0.012832 0.007409 0.000000 0.000000 0.014817 0.000000 0.000000 0.000000 0.006885 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 77.930 77.930 145.240 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 Se 196.106 n SELENOMETHIONINE L-peptide linking C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER 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 O4 S -2 96.063 SULFATE ION non-polymer C4 H9 N O3 119.119 y THREONINE 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 a conserved hypothetical protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution 10.2210/pdb4qdy/pdb pdb_00004qdy 100 1 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) PIXEL 2013-07-01 DECTRIS PILATUS 6M single crystal Si(111) bent MAD M x-ray 1 0.91837 1.0 0.97966 1.0 0.97895 1.0 BL11-1 SSRL 0.91837,0.97966,0.97895 SYNCHROTRON SSRL BEAMLINE BL11-1 24436.973 conserved hypothetical protein 1 man polymer 106.120 DI(HYDROXYETHYL)ETHER 2 syn non-polymer 96.063 SULFATE ION 1 syn non-polymer 18.015 water 12 nat water no yes GRQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASE(MSE)QESTRKFKVTADLTDAGVGTIEVP LSIEDLPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENV(MSE)VSDKEVSITSDQETLDRIDKIIA VLPTSERITGNYSGSVPLQAIDRNGVVLPAVITPFDTI(MSE)KVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN GRQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASEMQESTRKFKVTADLTDAGVGTIEVPLSIE DLPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENVMVSDKEVSITSDQETLDRIDKIIAVLPTSERI TGNYSGSVPLQAIDRNGVVLPAVITPFDTIMKVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN A JCSG-417515 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n TIGR4 sample NP_346007.1, SP_1560 170187 Streptococcus pneumoniae 562 Escherichia Coli PB1 Plasmid SpeedET 1 2.60 52.78 VAPOR DIFFUSION, SITTING DROP 42.0% polyethylene glycol 1500, 0.2M ammonium sulfate, 0.1M cesium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 Joint Center for Structural Genomics JCSG PSI:Biology software citation_author database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Structure summary Refinement description Database references Database references Derived calculations 1 0 2014-07-30 1 1 2014-12-24 1 2 2017-11-22 1 3 2018-01-24 1 4 2023-02-01 _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _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 2014-05-14 REL REL PEG DI(HYDROXYETHYL)ETHER SO4 SULFATE ION HOH water THE CONSTRUCT (RESIDUES 34-259) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. PEG 260 2 PEG PEG 301 A PEG 261 2 PEG PEG 302 A SO4 262 3 SO4 SO4 303 A HOH 263 4 HOH HOH 401 A HOH 264 4 HOH