOH 236 A HOH 97 4 HOH HOH 237 A HOH 98 4 HOH HOH 238 A HOH 99 4 HOH HOH 239 A HOH 100 4 HOH HOH 240 A HOH 101 4 HOH HOH 241 A HOH 102 4 HOH HOH 242 A HOH 103 4 HOH HOH 243 A HOH 104 4 HOH HOH 244 A HOH 105 4 HOH HOH 245 A HOH 106 4 HOH HOH 246 A HOH 107 4 HOH HOH 247 A HOH 108 4 HOH HOH 248 A HOH 109 4 HOH HOH 249 A HOH 110 4 HOH HOH 250 A HOH 111 4 HOH HOH 251 A HOH 112 4 HOH HOH 252 A HOH 113 4 HOH HOH 253 A HOH 114 4 HOH HOH 254 A HOH 115 4 HOH HOH 255 A HOH 116 4 HOH HOH 256 A HOH 117 4 HOH HOH 257 A HOH 118 4 HOH HOH 258 A HOH 119 4 HOH HOH 259 A HOH 120 4 HOH HOH 260 A HOH 121 4 HOH HOH 261 A HOH 122 4 HOH HOH 262 A HOH 123 4 HOH HOH 263 A HOH 124 4 HOH HOH 264 A HOH 125 4 HOH HOH 265 A HOH 126 4 HOH HOH 266 A HOH 127 4 HOH HOH 267 A HOH 128 4 HOH HOH 268 A HOH 129 4 HOH HOH 269 A HOH 130 4 HOH HOH 270 A HOH 131 4 HOH HOH 271 A HOH 132 4 HOH HOH 272 A HOH 133 4 HOH HOH 273 A HOH 134 4 HOH HOH 274 A HOH 135 4 HOH HOH 275 A HOH 136 4 HOH HOH 276 A HOH 137 4 HOH HOH 277 A HOH 138 4 HOH HOH 278 A HOH 139 4 HOH HOH 279 A HOH 140 4 HOH HOH 280 A HOH 141 4 HOH HOH 281 A HOH 142 4 HOH HOH 282 A HOH 143 4 HOH HOH 283 A HOH 144 4 HOH HOH 284 A HOH 145 4 HOH HOH 285 A HOH 146 4 HOH HOH 286 A HOH 147 4 HOH HOH 287 A HOH 148 4 HOH HOH 288 A HOH 149 4 HOH HOH 289 A HOH 150 4 HOH HOH 290 A HOH 151 4 HOH HOH 291 A HOH 152 4 HOH HOH 292 A HOH 153 4 HOH HOH 293 A HOH 154 4 HOH HOH 294 A HOH 155 4 HOH HOH 295 A HOH 156 4 HOH HOH 296 A HOH 157 4 HOH HOH 297 A HOH 158 4 HOH HOH 298 A HOH 159 4 HOH HOH 299 A HOH 160 4 HOH HOH 300 A HOH 161 4 HOH HOH 301 A HOH 162 4 HOH HOH 302 A HOH 163 4 HOH HOH 303 A HOH 164 4 HOH HOH 304 A HOH 165 4 HOH HOH 305 A HOH 166 4 HOH HOH 306 A HOH 167 4 HOH HOH 307 A HOH 168 4 HOH HOH 308 A HOH 169 4 HOH HOH 309 A HOH 170 4 HOH HOH 310 A HOH 171 4 HOH HOH 311 A HOH 172 4 HOH HOH 312 A HOH 173 4 HOH HOH 313 A HOH 174 4 HOH HOH 314 A HOH 175 4 HOH HOH 315 A HOH 176 4 HOH HOH 316 A HOH 177 4 HOH HOH 317 A HOH 178 4 HOH HOH 318 A HOH 179 4 HOH HOH 319 A HOH 180 4 HOH HOH 320 A HOH 181 4 HOH HOH 321 A HOH 182 4 HOH HOH 322 A HOH 183 4 HOH HOH 323 A HOH 184 4 HOH HOH 324 A HOH 185 4 HOH HOH 325 A HOH 186 4 HOH HOH 326 A HOH 187 4 HOH HOH 327 A HOH 188 4 HOH HOH 328 A HOH 189 4 HOH HOH 329 A HOH 190 4 HOH HOH 330 A HOH 191 4 HOH HOH 331 A HOH 192 4 HOH HOH 332 A HOH 193 4 HOH HOH 333 A HOH 194 4 HOH HOH 334 A HOH 195 4 HOH HOH 335 A HOH 196 4 HOH HOH 336 A HOH 197 4 HOH HOH 337 A HOH 198 4 HOH HOH 338 A HOH 199 4 HOH HOH 339 A GLY 0 n 1 GLY 0 A ALA 20 n 2 ALA 20 A ASP 21 n 3 