0.012138 0.000000 0.000000 0.000000 0.012138 0.000000 0.000000 0.000000 0.013451 0.00000 0.00000 0.00000 Chang, C. Hatzos, C. Abdullah, J. Joachimiak, A. Midwest Center for Structural Genomics (MCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 82.383 82.383 74.342 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 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 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 YfrE protein from Vibrio parahaemolyticus. 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 2007-10-04 ADSC QUANTUM 315 Double crystal SINGLE WAVELENGTH M x-ray 1 0.97857 1.0 19-ID APS 0.97857 SYNCHROTRON APS BEAMLINE 19-ID 10568.690 Putative YfrE protein Residues 146-235 2 man polymer 62.068 1,2-ETHANEDIOL 4 syn non-polymer 18.015 water 103 nat water no yes SNAVTATQLAAKATTLYYLHKQA(MSE)TDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPN LDRVTIIESINKAKKL(MSE) SNAVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPNLDRV TIIESINKAKKLM A,B APC91400.1 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 Vibrio Vibrio parahaemolyticus RIMD 2210633 / Serotype O3:K6 Escherichia sample VP1931 223926 Vibrio parahaemolyticus RIMD 2210633 562 Escherichia coli BL21(DE3) derivative Plasmid pMCSG7 1 2.98 58.78 VAPOR DIFFUSION, SITTING DROP 9.0 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K 289 Midwest Center for Structural Genomics MCSG PSI, Protein Structure Initiative repository Initial release Advisory Version format compliance 1 0 2007-12-04 1 1 2011-07-13 Y RCSB Y RCSB 2007-11-16 REL REL EDO 1,2-ETHANEDIOL HOH water EDO 301 2 EDO EDO 301 A EDO 302 2 EDO EDO 302 A EDO 304 2 EDO EDO 304 A EDO 303 2 EDO EDO 303 B HOH 3 3 HOH HOH 3 A HOH 5 3 HOH HOH 5 A HOH 7 3 HOH HOH 7 A HOH 9 3 HOH HOH 9 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 25 3 HOH HOH 25 A HOH 28 3 HOH HOH 28 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 33 3 HOH HOH 33 A HOH 35 3 HOH HOH 35 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 44 3 HOH HOH 44 A HOH 46 3 HOH HOH 46 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A HOH 50 3 HOH HOH 50 A HOH 56 3 HOH HOH 56 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 66 3 HOH HOH 66 A HOH 67 3 HOH HOH 67 A HOH 70 3 HOH HOH 70 A HOH 71 3 HOH HOH 71 A HOH 73 3 HOH HOH 73 A HOH 75 3 HOH HOH 75 A HOH 77 3 HOH HOH 77 A HOH 79 3 HOH HOH 79 A HOH 80 3 HOH HOH 80 A HOH 81 3 HOH HOH 81 A HOH 82 3 HOH HOH 82 A HOH 86 3 HOH HOH 86 A HOH 87 3 HOH HOH 87 A HOH 90 3 HOH HOH 90 A HOH 91 3 HOH HOH 91 A HOH 92 3 HOH HOH 92 A HOH 93 3 HOH HOH 93 A HOH 96 3 HOH HOH 96 A HOH 97 3 HOH HOH 97 