HOH 402 A HOH 265 4 HOH HOH 403 A HOH 266 4 HOH HOH 404 A HOH 267 4 HOH HOH 405 A HOH 268 4 HOH HOH 406 A HOH 269 4 HOH HOH 407 A HOH 270 4 HOH HOH 408 A HOH 271 4 HOH HOH 409 A HOH 272 4 HOH HOH 410 A HOH 273 4 HOH HOH 411 A HOH 274 4 HOH HOH 412 A GLY 0 n 1 GLY 0 A ARG 34 n 2 ARG 34 A GLN 35 n 3 GLN 35 A VAL 36 n 4 VAL 36 A LYS 37 n 5 LYS 37 A THR 38 n 6 THR 38 A GLU 39 n 7 GLU 39 A THR 40 n 8 THR 40 A TYR 41 n 9 TYR 41 A THR 42 n 10 THR 42 A ASN 43 n 11 ASN 43 A THR 44 n 12 THR 44 A VAL 45 n 13 VAL 45 A THR 46 n 14 THR 46 A ASN 47 n 15 ASN 47 A VAL 48 n 16 VAL 48 A PRO 49 n 17 PRO 49 A ILE 50 n 18 ILE 50 A ASP 51 n 19 ASP 51 A ILE 52 n 20 ILE 52 A ARG 53 n 21 ARG 53 A TYR 54 n 22 TYR 54 A ASN 55 n 23 ASN 55 A SER 56 n 24 SER 56 A ASP 57 n 25 ASP 57 A LYS 58 n 26 LYS 58 A TYR 59 n 27 TYR 59 A PHE 60 n 28 PHE 60 A ILE 61 n 29 ILE 61 A SER 62 n 30 SER 62 A GLY 63 n 31 GLY 63 A PHE 64 n 32 PHE 64 A ALA 65 n 33 ALA 65 A SER 66 n 34 SER 66 A GLU 67 n 35 GLU 67 A VAL 68 n 36 VAL 68 A SER 69 n 37 SER 69 A VAL 70 n 38 VAL 70 A VAL 71 n 39 VAL 71 A LEU 72 n 40 LEU 72 A THR 73 n 41 THR 73 A GLY 74 n 42 GLY 74 A ALA 75 n 43 ALA 75 A ASN 76 n 44 ASN 76 A ARG 77 n 45 ARG 77 A LEU 78 n 46 LEU 78 A SER 79 n 47 SER 79 A LEU 80 n 48 LEU 80 A ALA 81 n 49 ALA 81 A SER 82 n 50 SER 82 A GLU 83 n 51 GLU 83 A MSE 84 n 52 MSE 84 A GLN 85 n 53 GLN 85 A GLU 86 n 54 GLU 86 A SER 87 n 55 SER 87 A THR 88 n 56 THR 88 A ARG 89 n 57 ARG 89 A LYS 90 n 58 LYS 90 A PHE 91 n 59 PHE 91 A LYS 92 n 60 LYS 92 A VAL 93 n 61 VAL 93 A THR 94 n 62 THR 94 A ALA 95 n 63 ALA 95 A ASP 96 n 64 ASP 96 A LEU 97 n 65 LEU 97 A THR 98 n 66 THR 98 A ASP 99 n 67 ASP 99 A ALA 100 n 68 ALA 100 A GLY 101 n 69 GLY 101 A VAL 102 n 70 VAL 102 A GLY 103 n 71 GLY 103 A THR 104 n 72 THR 104 A ILE 105 n 73 ILE 105 A GLU 106 n 74 GLU 106 A VAL 107 n 75 VAL 107 A PRO 108 n 76 PRO 108 A LEU 109 n 77 LEU 109 A SER 110 n 78 SER 110 A ILE 111 n 79 ILE 111 A GLU 112 n 80 GLU 112 A ASP 113 n 81 ASP 113 A LEU 114 n 82 LEU 114 A PRO 115 n 83 PRO 115 A ASN 116 n 84 ASN 116 A GLY 117 n 85 GLY 117 A LEU 118 n 86 LEU 118 A THR 119 n 87 THR 119 A ALA 120 n 88 ALA 120 A VAL 121 n 89 VAL 121 A ALA 122 n 90 ALA 122 A THR 123 n 91 THR 123 A PRO 124 n 92 PRO 124 A GLN 125 n 93 GLN 125 A LYS 126 n 94 LYS 126 A ILE 127 n 95 ILE 127 A THR 128 n 96 THR 128 A VAL 129 n 97 VAL 129 A LYS 130 n 98 LYS 130 A ILE 131 n 99 ILE 131 A GLY 132 n 100 GLY 132 A LYS 133 n 101 LYS 133 A LYS 134 n 102 LYS 134 A ALA 135 n 103 ALA 135 A GLN 136 n 104 GLN 136 A LYS 137 n 105 LYS 137 A ASP 138 n 106 ASP 138 A LYS 139 n 107 LYS 139 A VAL 140 n 108 VAL 140 A LYS 141 n 109 