0.024652 0.000000 0.000000 0.000000 0.009915 0.000000 0.000000 0.000000 0.008359 0.000000 0.000000 0.000000 Ramagopal, U.A. Toro, R. 0000-0002-2487-9713 Burley, S.K. Almo, S.C. New York SGX Research Center for Structural Genomics (NYSGXRC) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 40.565 100.860 119.634 C10 H13 N5 O4 267.241 ADENOSINE non-polymer 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 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 probable rRNA-methyltransferase from Porphyromonas gingivalis 0000-0002-2487-9713 100 1 CCD 2009-08-14 ADSC QUANTUM 315 SINGLE WAVELENGTH x-ray 1 0.9793 1.0 X29A NSLS 0.9793 SYNCHROTRON NSLS BEAMLINE X29A 29200.488 Probable r-RNA methyltransferase 2 man polymer 267.241 ADENOSINE 2 syn non-polymer 18.015 water 136 nat water no yes (MSE)SLSLPLFYAPDIEQSDRLPDDEAGHILRVLR(MSE)QAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQ KPWRDRITIAIAPTKQSER(MSE)EW(MSE)LEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISA(MSE)KQSLKAS FPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRAEITQGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVS LGESRLRTETAGLVACQWIHTLQACYRIGEGHHHHHH MSLSLPLFYAPDIEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRIT IAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAMKQSLKASFPVIRVNIPIQTVIADTPKA AVRLIAYVDEAVRAEITQGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIH TLQACYRIGEGHHHHHH A,B NYSGXRC-11285c 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n ATCC 33277 /DSM 20709 /JCM 12257 sample PGN_0201 431947 Porphyromonas gingivalis ATCC 33277 469008 Escherichia coli BL21(DE3) BC-pSGX4(BC) 1 2.10 41.30 VAPOR DIFFUSION, SITTING DROP 6.5 0.1 M Bis-Tris pH 6.5, 25% PEG 3350, 0.2M Ammonium Acetate, Vapor diffusion, Sitting drop, temperature 298K 298 New York SGX Research Center for Structural Genomics NYSGXRC PSI, Protein Structure Initiative audit_author citation_author struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Database references Derived calculations Structure summary 1 0 2010-01-19 1 1 2011-07-13 1 2 2021-02-10 _audit_author.identifier_ORCID _citation_author.identifier_ORCID _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_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_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 2009-11-30 REL REL ADN ADENOSINE HOH water ASSIGNMENT OF BOUND LIGAND "ADN" IS PURELY BASED ON DENSITY ADN 300 2 ADN ADN 300 A ADN 300 2 ADN ADN 300 B HOH 1 3 HOH HOH 256 A HOH 2 3 HOH HOH 257 A HOH 5 3 HOH HOH 258 A HOH 6 3 HOH HOH 259 A HOH 7 3 HOH HOH 260 A HOH 8 3 HOH HOH 261 A HOH 9 3 HOH HOH 262 A HOH 10 3 HOH HOH 263 A HOH 11 3 HOH HOH 264 A HOH 12 3 HOH HOH 265 A HOH 13 3 HOH HOH 266 A HOH 14 3 HOH HOH 267 A HOH 15 3 HOH HOH 268 A HOH 16 3 HOH HOH 269 A HOH 17 3 HOH HOH 270 A HOH 18 3 HOH HOH 271 A HOH 20 3 HOH HOH 272 A HOH 21 3 HOH HOH 273 A HOH 23 3 HOH HOH 274 A HOH 24 3 HOH HOH 275 A HOH 26 3 HOH HOH 276 A HOH 29 3 HOH HOH 277 A HOH 32 3 HOH HOH 278 A HOH 33 3 HOH HOH 279 A HOH 35 3 HOH HOH 280 A HOH 37 3 HOH HOH 281 A HOH 38 3 HOH HOH 282 A HOH 39 3 HOH HOH 283 A HOH 40 3 HOH HOH 284 A HOH 41 3 HOH HOH 285 A HOH 42 3 HOH HOH 286 A HOH 44 3 HOH HOH 287 A HOH 45 3 HOH HOH 288 A HOH 48 3 HOH HOH 289 A HOH 49 3 HOH HOH 290 A HOH 50 3 HOH