ASP 21 A ASP 22 n 4 ASP 22 A ASP 23 n 5 ASP 23 A LYS 24 n 6 LYS 24 A PRO 25 n 7 PRO 25 A ILE 26 n 8 ILE 26 A GLN 27 n 9 GLN 27 A VAL 28 n 10 VAL 28 A THR 29 n 11 THR 29 A GLN 30 n 12 GLN 30 A MSE 31 n 13 MSE 31 A PRO 32 n 14 PRO 32 A GLN 33 n 15 GLN 33 A LEU 34 n 16 LEU 34 A ALA 35 n 17 ALA 35 A GLN 36 n 18 GLN 36 A GLN 37 n 19 GLN 37 A PHE 38 n 20 PHE 38 A ILE 39 n 21 ILE 39 A LYS 40 n 22 LYS 40 A GLN 41 n 23 GLN 41 A HIS 42 n 24 HIS 42 A PHE 43 n 25 PHE 43 A SER 44 n 26 SER 44 A ASP 45 n 27 ASP 45 A SER 46 n 28 SER 46 A LYS 47 n 29 LYS 47 A VAL 48 n 30 VAL 48 A ALA 49 n 31 ALA 49 A LEU 50 n 32 LEU 50 A ALA 51 n 33 ALA 51 A LYS 52 n 34 LYS 52 A MSE 53 n 35 MSE 53 A GLU 54 n 36 GLU 54 A SER 55 n 37 SER 55 A ASP 56 n 38 ASP 56 A PHE 57 n 39 PHE 57 A LEU 58 n 40 LEU 58 A TYR 59 n 41 TYR 59 A LYS 60 n 42 LYS 60 A SER 61 n 43 SER 61 A TYR 62 n 44 TYR 62 A GLU 63 n 45 GLU 63 A VAL 64 n 46 VAL 64 A ILE 65 n 47 ILE 65 A PHE 66 n 48 PHE 66 A THR 67 n 49 THR 67 A ASN 68 n 50 ASN 68 A GLY 69 n 51 GLY 69 A ASN 70 n 52 ASN 70 A LYS 71 n 53 LYS 71 A VAL 72 n 54 VAL 72 A GLU 73 n 55 GLU 73 A PHE 74 n 56 PHE 74 A ASP 75 n 57 ASP 75 A LYS 76 n 58 LYS 76 A LYS 77 n 59 LYS 77 A GLY 78 n 60 GLY 78 A ASN 79 n 61 ASN 79 A TRP 80 n 62 TRP 80 A GLU 81 n 63 GLU 81 A GLU 82 n 64 GLU 82 A VAL 83 n 65 VAL 83 A ASP 84 n 66 ASP 84 A CYS 85 n 67 CYS 85 A LYS 86 n 68 LYS 86 A HIS 87 n 69 HIS 87 A THR 88 n 70 THR 88 A SER 89 n 71 SER 89 A VAL 90 n 72 VAL 90 A PRO 91 n 73 PRO 91 A VAL 92 n 74 VAL 92 A ALA 93 n 75 ALA 93 A ILE 94 n 76 ILE 94 A ILE 95 n 77 ILE 95 A PRO 96 n 78 PRO 96 A ALA 97 n 79 ALA 97 A ALA 98 n 80 ALA 98 A ILE 99 n 81 ILE 99 A GLN 100 n 82 GLN 100 A LYS 101 n 83 LYS 101 A TYR 102 n 84 TYR 102 A VAL 103 n 85 VAL 103 A THR 104 n 86 THR 104 A THR 105 n 87 THR 105 A ASN 106 n 88 ASN 106 A TYR 107 n 89 TYR 107 A PRO 108 n 90 PRO 108 A ASP 109 n 91 ASP 109 A ALA 110 n 92 ALA 110 A LYS 111 n 93 LYS 111 A VAL 112 n 94 VAL 112 A LEU 113 n 95 LEU 113 A LYS 114 n 96 LYS 114 A ILE 115 n 97 ILE 115 A GLU 116 n 98 GLU 116 A ARG 117 n 99 ARG 117 A ASP 118 n 100 ASP 118 A LYS 119 n 101 LYS 119 A LYS 120 n 102 LYS 120 A ASP 121 n 103 ASP 121 A TYR 122 n 104 TYR 122 A GLU 123 n 105 GLU 123 A VAL 124 n 106 VAL 124 A LYS 125 n 107 LYS 125 A LEU 126 n 108 LEU 126 A SER 127 n 109 SER 127 A ASN 128 n 110 ASN 128 A ARG 129 n 111 ARG 129 A THR 130 n 112 THR 130 A GLU 131 n 113 GLU 131 A LEU 132 n 114 LEU 132 A LYS 133 n 115 LYS 133 A PHE 134 n 116 PHE 134 A ASP 135 n 117 ASP 135 A LEU 136 n 118 LEU 136 A LYS 137 n 119 