LYS 141 A ILE 142 n 110 ILE 142 A VAL 143 n 111 VAL 143 A PRO 144 n 112 PRO 144 A GLU 145 n 113 GLU 145 A ILE 146 n 114 ILE 146 A ASP 147 n 115 ASP 147 A PRO 148 n 116 PRO 148 A SER 149 n 117 SER 149 A GLN 150 n 118 GLN 150 A ILE 151 n 119 ILE 151 A ASP 152 n 120 ASP 152 A SER 153 n 121 SER 153 A ARG 154 n 122 ARG 154 A VAL 155 n 123 VAL 155 A GLN 156 n 124 GLN 156 A ILE 157 n 125 ILE 157 A GLU 158 n 126 GLU 158 A ASN 159 n 127 ASN 159 A VAL 160 n 128 VAL 160 A MSE 161 n 129 MSE 161 A VAL 162 n 130 VAL 162 A SER 163 n 131 SER 163 A ASP 164 n 132 ASP 164 A LYS 165 n 133 LYS 165 A GLU 166 n 134 GLU 166 A VAL 167 n 135 VAL 167 A SER 168 n 136 SER 168 A ILE 169 n 137 ILE 169 A THR 170 n 138 THR 170 A SER 171 n 139 SER 171 A ASP 172 n 140 ASP 172 A GLN 173 n 141 GLN 173 A GLU 174 n 142 GLU 174 A THR 175 n 143 THR 175 A LEU 176 n 144 LEU 176 A ASP 177 n 145 ASP 177 A ARG 178 n 146 ARG 178 A ILE 179 n 147 ILE 179 A ASP 180 n 148 ASP 180 A LYS 181 n 149 LYS 181 A ILE 182 n 150 ILE 182 A ILE 183 n 151 ILE 183 A ALA 184 n 152 ALA 184 A VAL 185 n 153 VAL 185 A LEU 186 n 154 LEU 186 A PRO 187 n 155 PRO 187 A THR 188 n 156 THR 188 A SER 189 n 157 SER 189 A GLU 190 n 158 GLU 190 A ARG 191 n 159 ARG 191 A ILE 192 n 160 ILE 192 A THR 193 n 161 THR 193 A GLY 194 n 162 GLY 194 A ASN 195 n 163 ASN 195 A TYR 196 n 164 TYR 196 A SER 197 n 165 SER 197 A GLY 198 n 166 GLY 198 A SER 199 n 167 SER 199 A VAL 200 n 168 VAL 200 A PRO 201 n 169 PRO 201 A LEU 202 n 170 LEU 202 A GLN 203 n 171 GLN 203 A ALA 204 n 172 ALA 204 A ILE 205 n 173 ILE 205 A ASP 206 n 174 ASP 206 A ARG 207 n 175 ARG 207 A ASN 208 n 176 ASN 208 A GLY 209 n 177 GLY 209 A VAL 210 n 178 VAL 210 A VAL 211 n 179 VAL 211 A LEU 212 n 180 LEU 212 A PRO 213 n 181 PRO 213 A ALA 214 n 182 ALA 214 A VAL 215 n 183 VAL 215 A ILE 216 n 184 ILE 216 A THR 217 n 185 THR 217 A PRO 218 n 186 PRO 218 A PHE 219 n 187 PHE 219 A ASP 220 n 188 ASP 220 A THR 221 n 189 THR 221 A ILE 222 n 190 ILE 222 A MSE 223 n 191 MSE 223 A LYS 224 n 192 LYS 224 A VAL 225 n 193 VAL 225 A THR 226 n 194 THR 226 A THR 227 n 195 THR 227 A LYS 228 n 196 LYS 228 A PRO 229 n 197 PRO 229 A VAL 230 n 198 VAL 230 A n 199 231 A n 200 232 A n 201 233 A n 202 234 A n 203 235 A n 204 236 A n 205 237 A n 206 238 A n 207 239 A n 208 240 A n 209 241 A n 210 242 A n 211 243 A n 212 244 A n 213 245 A n 214 246 A n 215 247 A n 216 248 A n 217 249 A n 218 250 A n 219 251 A n 220 252 A n 221 253 A n 222 254 A n 223 255 A n 224 256 A n 225 257 A n 226 258 A n 227 259 A 0.4861 0.2692 0.1977 1.7953 -0.8692 1.2657 0.1081 0.0928 -0.0710 -0.0466 -0.0986 0.0079 0.1905 0.0517 -0.0095 0.0700 0.2058 