HOH 291 A HOH 55 3 HOH HOH 292 A HOH 56 3 HOH HOH 293 A HOH 58 3 HOH HOH 294 A HOH 60 3 HOH HOH 295 A HOH 62 3 HOH HOH 296 A HOH 66 3 HOH HOH 297 A HOH 69 3 HOH HOH 298 A HOH 70 3 HOH HOH 299 A HOH 71 3 HOH HOH 301 A HOH 76 3 HOH HOH 302 A HOH 78 3 HOH HOH 303 A HOH 81 3 HOH HOH 304 A HOH 84 3 HOH HOH 305 A HOH 86 3 HOH HOH 306 A HOH 87 3 HOH HOH 307 A HOH 89 3 HOH HOH 308 A HOH 90 3 HOH HOH 309 A HOH 92 3 HOH HOH 310 A HOH 93 3 HOH HOH 311 A HOH 94 3 HOH HOH 312 A HOH 95 3 HOH HOH 313 A HOH 96 3 HOH HOH 314 A HOH 97 3 HOH HOH 315 A HOH 100 3 HOH HOH 316 A HOH 101 3 HOH HOH 317 A HOH 104 3 HOH HOH 318 A HOH 105 3 HOH HOH 319 A HOH 106 3 HOH HOH 320 A HOH 108 3 HOH HOH 321 A HOH 110 3 HOH HOH 322 A HOH 113 3 HOH HOH 323 A HOH 114 3 HOH HOH 324 A HOH 119 3 HOH HOH 325 A HOH 120 3 HOH HOH 326 A HOH 123 3 HOH HOH 327 A HOH 124 3 HOH HOH 328 A HOH 126 3 HOH HOH 329 A HOH 127 3 HOH HOH 330 A HOH 128 3 HOH HOH 331 A HOH 129 3 HOH HOH 332 A HOH 131 3 HOH HOH 333 A HOH 133 3 HOH HOH 334 A HOH 134 3 HOH HOH 335 A HOH 135 3 HOH HOH 336 A HOH 136 3 HOH HOH 337 A HOH 137 3 HOH HOH 338 A HOH 3 3 HOH HOH 256 B HOH 4 3 HOH HOH 257 B HOH 19 3 HOH HOH 258 B HOH 22 3 HOH HOH 259 B HOH 25 3 HOH HOH 260 B HOH 27 3 HOH HOH 261 B HOH 28 3 HOH HOH 262 B HOH 30 3 HOH HOH 263 B HOH 31 3 HOH HOH 264 B HOH 34 3 HOH HOH 265 B HOH 36 3 HOH HOH 266 B HOH 43 3 HOH HOH 267 B HOH 46 3 HOH HOH 268 B HOH 51 3 HOH HOH 269 B HOH 52 3 HOH HOH 270 B HOH 53 3 HOH HOH 271 B HOH 54 3 HOH HOH 272 B HOH 57 3 HOH HOH 273 B HOH 59 3 HOH HOH 274 B HOH 61 3 HOH HOH 275 B HOH 63 3 HOH HOH 276 B HOH 64 3 HOH HOH 277 B HOH 65 3 HOH HOH 278 B HOH 67 3 HOH HOH 279 B HOH 68 3 HOH HOH 280 B HOH 72 3 HOH HOH 281 B HOH 73 3 HOH HOH 282 B HOH 74 3 HOH HOH 283 B HOH 75 3 HOH HOH 284 B HOH 77 3 HOH HOH 285 B HOH 79 3 HOH HOH 286 B HOH 80 3 HOH HOH 287 B HOH 82 3 HOH HOH 288 B HOH 83 3 HOH HOH 289 B HOH 85 3 HOH HOH 290 B HOH 88 3 HOH HOH 291 B HOH 91 3 HOH HOH 292 B HOH 98 3 HOH HOH 293 B HOH 99 3 HOH HOH 294 B HOH 102 3 HOH HOH 295 B HOH 103 3 HOH HOH 296 B HOH 107 3 HOH HOH 297 B HOH 109 3 HOH HOH 298 B HOH 111 3 HOH HOH 299 B HOH 112 3 HOH HOH 301 B HOH 115 3 HOH HOH 302 B HOH 116 3 HOH HOH 303 B HOH 117 3 HOH HOH 304 B HOH 118 3 HOH HOH 305 B HOH 121 3 HOH HOH 306 B HOH 122 3 HOH HOH 307 B HOH 125 3 HOH HOH 308 B HOH 130 3 HOH HOH 309 B HOH 132 3 HOH HOH 310 B n 1 -1 A n 2 0 A n 3 1 A n 4 2 A LEU 3 n 5 LEU 3 A PRO 4 n 6 PRO 4 A LEU 5 n 7 LEU 5 A PHE 6 n 8 PHE 6 A TYR 7 n 9 TYR 7 A ALA 8 n 10 ALA 8 A PRO 9 n 11 PRO 9 A ASP 10 n 12 ASP 10 A ILE 11 n 13 ILE 11 A GLU 12 n 14 GLU 12 A GLN 13 n 15 GLN 13 A SER 14 n 16 SER 14 A ASP 15 n 17 ASP 15 A ARG 16 n 18 ARG 16 A LEU 17 n 19 LEU 17 A PRO 18 n 20 PRO 18 A ASP 19 n 21 ASP 19 A ASP 20 n 22 ASP 20 A GLU 21 n 23 GLU 21 A ALA 22 n 24 ALA 22 A GLY 23 n 25 GLY 23 A HIS 24 n 26 HIS 24 A ILE 25 n 27 ILE 25 A LEU 26 n 28 LEU 26 A ARG 27 n 29 ARG 27 A VAL 28 n 30 VAL 28 A LEU 29 n 31 LEU 29 A ARG 30 n 32 ARG 30 A MSE 31 n 33 MSE 31 A GLN 32 n 34 GLN 32 A ALA 33 n 35 ALA 33 A GLY 34 n 36 GLY 34 A ASP 35 n 37 ASP 35 A ARG 36 n 38 ARG 36 A LEU 37 n 39 LEU 37 A ARG 38 n 40 ARG 38 A LEU 39 n 41 LEU 39 A THR 40 n 42 THR 40 A ASP 41 n 43 ASP 41 A GLY 42 n 44 GLY 42 A ARG 43 n 45 ARG 43 A GLY 44 n 46 GLY 44 A SER 45 n 47 