LYS 137 A PHE 138 n 120 PHE 138 A ASN 139 n 121 ASN 139 A LEU 140 n 122 LEU 140 A ILE 141 n 123 ILE 141 A ASP 142 n 124 ASP 142 A ILE 143 n 125 ILE 143 A ASP 144 n 126 ASP 144 A ASN 145 n 127 ASN 145 A 1.2557 0.0120 0.1457 0.3124 0.0582 0.4953 0.0117 -0.0362 -0.0013 0.0069 -0.0177 -0.0076 0.0011 0.0328 0.0060 -0.0143 -0.0043 -0.0026 -0.0308 0.0052 -0.0250 refined 5.4168 48.0223 9.8704 X-RAY DIFFRACTION A 0 A 1 A 145 A 127 X-RAY DIFFRACTION 1 author_and_software_defined_assembly PISA 2 dimeric author_defined_assembly 1 monomeric gel filtration light scattering gel filtration light scattering 3320 -77 12730 A GLU 54 A OE1 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 54 A OE2 GLU 36 1_555 50.3 A GLU 54 A OE1 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 63 A OE2 GLU 45 1_555 76.4 A GLU 54 A OE2 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 63 A OE2 GLU 45 1_555 126.6 A GLU 54 A OE1 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE1 GLU 55 1_555 127.7 A GLU 54 A OE2 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE1 GLU 55 1_555 129.1 A GLU 63 A OE2 GLU 45 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE1 GLU 55 1_555 79.3 A GLU 54 A OE1 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE2 GLU 55 1_555 81.6 A GLU 54 A OE2 GLU 36 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE2 GLU 55 1_555 81.7 A GLU 63 A OE2 GLU 45 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE2 GLU 55 1_555 89.8 A GLU 73 A OE1 GLU 55 1_555 A CA 1 B CA CA 1_555 A GLU 73 A OE2 GLU 55 1_555 52.6 A GLU 73 A OE1 GLU 55 1_555 A CA 2 C CA CA 1_555 A GLU 82 A OE1 GLU 64 1_555 90.5 A GLU 73 A OE1 GLU 55 1_555 A CA 2 C CA CA 1_555 A HOH 146 G O HOH 1_555 80.1 A GLU 82 A OE1 GLU 64 1_555 A CA 2 C CA CA 1_555 A HOH 146 G O HOH 1_555 105.2 A GLU 73 A OE1 GLU 55 1_555 A CA 2 C CA CA 1_555 A HOH 158 G O HOH 1_555 153.2 A GLU 82 A OE1 GLU 64 1_555 A CA 2 C CA CA 1_555 A HOH 158 G O HOH 1_555 85.6 A HOH 146 G O HOH 1_555 A CA 2 C CA CA 1_555 A HOH 158 G O HOH 1_555 75.4 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A EDO 5 B F O2 EDO 1_555 19.1 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A EDO 5 A F O1 EDO 1_555 60.8 A EDO 5 B F O2 EDO 1_555 A CA 3 D CA CA 1_555 A EDO 5 A F O1 EDO 1_555 73.5 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A GLU 123 A A OE2 GLU 105 1_555 68.0 A EDO 5 B F O2 EDO 1_555 A CA 3 D CA CA 1_555 A GLU 123 A A OE2 GLU 105 1_555 80.2 A EDO 5 A F O1 EDO 1_555 A CA 3 D CA CA 1_555 A GLU 123 A A OE2 GLU 105 1_555 91.2 