0.0271 -0.1025 -0.0217 -0.0487 refined 36.5669 -2.8805 44.4506 X-RAY DIFFRACTION A 33 A 230 X-RAY DIFFRACTION 1 { A|33-230} author_and_software_defined_assembly PISA 2 dimeric 3870 -24 20940 A MSE 84 SELENOMETHIONINE A MSE 52 MET A MSE 161 SELENOMETHIONINE A MSE 129 MET A MSE 223 SELENOMETHIONINE A MSE 191 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 4_655 -x+1,-y,z crystal symmetry operation 77.9300000000 0.0000000000 0.0000000000 A O GLU 112 A O GLU 80 A N LYS 92 A N LYS 60 A O VAL 93 A O VAL 61 A N ASP 51 A N ASP 19 A N VAL 45 A N VAL 13 A O VAL 70 A O VAL 38 A N SER 69 A N SER 37 A O THR 123 A O THR 91 A N PHE 60 A N PHE 28 A O GLY 132 A O GLY 100 A O VAL 129 A O VAL 97 A N ILE 105 A N ILE 73 A N PHE 60 A N PHE 28 A O GLY 132 A O GLY 100 A N ALA 135 A N ALA 103 A O SER 171 A O SER 139 A N THR 170 A N THR 138 A O VAL 215 A O VAL 183 A N VAL 143 A N VAL 111 A O ILE 182 A O ILE 150 A N ILE 183 A N ILE 151 A O GLN 203 A O GLN 171 A N TYR 196 A N TYR 164 A O VAL 225 A O VAL 193 A O THR 226 A O THR 194 A N ASN 159 A N ASN 127 1 A CG ARG 34 A CG ARG 2 1 Y 1 A CD ARG 34 A CD ARG 2 1 Y 1 A NE ARG 34 A NE ARG 2 1 Y 1 A CZ ARG 34 A CZ ARG 2 1 Y 1 A NH1 ARG 34 A NH1 ARG 2 1 Y 1 A NH2 ARG 34 A NH2 ARG 2 1 Y 1 A CG LYS 37 A CG LYS 5 1 Y 1 A CD LYS 37 A CD LYS 5 1 Y 1 A CE LYS 37 A CE LYS 5 1 Y 1 A NZ LYS 37 A NZ LYS 5 1 Y 1 A CG GLU 39 A CG GLU 7 1 Y 1 A CD GLU 39 A CD GLU 7 1 Y 1 A OE1 GLU 39 A OE1 GLU 7 1 Y 1 A OE2 GLU 39 A OE2 GLU 7 1 Y 1 A CG ASN 43 A CG ASN 11 1 Y 1 A OD1 ASN 43 A OD1 ASN 11 1 Y 1 A ND2 ASN 43 A ND2 ASN 11 1 Y 1 A CG LYS 90 A CG LYS 58 1 Y 1 A CD LYS 90 A CD LYS 58 1 Y 1 A CE LYS 90 A CE LYS 58 1 Y 1 A NZ LYS 90 A NZ LYS 58 1 Y 1 A CG LYS 92 A CG LYS 60 1 Y 1 A CD LYS 92 A CD LYS 60 1 Y 1 A CE LYS 92 A CE LYS 60 1 Y 1 A NZ LYS 92 A NZ LYS 60 1 Y 1 A CG ASP 99 A CG ASP 67 1 Y 1 A OD1 ASP 99 A OD1 ASP 67 1 Y 1 A OD2 ASP 99 A OD2 ASP 67 1 Y 1 A CG LYS 133 A CG LYS 101 1 Y 1 A CD LYS 133 A CD LYS 101 1 Y 1 A CE LYS 133 A CE LYS 101 1 Y 1 A NZ LYS 133 A NZ LYS 101 1 Y 1 A CG LYS 137 A CG LYS 105 1 Y 1 A CD LYS 137 A CD LYS 105 1 Y 1 A CE LYS 137 A CE LYS 105 1 Y 1 A NZ LYS 137 A NZ LYS 105 1 Y 1 A CG LYS 141 A CG LYS 109 1 Y 1 A CD LYS 141 A CD LYS 109 1 Y 1 A CE LYS 141 A CE LYS 109 1 Y 1 A NZ LYS 141 A NZ LYS 109 1 Y 1 A CG ARG 154 A CG ARG 122 1 Y 1 A CD ARG 154 A CD ARG 122 1 Y 1 A NE ARG 154 A NE ARG 122 1 Y 1 A CZ ARG 154 A CZ ARG 122 1 Y 1 A NH1 ARG 154 A NH1 ARG 122 1 Y 1 A NH2 ARG 154 A NH2 ARG 122 1 Y 1 A CG GLN 156 A CG GLN 124 1 Y 1 A CD GLN 156 A CD GLN 124 1 Y 1 A OE1 GLN 156 A OE1 GLN 124 1 Y 1 A NE2 GLN 156 A NE2 GLN 124 1 Y 1 A CD