SER 45 A PHE 46 n 48 PHE 46 A PHE 47 n 49 PHE 47 A ASP 48 n 50 ASP 48 A ALA 49 n 51 ALA 49 A VAL 50 n 52 VAL 50 A ILE 51 n 53 ILE 51 A GLU 52 n 54 GLU 52 A THR 53 n 55 THR 53 A ALA 54 n 56 ALA 54 A ASP 55 n 57 ASP 55 A ARG 56 n 58 ARG 56 A LYS 57 n 59 LYS 57 A SER 58 n 60 SER 58 A CYS 59 n 61 CYS 59 A TYR 60 n 62 TYR 60 A VAL 61 n 63 VAL 61 A SER 62 n 64 SER 62 A VAL 63 n 65 VAL 63 A CYS 64 n 66 CYS 64 A GLY 65 n 67 GLY 65 A GLN 66 n 68 GLN 66 A GLU 67 n 69 GLU 67 A SER 68 n 70 SER 68 A TRP 69 n 71 TRP 69 A GLN 70 n 72 GLN 70 A LYS 71 n 73 LYS 71 A PRO 72 n 74 PRO 72 A TRP 73 n 75 TRP 73 A ARG 74 n 76 ARG 74 A ASP 75 n 77 ASP 75 A ARG 76 n 78 ARG 76 A ILE 77 n 79 ILE 77 A THR 78 n 80 THR 78 A ILE 79 n 81 ILE 79 A ALA 80 n 82 ALA 80 A ILE 81 n 83 ILE 81 A ALA 82 n 84 ALA 82 A PRO 83 n 85 PRO 83 A THR 84 n 86 THR 84 A LYS 85 n 87 LYS 85 A GLN 86 n 88 GLN 86 A SER 87 n 89 SER 87 A GLU 88 n 90 GLU 88 A ARG 89 n 91 ARG 89 A MSE 90 n 92 MSE 90 A GLU 91 n 93 GLU 91 A TRP 92 n 94 TRP 92 A MSE 93 n 95 MSE 93 A LEU 94 n 96 LEU 94 A GLU 95 n 97 GLU 95 A LYS 96 n 98 LYS 96 A LEU 97 n 99 LEU 97 A VAL 98 n 100 VAL 98 A GLU 99 n 101 GLU 99 A ILE 100 n 102 ILE 100 A GLY 101 n 103 GLY 101 A VAL 102 n 104 VAL 102 A ASP 103 n 105 ASP 103 A GLU 104 n 106 GLU 104 A VAL 105 n 107 VAL 105 A VAL 106 n 108 VAL 106 A PHE 107 n 109 PHE 107 A ILE 108 n 110 ILE 108 A GLU 109 n 111 GLU 109 A SER 110 n 112 SER 110 A GLU 111 n 113 GLU 111 A HIS 112 n 114 HIS 112 A SER 113 n 115 SER 113 A GLU 114 n 116 GLU 114 A ARG 115 n 117 ARG 115 A ARG 116 n 118 ARG 116 A ARG 117 n 119 ARG 117 A ILE 118 n 120 ILE 118 A LYS 119 n 121 LYS 119 A ALA 120 n 122 ALA 120 A GLU 121 n 123 GLU 121 A ARG 122 n 124 ARG 122 A LEU 123 n 125 LEU 123 A GLU 124 n 126 GLU 124 A ARG 125 n 127 ARG 125 A ILE 126 n 128 ILE 126 A ALA 127 n 129 ALA 127 A ILE 128 n 130 ILE 128 A SER 129 n 131 SER 129 A ALA 130 n 132 ALA 130 A MSE 131 n 133 MSE 131 A LYS 132 n 134 LYS 132 A GLN 133 n 135 GLN 133 A SER 134 n 136 SER 134 A LEU 135 n 137 LEU 135 A LYS 136 n 138 LYS 136 A ALA 137 n 139 ALA 137 A SER 138 n 140 SER 138 A PHE 139 n 141 PHE 139 A PRO 140 n 142 PRO 140 A VAL 141 n 143 VAL 141 A ILE 142 n 144 ILE 142 A ARG 143 n 145 ARG 143 A VAL 144 n 146 VAL 144 A ASN 145 n 147 ASN 145 A ILE 146 n 148 ILE 146 A PRO 147 n 149 PRO 147 A ILE 148 n 150 ILE 148 A GLN 149 n 151 GLN 149 A THR 150 n 152 THR 150 A VAL 151 n 153 VAL 151 A ILE 152 n 154 ILE 152 A ALA 153 n 155 ALA 153 A ASP 154 n 156 ASP 154 A THR 155 n 157 THR 155 A PRO 156 n 158 PRO 156 A LYS 157 n 159 LYS 157 A ALA 158 n 160 ALA 158 A ALA 159 n 161 ALA 159 A VAL 160 n 162 VAL 160 A ARG 161 n 163 ARG 161 A LEU 162 n 164 LEU 162 A ILE 163 n 165 ILE 163 A ALA 164 n 166 ALA 164 A TYR 165 n 167 TYR 165 A VAL 166 n 168 VAL 166 A ASP 167 n 169 ASP 167 A GLU 168 n 170 GLU 168 A ALA 169 n 171 ALA 169 A VAL 170 n 172 VAL 170 A ARG 171 n 173 ARG 171 A n 174 172 A n 175 173 A n 176 174 A n 177 175 A n 178 176 A GLY 177 n 179 GLY 177 A ARG 178 n 180 ARG 178 A GLY 179 n 181 GLY 179 A TYR 180 n 182 TYR 180 A PRO 181 n 183 PRO 181 A SER 182 n 184 SER 182 A ASP 183 n 185 ASP 183 A PHE 184 n 186 PHE 184 A TYR 185 n 187 TYR 185 A HIS 186 n 188 HIS 186 A VAL 187 n 189 VAL 187 A GLY 188 n 190 GLY 188 A GLN 189 n 191 GLN 189 A ASP 190 