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 336 B G O HOH 1_555 100.4 A EDO 5 B F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 336 B G O HOH 1_555 104.8 A EDO 5 A F O1 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 336 B G O HOH 1_555 45.3 A GLU 123 A A OE2 GLU 105 1_555 A CA 3 D CA CA 1_555 A HOH 336 B G O HOH 1_555 128.5 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 A G O HOH 1_555 131.1 A EDO 5 B F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 A G O HOH 1_555 146.9 A EDO 5 A F O1 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 A G O HOH 1_555 73.5 A GLU 123 A A OE2 GLU 105 1_555 A CA 3 D CA CA 1_555 A HOH 337 A G O HOH 1_555 98.0 A HOH 336 B G O HOH 1_555 A CA 3 D CA CA 1_555 A HOH 337 A G O HOH 1_555 50.9 A EDO 5 A F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 95.4 A EDO 5 B F O2 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 114.3 A EDO 5 A F O1 EDO 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 67.8 A GLU 123 A A OE2 GLU 105 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 50.8 A HOH 336 B G O HOH 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 82.9 A HOH 337 A G O HOH 1_555 A CA 3 D CA CA 1_555 A HOH 337 B G O HOH 1_555 48.9 A MSE 31 SELENOMETHIONINE A MSE 13 MET A MSE 53 SELENOMETHIONINE A MSE 35 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 A N LYS 24 A N LYS 6 A O MSE 53 A O MSE 35 A N LEU 50 A N LEU 32 A O ILE 65 A O ILE 47 A N TYR 62 A N TYR 44 A O PHE 74 A O PHE 56 A N LYS 71 A N LYS 53 A O ASP 84 A O ASP 66 A N VAL 83 A N VAL 65 A O ILE 115 A O ILE 97 A N LEU 113 A N LEU 95 A O LYS 125 A O LYS 107 A N TYR 122 A N TYR 104 A O PHE 134 A O PHE 116 A N LYS 133 A N LYS 115 A O ILE 141 A O ILE 123 1 A CA 3 D CA 1 A HOH 334 G HOH 1 A CD LYS 24 A CD LYS 6 1 Y 1 A CE LYS 24 A CE LYS 6 1 Y 1 A NZ LYS 24 A NZ LYS 6 1 Y 1 A CG ASP 45 A CG ASP 27 1 Y 1 A OD1 ASP 45 A OD1 ASP 27 1 Y 1 A OD2 ASP 45 A OD2 ASP 27 1 Y 1 A CD LYS 47 A CD LYS 29 1 Y 1 A CE LYS 47 A CE LYS 29 1 Y 1 A NZ LYS 47 A NZ LYS 29 1 Y 1 A CD LYS 60 A CD LYS 42 1 Y 1 A CE LYS 60 A CE LYS 42 1 Y 1 A NZ LYS 60 A NZ LYS 42 1 Y 1 A NZ LYS 76 A NZ LYS 58 1 Y 1 A CE LYS 77 A CE LYS 59 1 Y 1 A NZ LYS 77 A NZ LYS 59 1 Y 1 A CE LYS 111 A CE LYS 93 1 Y 1 A NZ LYS 111 A NZ LYS 93 1 Y 1 A CE LYS 120 A CE LYS 102 1 Y 1 A NZ LYS 120 A NZ LYS 102 1 Y 1 A CZ ARG 129 A CZ ARG 111 1 Y 1 A NH1 ARG 129 A NH1 ARG 111 1 Y 1 A NH2 ARG 129 A NH2 ARG 111 1 Y 1 A THR 88 -136.51 -108.94 1 A ARG 129 84.18 -6.44 10.575 -0.28 0.00 0.15 0.24 0.00 0.17 0.969 0.955 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.ETHYLENE GLYCOL AND CALCIUM IONS FROM THE CRYSTALLIZATION COND ARE MODELED IN THIS STRUCTURE. 