LYS 181 A CD LYS 149 1 Y 1 A CE LYS 181 A CE LYS 149 1 Y 1 A NZ LYS 181 A NZ LYS 149 1 Y 1 A CG LYS 224 A CG LYS 192 1 Y 1 A CD LYS 224 A CD LYS 192 1 Y 1 A CE LYS 224 A CE LYS 192 1 Y 1 A NZ LYS 224 A NZ LYS 192 1 Y 1 A CG LYS 228 A CG LYS 196 1 Y 1 A CD LYS 228 A CD LYS 196 1 Y 1 A CE LYS 228 A CE LYS 196 1 Y 1 A NZ LYS 228 A NZ LYS 196 1 Y 1 A ALA 231 A ALA 199 1 Y 1 A PRO 232 A PRO 200 1 Y 1 A SER 233 A SER 201 1 Y 1 A SER 234 A SER 202 1 Y 1 A SER 235 A SER 203 1 Y 1 A THR 236 A THR 204 1 Y 1 A SER 237 A SER 205 1 Y 1 A ASN 238 A ASN 206 1 Y 1 A SER 239 A SER 207 1 Y 1 A SER 240 A SER 208 1 Y 1 A THR 241 A THR 209 1 Y 1 A SER 242 A SER 210 1 Y 1 A SER 243 A SER 211 1 Y 1 A SER 244 A SER 212 1 Y 1 A SER 245 A SER 213 1 Y 1 A GLU 246 A GLU 214 1 Y 1 A THR 247 A THR 215 1 Y 1 A SER 248 A SER 216 1 Y 1 A SER 249 A SER 217 1 Y 1 A SER 250 A SER 218 1 Y 1 A THR 251 A THR 219 1 Y 1 A LYS 252 A LYS 220 1 Y 1 A ALA 253 A ALA 221 1 Y 1 A THR 254 A THR 222 1 Y 1 A SER 255 A SER 223 1 Y 1 A SER 256 A SER 224 1 Y 1 A LYS 257 A LYS 225 1 Y 1 A THR 258 A THR 226 1 Y 1 A ASN 259 A ASN 227 1 Y 1 A ARG 34 -93.70 -154.46 1 A SER 171 -170.20 -167.02 1 A ALA 184 -103.91 74.72 138.770 65.2071 17.160 -13.3819 0.0000 0.0000 -13.3819 0.0000 26.7639 0.8878 0.8243 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL PHASES (MAD) WERE USED AS RESTRAINTS DURING REFINEMENT. 4. POLYETHYLENE GLYCOL FRAGMENTS (PEG) AND SULFATE FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE 0.2878 0.2323 0.2346 2.7400 39.330 342 7370 4.6400 99.9200 1.000 0.500 RANDOM 1 THROUGHOUT 0.000 MAD 0.482 2.7400 39.330 12 1479 19 0 1448 685 SINUSOIDAL 10.000 37 HARMONIC 2.000 211 HARMONIC 5.000 1482 HARMONIC 20.000 228 SEMIHARMONIC 10.000 1658 SEMIHARMONIC 4.000 0.008 1482 HARMONIC 2.000 1.070 2026 HARMONIC 2.000 2.060 1.460 0.2520 0.2695 0.2688 3.0600 84 1936 2020 5 4.1600 99.9200 69.717 2.74 39.330 4QDY 7389 -3.000 0.139 1 18.360 99.700 0.013 2.740 2.840 2.7 9325 727 1 100.000 0.013 2.840 2.950 3.6 8626 691 1 100.000 0.013 2.950 3.080 4.6 7716 693 1 99.600 0.013 3.080 3.250 8.0 9991 745 1 99.600 0.013 3.250 3.450 10.5 9368 704 1 99.700 0.013 3.450 3.710 15.0 9286 721 1 100.000 0.013 3.710 4.080 19.7 9023 729 1 100.000 0.013 4.080 4.670 29.6 8460 753 1 99.900 0.013 4.670 5.860 36.5 9576 767 1 100.000 0.013 5.860 45.7 9177 858 1 98.500 model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package phasing Eric de La Fortelle sharp-develop@globalphasing.com http://www.globalphasing.com/sharp/ SHARP package data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package refinement Gerard Bricogne