n 192 ASP 190 A VAL 191 n 193 VAL 191 A LEU 192 n 194 LEU 192 A ILE 193 n 195 ILE 193 A LEU 194 n 196 LEU 194 A ILE 195 n 197 ILE 195 A GLY 196 n 198 GLY 196 A PRO 197 n 199 PRO 197 A GLU 198 n 200 GLU 198 A GLY 199 n 201 GLY 199 A ASP 200 n 202 ASP 200 A PHE 201 n 203 PHE 201 A SER 202 n 204 SER 202 A PRO 203 n 205 PRO 203 A SER 204 n 206 SER 204 A GLU 205 n 207 GLU 205 A VAL 206 n 208 VAL 206 A GLU 207 n 209 GLU 207 A SER 208 n 210 SER 208 A ALA 209 n 211 ALA 209 A LEU 210 n 212 LEU 210 A LEU 211 n 213 LEU 211 A ALA 212 n 214 ALA 212 A GLY 213 n 215 GLY 213 A PHE 214 n 216 PHE 214 A ALA 215 n 217 ALA 215 A PRO 216 n 218 PRO 216 A VAL 217 n 219 VAL 217 A SER 218 n 220 SER 218 A LEU 219 n 221 LEU 219 A GLY 220 n 222 GLY 220 A GLU 221 n 223 GLU 221 A SER 222 n 224 SER 222 A ARG 223 n 225 ARG 223 A LEU 224 n 226 LEU 224 A ARG 225 n 227 ARG 225 A THR 226 n 228 THR 226 A GLU 227 n 229 GLU 227 A THR 228 n 230 THR 228 A ALA 229 n 231 ALA 229 A GLY 230 n 232 GLY 230 A LEU 231 n 233 LEU 231 A VAL 232 n 234 VAL 232 A ALA 233 n 235 ALA 233 A CYS 234 n 236 CYS 234 A GLN 235 n 237 GLN 235 A TRP 236 n 238 TRP 236 A ILE 237 n 239 ILE 237 A HIS 238 n 240 HIS 238 A THR 239 n 241 THR 239 A LEU 240 n 242 LEU 240 A GLN 241 n 243 GLN 241 A ALA 242 n 244 ALA 242 A CYS 243 n 245 CYS 243 A TYR 244 n 246 TYR 244 A ARG 245 n 247 ARG 245 A ILE 246 n 248 ILE 246 A GLY 247 n 249 GLY 247 A n 250 248 A n 251 249 A n 252 250 A n 253 251 A n 254 252 A n 255 253 A n 256 254 A n 257 255 A n 1 -1 B n 2 0 B n 3 1 B n 4 2 B LEU 3 n 5 LEU 3 B PRO 4 n 6 PRO 4 B LEU 5 n 7 LEU 5 B PHE 6 n 8 PHE 6 B TYR 7 n 9 TYR 7 B ALA 8 n 10 ALA 8 B PRO 9 n 11 PRO 9 B ASP 10 n 12 ASP 10 B ILE 11 n 13 ILE 11 B GLU 12 n 14 GLU 12 B GLN 13 n 15 GLN 13 B SER 14 n 16 SER 14 B ASP 15 n 17 ASP 15 B ARG 16 n 18 ARG 16 B LEU 17 n 19 LEU 17 B PRO 18 n 20 PRO 18 B ASP 19 n 21 ASP 19 B ASP 20 n 22 ASP 20 B GLU 21 n 23 GLU 21 B ALA 22 n 24 ALA 22 B GLY 23 n 25 GLY 23 B HIS 24 n 26 HIS 24 B ILE 25 n 27 ILE 25 B LEU 26 n 28 LEU 26 B ARG 27 n 29 ARG 27 B VAL 28 n 30 VAL 28 B LEU 29 n 31 LEU 29 B ARG 30 n 32 ARG 30 B MSE 31 n 33 MSE 31 B GLN 32 n 34 GLN 32 B ALA 33 n 35 ALA 33 B GLY 34 n 36 GLY 34 B ASP 35 n 37 ASP 35 B ARG 36 n 38 ARG 36 B LEU 37 n 39 LEU 37 B ARG 38 n 40 ARG 38 B LEU 39 n 41 LEU 39 B THR 40 n 42 THR 40 B ASP 41 n 43 ASP 41 B GLY 42 n 44 GLY 42 B ARG 43 n 45 ARG 43 B GLY 44 n 46 GLY 44 B SER 45 n 47 SER 45 B PHE 46 n 48 PHE 46 B PHE 47 n 49 PHE 47 B ASP 48 n 50 ASP 48 B ALA 49 n 51 ALA 49 B VAL 50 n 52 VAL 50 B ILE 51 n 53 ILE 51 B GLU 52 n 54 GLU 52 B THR 53 n 55 THR 53 B ALA 54 n 56 ALA 54 B ASP 55 n 57 ASP 55 B ARG 56 n 58 ARG 56 B LYS 57 n 59 LYS 57 B SER 58 n 60 SER 58 B CYS 59 n 61 CYS 59 B TYR 60 n 62 TYR 60 B VAL 61 n 63 VAL 61 B SER 62 n 64 SER 62 B VAL 63 n 65 VAL 63 B CYS 64 n 66 CYS 64 B GLY 65 n 67 GLY 65 B GLN 66 n 68 GLN 66 B GLU 67 n 69 GLU 67 B SER 68 n 70 SER 68 B TRP 69 n 71 TRP 69 B GLN 70 n 72 GLN 70 B LYS 71 n 73 LYS 71 B PRO 72 n 74 PRO 72 B TRP 73 n 75 TRP 73 B ARG 74 n 76 ARG 74 B ASP 75 n 77 ASP 75 B ARG 76 n 78 ARG 76 B ILE 77 n 79 ILE 77 B THR 78 n 80 THR 78 B ILE 79 n 81 ILE 79 B ALA 80 n 82 ALA 80 B ILE 81 n 83 ILE 81 B ALA 82 n 84 ALA 82 B PRO 83 n 85 PRO 83 B THR 84 n 86 THR 84 B LYS 85 n 87 LYS 85 B GLN 86 n 88 GLN 