0.19824 0.16034 0.16228 1.40 24.922 1172 23150 5.1 90.53 2.134 0.045 RANDOM LIKELY RESIDUAL 1 THROUGHOUT MAD 0.066 0.071 0.80 0.80 1.20 MAXIMUM LIKELIHOOD WITH PHASES MASK 1.40 24.922 194 1218 11 0 1013 0.018 0.022 1131 0.001 0.020 771 1.559 1.965 1539 1.096 3.000 1902 6.603 5.000 146 35.122 26.731 52 11.482 15.000 209 11.545 15.000 1 0.102 0.200 168 0.008 0.021 1293 0.003 0.020 207 1.626 3.000 697 0.510 3.000 271 2.615 5.000 1150 3.931 8.000 434 5.984 11.000 389 0.299 0.258 1.437 76 1644 20 91.98 1.40 24.922 3DB7 23150 -3.00 0.042 1 10.440 2.149 90.5 0.536 1.40 1.45 1.5 1 0.369 1.45 1.51 2.0 1 0.281 1.51 1.58 2.7 1 0.211 1.58 1.66 3.6 1 0.155 1.66 1.76 4.8 1 0.093 1.76 1.90 7.4 1 0.046 1.90 2.09 12.4 1 0.036 2.09 2.39 16.0 1 0.027 2.39 3.01 20.8 1 0.017 3.01 24.92 32.1 1 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 September 10, 2007 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 3.004 data reduction XDS phasing SHELXD phasing autoSHARP Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution 1 N N 2 N N 2 N N 2 N N 3 N N 3 N N 4 N N AUTHORS STATE THAT ONLY WHEN CA1 AND CA2 ARE INCLUDED IN THE CALCULATION, DOES PISA (v1.14) PREDICT THAT A STABLE DIMER COULD BE A PROBABLE QUATERNARY STRUCTURE. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING (SEC+SLS) WITHOUT ADDED CALCIUM SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. WHEN A SAMPLE WAS RUN WITH 0.2 M CALCIUM CHLORIDE IN THE MOBILE PHASE (SIMILAR CONCENTRATION TO THAT IN THE CRYSTALLIZATION REAGENT), THE SEC+SLS RESULTS SHOWED PRIMARILY DIMER. A GLY 0 A GLY 1 HELX_P A ASP 23 A ASP 5 5 1 5 A GLN 27 A GLN 9 HELX_P A MSE 31 A MSE 13 5 2 5 A PRO 32 A PRO 14 HELX_P A PHE 43 A PHE 25 1 3 12 A PRO 91 A PRO 73 HELX_P A ILE 95 A ILE 77 5 4 5 A PRO 96 A PRO 78 HELX_P A TYR 107 A TYR 89 1 5 12 covale 1.331 both A A GLN 30 A C GLN 12 1_555 A MSE 31 A N MSE 13 1_555 covale 1.313 both B A GLN 30 A C GLN 12 1_555 A MSE 31 A N MSE 13 1_555 covale 1.348 both A A MSE 31 A C MSE 13 1_555 A PRO 32 A N PRO 14 1_555 covale 1.336 both B A MSE 31 A C MSE 13 1_555 A PRO 32 A N PRO 14 1_555 covale 1.322 both A LYS 52 A C LYS 34 1_555 A MSE 53 A N MSE 35 1_555 covale 1.332 both A MSE 53 A C MSE 35 1_555 A GLU 54 A N GLU 36 1_555 metalc 2.463 A CA 1 B CA CA 1_555 A GLU 54 A OE1 GLU 36 1_555 metalc 2.691 A CA 1 B CA CA 1_555 A GLU 54 A OE2 GLU 36 1_555 metalc 2.344 A CA 1 B CA CA 1_555 A GLU 63 