buster-develop@GlobalPhasing.com http://www.globalphasing.com/buster/ BUSTER-TNT program 2.10.0 data reduction XDS phasing SHELXD refinement BUSTER 2.10.0 Y Crystal structure of a YbbR-like protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution 1 N N 2 N N 2 N N 3 N N 4 N N A ASN 76 A ASN 44 HELX_P A GLN 85 A GLN 53 1 1 10 A GLN 173 A GLN 141 HELX_P A ARG 178 A ARG 146 1 2 6 covale 1.343 both A GLU 83 A C GLU 51 1_555 A MSE 84 A N MSE 52 1_555 covale 1.350 both A MSE 84 A C MSE 52 1_555 A GLN 85 A N GLN 53 1_555 covale 1.341 both A VAL 160 A C VAL 128 1_555 A MSE 161 A N MSE 129 1_555 covale 1.339 both A MSE 161 A C MSE 129 1_555 A VAL 162 A N VAL 130 1_555 covale 1.346 both A ILE 222 A C ILE 190 1_555 A MSE 223 A N MSE 191 1_555 covale 1.343 both A MSE 223 A C MSE 191 1_555 A LYS 224 A N LYS 192 1_555 STRUCTURAL GENOMICS, UNKNOWN FUNCTION Two YbbR domains, PF07949 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION A THR 123 A THR 91 1 A PRO 124 A PRO 92 1.48 A THR 217 A THR 185 1 A PRO 218 A PRO 186 0.13 Q97PP3_STRPN UNP 1 34 Q97PP3 RQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASEMQESTRKFKVTADLTDAGVGTIEVPLSIED LPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENVMVSDKEVSITSDQETLDRIDKIIAVLPTSERIT GNYSGSVPLQAIDRNGVVLPAVITPFDTIMKVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN 34 259 4QDY 34 259 Q97PP3 A 1 2 227 1 expression tag GLY 0 4QDY A Q97PP3 UNP 1 5 3 4 5 anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel A SER 110 A SER 78 A GLU 112 A GLU 80 A LYS 92 A LYS 60 A ASP 96 A ASP 64 A TYR 41 A TYR 9 A ARG 53 A ARG 21 A GLU 67 A GLU 35 A GLY 74 A GLY 42 A THR 119 A THR 87 A THR 123 A THR 91 A TYR 59 A TYR 27 A SER 62 A SER 30 A LYS 126 A LYS 94 A LYS 139 A LYS 107 A GLY 103 A GLY 71 A PRO 108 A PRO 76 A TYR 59 A TYR 27 A SER 62 A SER 30 A LYS 126 A LYS 94 A LYS 139 A LYS 107 A VAL 167 A VAL 135 A ASP 172 A ASP 140 A VAL 215 A VAL 183 A THR 217 A THR 185 A ILE 142 A ILE 110 A GLU 145 A GLU 113 A LYS 181 A LYS 149 A VAL 185 A VAL 153 A TYR 196 A TYR 164 A ILE 205 A ILE 173 A ASP 220 A ASP 188 A LYS 228 A LYS 196 A GLN 156 A GLN 124 A VAL 162 A VAL 130 BINDING SITE FOR RESIDUE PEG A 301 A PEG 301 Software 6 BINDING SITE FOR RESIDUE PEG A 302 A PEG 302 Software 3 BINDING SITE FOR RESIDUE SO4 A 303 A SO4 303 Software 3 A GLY 63 A GLY 31 6 1_555 A PHE 64 A PHE 32 6 1_555 A ALA 65 A ALA 33 6 1_555 A LEU 212 A LEU 180 6 4_655 A PRO 213 A PRO 181 6 4_655 A ALA 214 A ALA 182 6 4_655 A ASN 55 A ASN 23 3 1_555 A LYS 58 A LYS 26 3 1_555 A TYR 59 A TYR 27 3 1_555 A TYR 41 A TYR 9 3 1_555 A ARG 77 A ARG 45 3 1_555 A GLU 145 A GLU 113 3 6_554 181 P 64 2 2