86 B SER 87 n 89 SER 87 B GLU 88 n 90 GLU 88 B ARG 89 n 91 ARG 89 B MSE 90 n 92 MSE 90 B GLU 91 n 93 GLU 91 B TRP 92 n 94 TRP 92 B MSE 93 n 95 MSE 93 B LEU 94 n 96 LEU 94 B GLU 95 n 97 GLU 95 B LYS 96 n 98 LYS 96 B LEU 97 n 99 LEU 97 B VAL 98 n 100 VAL 98 B GLU 99 n 101 GLU 99 B ILE 100 n 102 ILE 100 B GLY 101 n 103 GLY 101 B VAL 102 n 104 VAL 102 B ASP 103 n 105 ASP 103 B GLU 104 n 106 GLU 104 B VAL 105 n 107 VAL 105 B VAL 106 n 108 VAL 106 B PHE 107 n 109 PHE 107 B ILE 108 n 110 ILE 108 B GLU 109 n 111 GLU 109 B SER 110 n 112 SER 110 B GLU 111 n 113 GLU 111 B HIS 112 n 114 HIS 112 B SER 113 n 115 SER 113 B GLU 114 n 116 GLU 114 B ARG 115 n 117 ARG 115 B ARG 116 n 118 ARG 116 B ARG 117 n 119 ARG 117 B ILE 118 n 120 ILE 118 B LYS 119 n 121 LYS 119 B ALA 120 n 122 ALA 120 B GLU 121 n 123 GLU 121 B ARG 122 n 124 ARG 122 B LEU 123 n 125 LEU 123 B GLU 124 n 126 GLU 124 B ARG 125 n 127 ARG 125 B ILE 126 n 128 ILE 126 B ALA 127 n 129 ALA 127 B ILE 128 n 130 ILE 128 B SER 129 n 131 SER 129 B ALA 130 n 132 ALA 130 B MSE 131 n 133 MSE 131 B LYS 132 n 134 LYS 132 B GLN 133 n 135 GLN 133 B SER 134 n 136 SER 134 B LEU 135 n 137 LEU 135 B LYS 136 n 138 LYS 136 B ALA 137 n 139 ALA 137 B SER 138 n 140 SER 138 B PHE 139 n 141 PHE 139 B PRO 140 n 142 PRO 140 B VAL 141 n 143 VAL 141 B ILE 142 n 144 ILE 142 B ARG 143 n 145 ARG 143 B VAL 144 n 146 VAL 144 B ASN 145 n 147 ASN 145 B ILE 146 n 148 ILE 146 B PRO 147 n 149 PRO 147 B ILE 148 n 150 ILE 148 B GLN 149 n 151 GLN 149 B THR 150 n 152 THR 150 B VAL 151 n 153 VAL 151 B ILE 152 n 154 ILE 152 B ALA 153 n 155 ALA 153 B ASP 154 n 156 ASP 154 B THR 155 n 157 THR 155 B PRO 156 n 158 PRO 156 B LYS 157 n 159 LYS 157 B ALA 158 n 160 ALA 158 B ALA 159 n 161 ALA 159 B VAL 160 n 162 VAL 160 B ARG 161 n 163 ARG 161 B LEU 162 n 164 LEU 162 B ILE 163 n 165 ILE 163 B ALA 164 n 166 ALA 164 B TYR 165 n 167 TYR 165 B VAL 166 n 168 VAL 166 B ASP 167 n 169 ASP 167 B GLU 168 n 170 GLU 168 B ALA 169 n 171 ALA 169 B VAL 170 n 172 VAL 170 B ARG 171 n 173 ARG 171 B n 174 172 B n 175 173 B n 176 174 B n 177 175 B n 178 176 B GLY 177 n 179 GLY 177 B ARG 178 n 180 ARG 178 B GLY 179 n 181 GLY 179 B TYR 180 n 182 TYR 180 B PRO 181 n 183 PRO 181 B SER 182 n 184 SER 182 B ASP 183 n 185 ASP 183 B PHE 184 n 186 PHE 184 B TYR 185 n 187 TYR 185 B HIS 186 n 188 HIS 186 B VAL 187 n 189 VAL 187 B GLY 188 n 190 GLY 188 B GLN 189 n 191 GLN 189 B ASP 190 n 192 ASP 190 B VAL 191 n 193 VAL 191 B LEU 192 n 194 LEU 192 B ILE 193 n 195 ILE 193 B LEU 194 n 196 LEU 194 B ILE 195 n 197 ILE 195 B GLY 196 n 198 GLY 196 B PRO 197 n 199 PRO 197 B GLU 198 n 200 GLU 198 B GLY 199 n 201 GLY 199 B ASP 200 n 202 ASP 200 B PHE 201 n 203 PHE 201 B SER 202 n 204 SER 202 B PRO 203 n 205 PRO 203 B SER 204 n 206 SER 204 B GLU 205 n 207 GLU 205 B VAL 206 n 208 VAL 206 B GLU 207 n 209 GLU 207 B SER 208 n 210 SER 208 B ALA 209 n 211 ALA 209 B LEU 210 n 212 LEU 210 B LEU 211 n 213 LEU 211 B ALA 212 n 214 ALA 212 B GLY 213 n 215 GLY 213 B PHE 214 n 216 PHE 214 B ALA 215 n 217 ALA 215 B PRO 216 n 218 PRO 216 B VAL 217 n 219 VAL 217 B SER 218 n 220 SER 218 B LEU 219 n 221 LEU 219 B GLY 220 n 222 GLY 220 B GLU 221 n 223 GLU 221 B SER 222 n 224 SER 222 B ARG 223 n 225 ARG 223 B LEU 224 n 226 LEU 224 B ARG 225 n 227 ARG 225 B THR 226 