A HOH 98 3 HOH HOH 98 A HOH 99 3 HOH HOH 99 A HOH 101 3 HOH HOH 101 A HOH 103 3 HOH HOH 103 A HOH 1 3 HOH HOH 1 B HOH 2 3 HOH HOH 2 B HOH 4 3 HOH HOH 4 B HOH 6 3 HOH HOH 6 B HOH 8 3 HOH HOH 8 B HOH 10 3 HOH HOH 10 B HOH 11 3 HOH HOH 11 B HOH 16 3 HOH HOH 16 B HOH 17 3 HOH HOH 17 B HOH 18 3 HOH HOH 18 B HOH 19 3 HOH HOH 19 B HOH 20 3 HOH HOH 20 B HOH 21 3 HOH HOH 21 B HOH 22 3 HOH HOH 22 B HOH 23 3 HOH HOH 23 B HOH 24 3 HOH HOH 24 B HOH 26 3 HOH HOH 26 B HOH 27 3 HOH HOH 27 B HOH 29 3 HOH HOH 29 B HOH 32 3 HOH HOH 32 B HOH 34 3 HOH HOH 34 B HOH 36 3 HOH HOH 36 B HOH 37 3 HOH HOH 37 B HOH 38 3 HOH HOH 38 B HOH 39 3 HOH HOH 39 B HOH 40 3 HOH HOH 40 B HOH 43 3 HOH HOH 43 B HOH 45 3 HOH HOH 45 B HOH 47 3 HOH HOH 47 B HOH 51 3 HOH HOH 51 B HOH 52 3 HOH HOH 52 B HOH 53 3 HOH HOH 53 B HOH 54 3 HOH HOH 54 B HOH 55 3 HOH HOH 55 B HOH 57 3 HOH HOH 57 B HOH 58 3 HOH HOH 58 B HOH 61 3 HOH HOH 61 B HOH 62 3 HOH HOH 62 B HOH 63 3 HOH HOH 63 B HOH 64 3 HOH HOH 64 B HOH 65 3 HOH HOH 65 B HOH 68 3 HOH HOH 68 B HOH 69 3 HOH HOH 69 B HOH 72 3 HOH HOH 72 B HOH 74 3 HOH HOH 74 B HOH 76 3 HOH HOH 76 B HOH 78 3 HOH HOH 78 B HOH 83 3 HOH HOH 83 B HOH 84 3 HOH HOH 84 B HOH 85 3 HOH HOH 85 B HOH 88 3 HOH HOH 88 B HOH 89 3 HOH HOH 89 B HOH 94 3 HOH HOH 94 B HOH 95 3 HOH HOH 95 B HOH 100 3 HOH HOH 100 B HOH 102 3 HOH HOH 102 B n 1 143 A ALA 144 n 2 ASN 144 A ALA 145 n 3 ALA 145 A VAL 146 n 4 VAL 146 A THR 147 n 5 THR 147 A ALA 148 n 6 ALA 148 A THR 149 n 7 THR 149 A GLN 150 n 8 GLN 150 A LEU 151 n 9 LEU 151 A ALA 152 n 10 ALA 152 A ALA 153 n 11 ALA 153 A LYS 154 n 12 LYS 154 A ALA 155 n 13 ALA 155 A THR 156 n 14 THR 156 A THR 157 n 15 THR 157 A LEU 158 n 16 LEU 158 A TYR 159 n 17 TYR 159 A TYR 160 n 18 TYR 160 A LEU 161 n 19 LEU 161 A HIS 162 n 20 HIS 162 A LYS 163 n 21 LYS 163 A GLN 164 n 22 GLN 164 A ALA 165 n 23 ALA 165 A MSE 166 n 24 MSE 166 A THR 167 n 25 THR 167 A ASP 168 n 26 ASP 168 A GLU 169 n 27 GLU 169 A VAL 170 n 28 VAL 170 A SER 171 n 29 SER 171 A LEU 172 n 30 LEU 172 A LEU 173 n 31 LEU 173 A LEU 174 n 32 LEU 174 A GLU 175 n 33 GLU 175 A GLN 176 n 34 GLN 176 A ALA 177 n 35 ALA 177 A LEU 178 n 36 LEU 178 A GLN 179 n 37 GLN 179 A LEU 180 n 38 LEU 180 A GLU 181 n 39 GLU 181 A PRO 182 n 40 PRO 182 A TYR 183 n 41 TYR 183 A ASN 184 n 42 ASN 184 A GLU 185 n 43 GLU 185 A ALA 186 n 44 ALA 186 A ALA 187 n 45 ALA 187 A LEU 188 n 46 LEU 188 A SER 189 n 47 SER 189 A LEU 190 n 48 LEU 190 A ILE 191 n 49 ILE 191 A ALA 192 n 50 ALA 192 A ASN 193 n 51 ASN 193 A ASP 194 n 52 ASP 194 A HIS 195 n 53 HIS 195 A PHE 196 n 54 PHE 196 A ILE 197 n 55 ILE 197 A SER 198 n 56 SER 198 A PHE 