A OE2 GLU 45 1_555 metalc 2.508 A CA 1 B CA CA 1_555 A GLU 73 A OE1 GLU 55 1_555 metalc 2.506 A CA 1 B CA CA 1_555 A GLU 73 A OE2 GLU 55 1_555 metalc 2.314 A CA 2 C CA CA 1_555 A GLU 73 A OE1 GLU 55 1_555 metalc 2.279 A CA 2 C CA CA 1_555 A GLU 82 A OE1 GLU 64 1_555 metalc 2.416 A CA 2 C CA CA 1_555 A HOH 146 G O HOH 1_555 metalc 2.466 A CA 2 C CA CA 1_555 A HOH 158 G O HOH 1_555 metalc 2.497 A A CA 3 D CA CA 1_555 A EDO 5 F O2 EDO 1_555 metalc 2.519 B A CA 3 D CA CA 1_555 A EDO 5 F O2 EDO 1_555 metalc 2.460 A A CA 3 D CA CA 1_555 A EDO 5 F O1 EDO 1_555 metalc 2.292 A A CA 3 D CA CA 1_555 A GLU 123 A OE2 GLU 105 1_555 metalc 2.181 B A CA 3 D CA CA 1_555 A HOH 336 G O HOH 1_555 metalc 2.386 A A CA 3 D CA CA 1_555 A HOH 337 G O HOH 1_555 metalc 2.199 B A CA 3 D CA CA 1_555 A HOH 337 G O HOH 1_555 Ca-BINDING PROTEIN Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, ca-binding protein Q8A994_BACTN UNP 1 20 Q8A994 ADDDKPIQVTQMPQLAQQFIKQHFSDSKVALAKMESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSVPVAIIPAAI QKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN 20 145 3DB7 20 145 Q8A994 A 1 2 127 1 expression tag GLY 0 3DB7 A Q8A994 UNP 1 9 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A LYS 24 A LYS 6 A ILE 26 A ILE 8 A VAL 48 A VAL 30 A ASP 56 A ASP 38 A TYR 59 A TYR 41 A PHE 66 A PHE 48 A LYS 71 A LYS 53 A PHE 74 A PHE 56 A TRP 80 A TRP 62 A ASP 84 A ASP 66 A VAL 112 A VAL 94 A ARG 117 A ARG 99 A ASP 121 A ASP 103 A LEU 126 A LEU 108 A GLU 131 A GLU 113 A ASP 135 A ASP 117 A LEU 140 A LEU 122 A ASP 144 A ASP 126 BINDING SITE FOR RESIDUE CA A 1 A CA 1 Software 6 BINDING SITE FOR RESIDUE CA A 2 A CA 2 Software 6 BINDING SITE FOR RESIDUE CA A 3 A CA 3 Software 3 BINDING SITE FOR RESIDUE EDO A 4 A EDO 4 Software 4 BINDING SITE FOR RESIDUE EDO A 5 A EDO 5 Software 8 A GLU 54 A GLU 36 6 1_555 A GLU 63 A GLU 45 6 1_555 A GLU 73 A GLU 55 6 1_555 A ASP 142 A ASP 124 6 2_555 A ILE 143 A ILE 125 6 2_555 A ASP 144 A ASP 126 6 2_555 A GLU 73 A GLU 55 6 1_555 A GLU 82 A GLU 64 6 1_555 A ASP 142 A ASP 124 6 2_555 A ASP 144 A ASP 126 6 2_555 A HOH 146 G HOH 6 1_555 A HOH 158 G HOH 6 1_555 A GLU 123 A GLU 105 3 2_555 A HOH 336 G HOH 3 2_555 A HOH 337 G HOH 3 2_555 A ILE 26 A ILE 8 4 1_555 A GLN 27 A GLN 9 4 1_555 A ALA 51 A ALA 33 4 1_555 A LYS 137 A LYS 119 4 3_545 A GLU 116 A GLU 98 8 1_555 A ARG 117 A ARG 99 8 1_555 A ASP 121 A ASP 103 8 1_555 A GLU 123 A GLU 105 8 2_555 A LYS 133 A LYS 115 8 2_555 A HOH 255 G HOH 8 1_555 A HOH 336 G HOH 8 1_555 A HOH 337 G HOH 8 2_555 5 C 1 2 1