n 228 THR 226 B GLU 227 n 229 GLU 227 B THR 228 n 230 THR 228 B ALA 229 n 231 ALA 229 B GLY 230 n 232 GLY 230 B LEU 231 n 233 LEU 231 B VAL 232 n 234 VAL 232 B ALA 233 n 235 ALA 233 B CYS 234 n 236 CYS 234 B GLN 235 n 237 GLN 235 B TRP 236 n 238 TRP 236 B ILE 237 n 239 ILE 237 B HIS 238 n 240 HIS 238 B THR 239 n 241 THR 239 B LEU 240 n 242 LEU 240 B GLN 241 n 243 GLN 241 B ALA 242 n 244 ALA 242 B CYS 243 n 245 CYS 243 B TYR 244 n 246 TYR 244 B ARG 245 n 247 ARG 245 B n 248 246 B n 249 247 B n 250 248 B n 251 249 B n 252 250 B n 253 251 B n 254 252 B n 255 253 B n 256 254 B n 257 255 B software_defined_assembly PISA 2 dimeric 3990 -9 22300 A MSE 31 SELENOMETHIONINE A MSE 33 MET A MSE 90 SELENOMETHIONINE A MSE 92 MET A MSE 93 SELENOMETHIONINE A MSE 95 MET A MSE 131 SELENOMETHIONINE A MSE 133 MET B MSE 31 SELENOMETHIONINE B MSE 33 MET B MSE 90 SELENOMETHIONINE B MSE 92 MET B MSE 93 SELENOMETHIONINE B MSE 95 MET B MSE 131 SELENOMETHIONINE B MSE 133 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 A N PHE 6 A N PHE 8 A O ARG 38 A O ARG 40 A N LEU 37 A N LEU 39 A O ALA 49 A O ALA 51 A N PHE 46 A N PHE 48 A O GLU 67 A O GLU 69 A O ARG 143 A O ARG 145 A N PHE 107 A N PHE 109 A O VAL 106 A O VAL 108 A N ILE 81 A N ILE 83 A N ALA 80 A N ALA 82 A O ILE 193 A O ILE 195 A O LEU 192 A O LEU 194 A N LEU 162 A N LEU 164 A N ILE 163 A N ILE 165 A O ALA 215 A O ALA 217 B N PHE 6 B N PHE 8 B O ARG 38 B O ARG 40 B N LEU 37 B N LEU 39 B O ALA 49 B O ALA 51 B N GLU 52 B N GLU 54 B O TYR 60 B O TYR 62 B O ARG 143 B O ARG 145 B N PHE 107 B N PHE 109 B O VAL 106 B O VAL 108 B N ILE 81 B N ILE 83 B N ALA 80 B N ALA 82 B O ILE 195 B O ILE 197 B O LEU 194 B O LEU 196 B N LEU 162 B N LEU 164 B N ARG 161 B N ARG 163 B O ALA 215 B O ALA 217 1 A NE ARG 171 A NE ARG 173 1 Y 1 A CZ ARG 171 A CZ ARG 173 1 Y 1 A NH1 ARG 171 A NH1 ARG 173 1 Y 1 A NH2 ARG 171 A NH2 ARG 173 1 Y 1 B CG LEU 3 B CG LEU 5 1 Y 1 B CD1 LEU 3 B CD1 LEU 5 1 Y 1 B CD2 LEU 3 B CD2 LEU 5 1 Y 1 B CD1 TYR 244 B CD1 TYR 246 1 Y 1 B CD2 TYR 244 B CD2 TYR 246 1 Y 1 B CE1 TYR 244 B CE1 TYR 246 1 Y 1 B CE2 TYR 244 B CE2 TYR 246 1 Y 1 B CZ TYR 244 B CZ TYR 246 1 Y 1 B OH TYR 244 B OH TYR 246 1 Y 1 B CZ ARG 245 B CZ ARG 247 1 Y 1 B NH1 ARG 245 B NH1 ARG 247 1 Y 1 B NH2 ARG 245 B NH2 ARG 247 1 Y 1 A MSE -1 A MSE 1 1 Y 1 A SER 0 A SER 2 1 Y 1 A LEU 1 A LEU 3 1 Y 1 A SER 2 A SER 4 1 Y 1 A ALA 172 A ALA 174 1 Y 1 A GLU 173 A GLU 175 1 Y 1 A ILE 174 A ILE 176 1 Y 1 A THR 175 A THR 177 1 Y 1 A GLN 176 A GLN 178 1 Y 1 A GLU 248 A GLU 250 1 Y 1 A GLY 249 A GLY 251 1 Y 1 A HIS 250 A HIS 252 1 Y 1 A HIS 251 A HIS 253 1 Y 1 A HIS 252 A HIS 254 1 Y 1 A HIS 253 A HIS 255 1 Y 1 A HIS 254 A HIS 256 1 Y 1 A HIS 255 A HIS 257 1 Y 1 B MSE -1 B MSE 1 1 Y 1 B SER 0 B SER 2 1 Y 1 B LEU 1 B LEU 3 1 Y 1 B SER 2 B SER 4 1 Y 1 B ALA 172 B ALA 174 1 Y 1 B GLU 173 B GLU 175 1 Y 1 B ILE 174 B ILE 176 1 Y 1 B THR 175 B THR 177 1 Y 1 B GLN 176 B GLN 178 1 Y 1 B ILE 246 B ILE 248 1 Y 1 B GLY 247 B GLY 249 1 Y 1 B GLU 248 B GLU 250 1 Y 1 B GLY 249 B GLY 251 1 Y 1 B HIS 250 B HIS 252 1 Y 1 B HIS 251 B HIS 253 1 Y 1 B HIS 252 B HIS 254 1 Y 1 B HIS 253 B HIS 255 1 Y 1 B HIS 254 B HIS 256 1 Y 1 B HIS 255 B HIS 257 1 Y 1 9.32 1.50 119.30 128.62 A A A C N CA LEU PRO PRO 3 4 4 Y 1 -13.11 2.10 128.40 