199 n 57 PHE 199 A ARG 200 n 58 ARG 200 A PHE 201 n 59 PHE 201 A GLN 202 n 60 GLN 202 A GLU 203 n 61 GLU 203 A ALA 204 n 62 ALA 204 A ILE 205 n 63 ILE 205 A ASP 206 n 64 ASP 206 A THR 207 n 65 THR 207 A TRP 208 n 66 TRP 208 A VAL 209 n 67 VAL 209 A LEU 210 n 68 LEU 210 A LEU 211 n 69 LEU 211 A LEU 212 n 70 LEU 212 A ASP 213 n 71 ASP 213 A SER 214 n 72 SER 214 A ASN 215 n 73 ASN 215 A ASP 216 n 74 ASP 216 A PRO 217 n 75 PRO 217 A ASN 218 n 76 ASN 218 A LEU 219 n 77 LEU 219 A ASP 220 n 78 ASP 220 A ARG 221 n 79 ARG 221 A VAL 222 n 80 VAL 222 A THR 223 n 81 THR 223 A ILE 224 n 82 ILE 224 A ILE 225 n 83 ILE 225 A GLU 226 n 84 GLU 226 A SER 227 n 85 SER 227 A ILE 228 n 86 ILE 228 A ASN 229 n 87 ASN 229 A LYS 230 n 88 LYS 230 A ALA 231 n 89 ALA 231 A LYS 232 n 90 LYS 232 A LYS 233 n 91 LYS 233 A LEU 234 n 92 LEU 234 A MSE 235 n 93 MSE 235 A n 1 143 B n 2 144 B ALA 145 n 3 ALA 145 B ALA 146 n 4 VAL 146 B THR 147 n 5 THR 147 B ALA 148 n 6 ALA 148 B THR 149 n 7 THR 149 B GLN 150 n 8 GLN 150 B LEU 151 n 9 LEU 151 B ALA 152 n 10 ALA 152 B ALA 153 n 11 ALA 153 B LYS 154 n 12 LYS 154 B ALA 155 n 13 ALA 155 B THR 156 n 14 THR 156 B THR 157 n 15 THR 157 B LEU 158 n 16 LEU 158 B TYR 159 n 17 TYR 159 B TYR 160 n 18 TYR 160 B LEU 161 n 19 LEU 161 B HIS 162 n 20 HIS 162 B LYS 163 n 21 LYS 163 B GLN 164 n 22 GLN 164 B ALA 165 n 23 ALA 165 B MSE 166 n 24 MSE 166 B THR 167 n 25 THR 167 B ASP 168 n 26 ASP 168 B GLU 169 n 27 GLU 169 B VAL 170 n 28 VAL 170 B SER 171 n 29 SER 171 B LEU 172 n 30 LEU 172 B LEU 173 n 31 LEU 173 B LEU 174 n 32 LEU 174 B GLU 175 n 33 GLU 175 B GLN 176 n 34 GLN 176 B ALA 177 n 35 ALA 177 B LEU 178 n 36 LEU 178 B GLN 179 n 37 GLN 179 B LEU 180 n 38 LEU 180 B GLU 181 n 39 GLU 181 B PRO 182 n 40 PRO 182 B TYR 183 n 41 TYR 183 B ASN 184 n 42 ASN 184 B GLU 185 n 43 GLU 185 B ALA 186 n 44 ALA 186 B ALA 187 n 45 ALA 187 B LEU 188 n 46 LEU 188 B SER 189 n 47 SER 189 B LEU 190 n 48 LEU 190 B ILE 191 n 49 ILE 191 B ALA 192 n 50 ALA 192 B ASN 193 n 51 ASN 193 B ASP 194 n 52 ASP 194 B HIS 195 n 53 HIS 195 B PHE 196 n 54 PHE 196 B ILE 197 n 55 ILE 197 B SER 198 n 56 SER 198 B PHE 199 n 57 PHE 199 B ARG 200 n 58 ARG 200 B PHE 201 n 59 PHE 201 B GLN 202 n 60 GLN 202 B GLU 203 n 61 GLU 203 B ALA 204 n 62 ALA 204 B ILE 205 n 63 ILE 205 B ASP 206 n 64 ASP 206 B THR 207 n 65 THR 207 B TRP 208 n 66 TRP 208 B VAL 209 n 67 VAL 209 B LEU 210 n 68 LEU 210 B LEU 211 n 69 LEU 211 B LEU 212 n 70 LEU 212 B ASP 213 n 71 ASP 213 B SER 214 n 72 SER 214 B ASN 215 n 73 ASN 215 B ASP 216 n 74 ASP 216 B PRO 217 n 75 PRO 217 B ASN 218 n 76 ASN 218 B LEU 219 n 77 LEU 219 B ASP 220 