115.29 A A A C N CD LEU PRO PRO 3 4 4 Y 1 A PRO 4 -35.35 147.46 1 A ASP 75 72.74 -176.76 1 A ASP 75 72.74 -175.27 1 A VAL 166 -126.27 -53.11 1 A VAL 170 -66.71 80.49 1 A ARG 178 -93.04 -66.90 1 A ASP 200 63.28 171.70 1 B PRO 72 -79.70 24.13 1 B ASP 75 63.71 -171.17 1 B PHE 184 -132.64 -30.48 1 B ASP 200 71.52 169.87 68.36 32.555 13.91 -0.650 0.000 0.000 0.900 0.000 -0.250 0.947 0.913 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY 0.266 0.210 0.213 2.000 50 1723 33986 5.100 99.810 0.266 0.210 1.00 0.30 0.826 4.470 0.127 0.212 0.190 RANDOM 1 THROUGHOUT 0.00 SAD 0.212 0.190 0.800 0.800 1.400 MAXIMUM LIKELIHOOD MASK 2.000 50 136 3994 38 0 3820 0.016 0.022 3939 1.491 1.977 5343 6.324 5.000 486 33.305 22.652 181 16.542 15.000 684 17.017 15.000 45 0.103 0.200 597 0.008 0.021 2987 0.974 1.500 2417 1.785 2.000 3913 2.571 3.000 1522 4.320 4.500 1430 0.267 0.252 2.052 127 2287 2414 20 97.570 2.000 50 3KW2 34052 34052 0.102 0.146 1 19 11.6 100 0.9 2.0 2.07 2.6 0.82 11.7 100 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.005 data collection CBASS data reduction HKL-2000 data scaling HKL-2000 phasing PHENIX Probable r-RNA methyltransferase Crystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N A PRO 18 A PRO 20 HELX_P A ARG 27 A ARG 29 1 1 10 A GLN 86 A GLN 88 HELX_P A GLY 101 A GLY 103 1 2 16 A LYS 119 A LYS 121 HELX_P A SER 134 A SER 136 1 3 16 A ILE 148 A ILE 150 HELX_P A THR 155 A THR 157 1 4 8 A TYR 180 A TYR 182 HELX_P A PHE 184 A PHE 186 5 5 5 A SER 202 A SER 204 HELX_P A GLY 213 A GLY 215 1 6 12 A ARG 225 A ARG 227 HELX_P A TYR 244 A TYR 246 1 7 20 B PRO 18 B PRO 20 HELX_P B ARG 27 B ARG 29 1 8 10 B GLN 86 B GLN 88 HELX_P B GLY 101 B GLY 103 1 9 16 B LYS 119 B LYS 121 HELX_P B SER 134 B SER 136 1 10 16 B ILE 148 B ILE 150 HELX_P B THR 155 B THR 157 1 11 8 B TYR 180 B TYR 182 HELX_P B PHE 184 B PHE 186 5 12 5 B SER 202 B SER 204 HELX_P B GLY 213 B GLY 215 1 13 12 B ARG 225 B ARG 227 HELX_P B TYR 244 B TYR 246 1 14 20 covale 1.331 both A ARG 30 A C ARG 32 1_555 A MSE 31 A N MSE 33 1_555 covale 1.331 both A MSE 31 A C MSE 33 1_555 A GLN 32 A N GLN 34 1_555 covale 1.336 both A ARG 89 A C ARG 91 1_555 A MSE 90 A N MSE 92 1_555 covale 1.330 both A MSE 90 A C MSE 92 1_555 A GLU 91 A N GLU 93 1_555 covale 1.328 both A TRP 92 A C TRP 94 1_555 A MSE 93 A N MSE 95 1_555 covale 1.323 both A MSE 93 A C MSE 95 1_555 A LEU 94 A N LEU 96 1_555 covale 1.326 both A ALA 130 A C ALA 132 1_555 A MSE 131 A N MSE 133 1_555 covale 1.323 both A MSE 131 A C MSE 133 1_555 A LYS 132 A N LYS 134 1_555 covale 1.327 both B ARG 30 B C ARG 32 1_555 B MSE 31 B N MSE 33 1_555 covale 1.325 both B MSE 31 B C MSE 33 1_555 B GLN 32 B N GLN 34 1_555 covale 1.326 both A B ARG 89 B C ARG 91 1_555 B MSE 90 B N MSE 92 1_555 covale 1.331 both B B ARG 89 B C ARG 91 1_555 B MSE 90 B N MSE 92 1_555 covale 1.330 both A B MSE 90 B C MSE 92 1_555 B GLU 91 B N GLU 93 1_555 covale 1.333 both B B MSE 90 B C MSE 92 1_555 B GLU 91 B N GLU 93 1_555 covale 1.325 both B TRP 92 B C TRP 94 1_555 B MSE 93 B N MSE 95 1_555 covale 1.316 both B MSE 93 B C MSE 95 1_555 B LEU 94 B N LEU 96 1_555 covale 1.327 both B ALA 130 B C ALA 132 1_555 B MSE 131 B N MSE 133 1_555 covale 1.337 both B MSE 131 B C MSE 133 1_555 B LYS 132 B N LYS 134 1_555 TRANSFERASE structural genomics, unknown function, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, TRANSFERASE B2RH75_PORG3 UNP 1 2 B2RH75 SLPLFYAPDIEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAI APTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAMKQSLKASFPVIRVNIPIQTVIADTPKAAVR LIAYVDEAVRAEITQGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQ ACYRIGE 2 248 3KW2 2 248 B2RH75 A 1 4 250 2 248 3KW2 2 248 B2RH75 B 1 4 250 1 expression tag MSE -1 3KW2 A B2RH75 UNP 1 1 expression tag SER 0 3KW2 A B2RH75 UNP 2 1 expression tag LEU 1 3KW2 A B2RH75 UNP 3 1 expression tag GLY 249 3KW2 A B2RH75 UNP 251 1 expression tag HIS 250 3KW2 A B2RH75 UNP 252 1 expression tag HIS 251 3KW2 A B2RH75 UNP 253 1 expression tag HIS 252 3KW2 A B2RH75 UNP 254 1 expression tag HIS 253 3KW2 A B2RH75 UNP 255 1 expression tag HIS 254 3KW2 A B2RH75 UNP 256 1 expression tag HIS 255 3KW2 A B2RH75 UNP 257 2 expression tag MSE -1 3KW2 B B2RH75 UNP 1 2 expression tag SER 0 3KW2 B B2RH75 UNP 2 2 expression tag LEU 1 3KW2 B B2RH75 UNP 3 2 expression tag GLY 249 3KW2 B B2RH75 UNP 251 2 expression tag HIS 250 3KW2 B B2RH75 UNP 252 2 expression tag HIS 251 3KW2 B B2RH75 UNP 253 2 expression tag HIS 252 3KW2 B B2RH75 UNP 254 2 expression tag HIS 253 3KW2 B B2RH75 UNP 255 2 expression tag HIS 254 3KW2 B B2RH75 UNP 256 2 expression tag HIS 255 3KW2 B B2RH75 UNP 257 4 6 4 6 parallel anti-parallel anti-parallel parallel parallel parallel parallel parallel parallel anti-parallel anti-parallel parallel parallel parallel parallel parallel A LEU 5 A LEU 7 A TYR 7 A TYR 9 A ARG 36 A ARG 38 A THR 40 A THR 42 A SER 45 A SER 47 A ALA 54 A ALA 56 A CYS 59 A CYS 61 A SER 68 A SER 70 A VAL 141 A VAL 143 A PRO 147 A PRO 149 A GLU 104 A GLU 106 A GLU 109 A GLU 111 A ILE 77 A ILE 79 A ILE 81 A ILE 83 A VAL 191 A VAL 193 A ILE 195 A ILE 197 A VAL 160 A VAL 162 A ALA 164 A ALA 166 A ALA 215 A ALA 217 A VAL 217 A VAL 219 B LEU 5 B LEU 7 B TYR 7 B TYR 9 B ARG 36 B ARG 38 B THR 40 B THR 42 B SER 45 B SER 47 B ALA 54 B ALA 56 B CYS 59 B CYS 61 B SER 68 B SER 70 B VAL 141 B VAL 143 B PRO 147 B PRO 149 B GLU 104 B GLU 106 B GLU 109 B GLU 111 B ILE 77 B ILE 79 B ILE 81 B ILE 83 B VAL 191 B VAL 193 B ILE 195 B ILE 197 B VAL 160 B VAL 162 B ALA 164 B ALA 166 B ALA 215 B ALA 217 B VAL 217 B VAL 219 BINDING SITE FOR RESIDUE ADN A 300 A ADN 300 Software 15 BINDING SITE FOR RESIDUE ADN B 300 B ADN 300 Software 14 A ALA 164 A ALA 166 15 1_555 A TYR 165 A TYR 167 15 1_555 A VAL 166 A VAL 168 15 1_555 A ARG 178 A ARG 180 15 1_555 A ILE 195 A ILE 197 15 1_555 A GLY 196 A GLY 198 15 1_555 A PRO 197 A PRO 199 15 1_555 A ASP 200 A ASP 202 15 1_555 A SER 218 A SER 220 15 1_555 A LEU 219 A LEU 221 15 1_555 A GLY 220 A GLY 222 15 1_555 A SER 222 A SER 224 15 1_555 A LEU 224 A LEU 226 15 1_555 A THR 226 A THR 228 15 1_555 A ALA 229 A ALA 231 15 1_555 B ALA 164 B ALA 166 14 1_555 B TYR 165 B TYR 167 14 1_555 B ARG 178 B ARG 180 14 1_555 B ILE 195 B ILE 197 14 1_555 B GLY 196 B GLY 198 14 1_555 B PRO 197 B PRO 199 14 1_555 B ASP 200 B ASP 202 14 1_555 B VAL 217 B VAL 219 14 1_555 B SER 218 B SER 220 14 1_555 B LEU 219 B LEU 221 14 1_555 B GLY 220 B GLY 222 14 1_555 B LEU 224 B LEU 226 14 1_555 B THR 226 B THR 228 14 1_555 B ALA 229 B ALA 231 14 1_555 19 P 21 21 21