n 78 ASP 220 B ARG 221 n 79 ARG 221 B VAL 222 n 80 VAL 222 B THR 223 n 81 THR 223 B ILE 224 n 82 ILE 224 B ILE 225 n 83 ILE 225 B GLU 226 n 84 GLU 226 B SER 227 n 85 SER 227 B ILE 228 n 86 ILE 228 B ASN 229 n 87 ASN 229 B LYS 230 n 88 LYS 230 B ALA 231 n 89 ALA 231 B LYS 232 n 90 LYS 232 B LYS 233 n 91 LYS 233 B LEU 234 n 92 LEU 234 B MSE 235 n 93 MSE 235 B 4.3436 -2.0700 -0.3590 10.7714 3.6696 4.6088 -0.0049 0.2091 0.2037 -0.2629 -0.3630 -0.0273 -0.3452 0.2851 0.3679 -0.0305 -0.0853 -0.0228 -0.0941 -0.0001 -0.0843 refined 14.4415 41.7123 25.0253 X-RAY DIFFRACTION 6.3284 1.1827 0.0157 6.4069 1.3246 3.8446 -0.0375 -0.1628 0.4638 0.0242 -0.2209 0.5075 -0.0817 -0.1401 0.2584 -0.0957 -0.0370 0.0281 -0.0875 -0.0450 -0.0783 refined 2.8432 30.2731 27.2527 X-RAY DIFFRACTION 11.2478 -5.0760 -0.9073 8.6956 0.3039 5.7662 -0.0172 0.0647 0.3363 -0.1922 0.0177 -0.0048 -0.0173 0.3440 -0.0005 -0.0087 0.0055 0.0273 -0.1289 0.0172 -0.1700 refined 19.9125 25.6789 8.6960 X-RAY DIFFRACTION 6.2788 -1.0633 -1.4030 3.5559 -0.6648 2.4488 -0.1876 -0.1895 -0.4069 0.1663 0.0248 0.1179 0.2758 0.1389 0.1629 0.0848 0.0823 0.0281 -0.1698 0.0084 -0.1578 refined 19.4101 12.9811 19.6081 X-RAY DIFFRACTION A 145 A 3 A 180 A 38 X-RAY DIFFRACTION 1 A 181 A 39 A 235 A 93 X-RAY DIFFRACTION 2 B 145 B 3 B 180 B 38 X-RAY DIFFRACTION 3 B 181 B 39 B 235 B 93 X-RAY DIFFRACTION 4 author_and_software_defined_assembly PISA 1 monomeric author_and_software_defined_assembly PISA 1 monomeric A MSE 166 SELENOMETHIONINE A MSE 24 MET A MSE 235 SELENOMETHIONINE A MSE 93 MET B MSE 166 SELENOMETHIONINE B MSE 24 MET B MSE 235 SELENOMETHIONINE B MSE 93 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 CG ASN 144 A CG ASN 2 1 Y 1 A OD1 ASN 144 A OD1 ASN 2 1 Y 1 A ND2 ASN 144 A ND2 ASN 2 1 Y 1 B CG1 VAL 146 B CG1 VAL 4 1 Y 1 B CG2 VAL 146 B CG2 VAL 4 1 Y 1 A SER 143 A SER 1 1 Y 1 B SER 143 B SER 1 1 Y 1 B ASN 144 B ASN 2 1 Y 1 A B OD1 NZ ASN LYS 215 163 2.14 1_555 4_455 39.329 0.20 0.00 0.00 0.20 0.00 -0.40 0.954 0.945 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.21447 0.19093 0.1921 0.1921 2.15 41.20 726 14417 14417 5.0 99.83 7.786 0.104 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0 SAD 0.194 0.160 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.15 41.20 103 1566 16 0 1447 0.015 0.022 1498 1.256 1.973 2031 4.589 5.000 185 39.529 26.119 67 12.874 15.000 269 6.879 15.000 4 0.085 0.200 248 0.005 0.020 1086 0.195 0.200 724 0.298 0.200 1061 0.145 0.200 77 0.257 0.200 36 0.282 0.200 6 0.860 1.500 970 1.249 2.000 1494 2.514 3.000 614 3.429 4.500 536 0.221 0.178 2.206 56 985 20 99.71 39.7 2.15 50 3BEE 14481 14459 -3 0.059 1 55.96 11.6 99.9 0.416 2.15 2.23 7.11 1411 1 11.9 100 refinement REFMAC 5.2.0019 data collection SBC-Collect data reduction HKL-3000 data scaling HKL-3000 phasing HKL-3000 Putative YfrE protein Crystal structure of putative YfrE protein from Vibrio parahaemolyticus 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N A THR 147 A THR 5 HELX_P A LEU 161 A LEU 19 1 1 15 A THR 167 A THR 25 HELX_P A GLU 181 A GLU 39 1 2 15 A ASN 184 A ASN 42 HELX_P A SER 198 A SER 56 1 3 15 A ARG 200 A ARG 58 HELX_P A ASP 213 A ASP 71 1 4 14 A ASP 220 A ASP 78 HELX_P A MSE 235 A MSE 93 1 5 16 B THR 147 B THR 5 HELX_P B HIS 162 B HIS 20 1 6 16 B THR 167 B THR 25 HELX_P B GLU 181 B GLU 39 1 7 15 B ASN 184 B ASN 42 HELX_P B SER 198 B SER 56 1 8 15 B ARG 200 B ARG 58 HELX_P B LEU 212 B LEU 70 1 9 13 B ASP 220 B ASP 78 HELX_P B MSE 235 B MSE 93 1 10 16 covale 1.327 A ALA 165 A C ALA 23 1_555 A MSE 166 A N MSE 24 1_555 covale 1.327 A MSE 166 A C MSE 24 1_555 A THR 167 A N THR 25 1_555 covale 1.332 A LEU 234 A C LEU 92 1_555 A MSE 235 A N MSE 93 1_555 covale 1.327 B ALA 165 B C ALA 23 1_555 B MSE 166 B N MSE 24 1_555 covale 1.330 B MSE 166 B C MSE 24 1_555 B THR 167 B N THR 25 1_555 covale 1.335 B LEU 234 B C LEU 92 1_555 B MSE 235 B N MSE 93 1_555 STRUCTURAL GENOMICS, UNKNOWN FUNCTION putaive YfrE protein, Vibrio parahaemolyticus, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TPR repeat, UNKNOWN FUNCTION Q87ND7_VIBPA UNP 1 146 Q87ND7 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPNLDRVTII ESINKAKKLM 146 235 3BEE 146 235 Q87ND7 A 1 4 93 146 235 3BEE 146 235 Q87ND7 B 1 4 93 1 EXPRESSION TAG SER 143 3BEE A Q87ND7 UNP 1 1 EXPRESSION TAG ASN 144 3BEE A Q87ND7 UNP 2 1 EXPRESSION TAG ALA 145 3BEE A Q87ND7 UNP 3 2 EXPRESSION TAG SER 143 3BEE B Q87ND7 UNP 1 2 EXPRESSION TAG ASN 144 3BEE B Q87ND7 UNP 2 2 EXPRESSION TAG ALA 145 3BEE B Q87ND7 UNP 3 BINDING SITE FOR RESIDUE EDO A 301 Software 4 BINDING SITE FOR RESIDUE EDO A 302 Software 4 BINDING SITE FOR RESIDUE EDO B 303 Software 4 BINDING SITE FOR RESIDUE EDO A 304 Software 7 A THR 167 A THR 25 4 1_555 A ASP 168 A ASP 26 4 1_555 A GLU 169 A GLU 27 4 1_555 B LYS 232 B LYS 90 4 5_555 A ASN 193 A ASN 51 4 1_555 A TRP 208 A TRP 66 4 1_555 A SER 227 A SER 85 4 1_555 B GLN 164 B GLN 22 4 1_555 A HOH 101 G HOH 4 3_554 A TYR 160 A TYR 18 4 1_555 A LEU 212 A LEU 70 4 3_554 A ASP 213 A ASP 71 4 3_554 A HOH 90 G HOH 7 1_555 A ASP 168 A ASP 26 7 1_555 A GLU 169 A GLU 27 7 1_555 A LEU 172 A LEU 30 7 1_555 B ILE 225 B ILE 83 7 5_555 B ASN 229 B ASN 87 7 5_555 B LYS 232 B LYS 90 7 5_555 96 P 43 21 2