0.010669 0.000000 0.004485 0.000000 0.026867 0.000000 0.000000 0.000000 0.019274 0.00000 0.00000 0.00000 Van Roey, P. Silva, G.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 112.80 90.00 93.730 37.220 56.280 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 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 S 149.211 y METHIONINE 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 286 1123 1136 10.1006/jmbi.1998.2519 10047486 Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. 1999 10.2210/pdb1b24/pdb pdb_00001b24 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD 1997-09 BRANDEIS MAD M x-ray 1 0.9300 1.0 0.9785 1.0 0.9789 1.0 X12C NSLS 0.9300,0.9785,0.9789 SYNCHROTRON NSLS BEAMLINE X12C SELENOMETHIONYL PROTEIN 22181.473 Homing endonuclease I-DmoI 3.1.-.- 1 man polymer 18.015 water 78 nat water no yes MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPL(MSE)QFLIDELNVKSKIQIVKGDT RYELRVSSKKLYYYFAN(MSE)LERIRLFN(MSE)REQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVR NTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPPE MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYEL RVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGV YVLNISLRDRIKFVHTILSSHLNPLPPE A 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 Desulfurococcus Escherichia sample 1 SELENOMETHIONINE AUXOTROPH 188 2275 Desulfurococcus mobilis 562 Escherichia coli DL41(DE3) Biological sequence 1 2.01 33.3 MAD DATA TREATED AS A SPECIAL CASE OF MIR VAPOR DIFFUSION, HANGING DROP 8.5 HANGING DROP VAPOR-DIFFUSION METHOD: 4UL I-DMOI PROTEIN 1UL 20MM N-OCTYL-B- GLUCOPYRANOSIDE 4UL PRECIPITATING BUFFER: 30% PEG 3350 200MM SODIUM ACETATE 100MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP 4UL I-DMOI PROTEIN 1 1UL 20MM N-OCTYL-B-GLUCOPYRANOSIDE 2 4UL PRECIPITATING BUFFER 2 30% PEG 3350 2 200MM SODIUM ACETATE 2 100MM TRIS-HCL PH 8.5 2 database_2 entity entity_src_gen pdbx_struct_mod_residue struct_conn struct_ref struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Database references Derived calculations Source and taxonomy Structure summary 1 0 1999-03-24 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-12-21 _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _entity.pdbx_ec _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_seq_type _pdbx_struct_mod_residue.details _struct_conn.pdbx_leaving_atom_flag _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code BNL Y RCSB 1998-12-03 REL REL HOH water HOH 1 2 HOH HOH 189 A HOH 2 2 HOH HOH 190 A HOH 6 2 HOH HOH 191 A HOH 9 2 HOH HOH 192 A HOH 12 2 HOH HOH 193 A HOH 13 2 HOH HOH 194 A HOH 14 2 HOH HOH 195 A HOH 15 2 HOH HOH 196 A HOH 16 2 HOH HOH 197 A HOH 17 2 HOH HOH 198 A HOH 20 2 HOH HOH 199 A HOH 22 2 HOH HOH 200 A HOH 23 2 HOH HOH 201 A HOH 24 2 HOH HOH 202 A HOH 25 2 HOH HOH 203 A HOH 26 2 HOH HOH 204 A HOH 28 2 HOH HOH 205 A HOH 30 2 HOH HOH 206 A HOH 31 2 HOH HOH 207 A HOH 33 2 HOH HOH 208 A HOH 36 2 HOH HOH 209 A HOH 37 2 HOH HOH 210 A HOH 38 2 HOH HOH 211 A HOH 40 2 HOH HOH 212 A HOH 43 2 HOH HOH 213 A HOH 45 2 HOH HOH 214 A HOH 47 2 HOH HOH 215 A HOH 48 2 HOH HOH 216 A HOH 49 2 HOH HOH 217 A HOH 50 2 HOH HOH 218 A HOH 51 2 HOH HOH 219 A HOH 52 2 HOH HOH 220 A HOH 54 2 HOH HOH 221 A HOH 55 2 HOH HOH 222 A HOH 56 2 HOH HOH 223 A HOH 58 2 HOH HOH 224 A HOH 59 2 HOH HOH 225 A HOH 60 2 HOH HOH 226 A HOH 61 2 HOH HOH 227 A HOH 62 2 HOH HOH 228 A HOH 63 2 HOH HOH 229 A HOH 65 2 HOH HOH 230 A HOH 66 2 HOH HOH 231 A HOH 67 2 HOH HOH 232 A HOH 68 2 HOH HOH 233 A HOH 71 2 HOH HOH 234 A HOH 72 2 HOH HOH 235 A HOH 73 2 HOH HOH 236 A HOH 74 2 HOH HOH 237 A HOH 75 2 HOH HOH 238 A HOH 76 2 HOH HOH 239 A HOH 80 2 HOH HOH 240 A HOH 81 2 HOH HOH 241 A HOH 82 2 HOH HOH 242 A HOH 83 2 HOH HOH 243 A HOH 87 2 HOH HOH 244 A HOH 91 2 HOH HOH 245 A HOH 92 2 HOH HOH 246 A HOH 93 2 HOH HOH 247 A HOH 94 2 HOH HOH 248 A HOH 95 2 HOH HOH 249 A HOH 96 2 HOH HOH 250 A HOH 100 2 HOH HOH 251 A HOH 101 2 HOH HOH 252 A HOH 102 2 HOH HOH 253 A HOH 103 2 HOH HOH 254 A HOH 104 2 HOH HOH 255 A HOH 106 2 HOH HOH 256 A HOH 107 2 HOH HOH 257 A HOH 108 2 HOH HOH 258 A HOH 109 2 HOH HOH 259 A HOH 111 2 HOH HOH 260 A HOH 112 2 HOH HOH 261 A HOH 113 2 HOH HOH 262 A HOH 116 2 HOH HOH 263 A HOH 117 2 HOH HOH 264 A HOH 118 2 HOH HOH 265 A HOH 119 2 HOH HOH 266 A n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A VAL 7 n 7 VAL 7 A SER 8 n 8 SER 8 A GLY 9 n 9 GLY 9 A ILE 10 n 10 ILE 10 A SER 11 n 11 SER 11 A ALA 12 n 12 ALA 12 A TYR 13 n 13 TYR 13 A LEU 14 n 14 LEU 14 A LEU 15 n 15 LEU 15 A GLY 16 n 16 GLY 16 A LEU 17 n 17 LEU 17 A ILE 18 n 18 ILE 18 A ILE 19 n 19 ILE 19 A GLY 20 n 20 GLY 20 A ASP 21 n 21 ASP 21 A GLY 22 n 22 GLY 22 A GLY 23 n 23 GLY 23 A LEU 24 n 24 LEU 24 A TYR 25 n 25 TYR 25 A LYS 26 n 26 LYS 26 A LEU 27 n 27 LEU 27 A LYS 28 n 28 LYS 28 A TYR 29 n 29 TYR 29 A LYS 30 n 30 LYS 30 A GLY 31 n 31 GLY 31 A ASN 32 n 32 ASN 32 A ARG 33 n 33 ARG 33 A SER 34 n 34 SER 34 A GLU 35 n 35 GLU 35 A TYR 36 n 36 TYR 36 A ARG 37 n 37 ARG 37 A VAL 38 n 38 VAL 38 A VAL 39 n 39 VAL 39 A ILE 40 n 40 ILE 40 A THR 41 n 41 THR 41 A GLN 42 n 42 GLN 42 A LYS 43 n 43 LYS 43 A SER 44 n 44 SER 44 A GLU 45 n 45 GLU 45 A ASN 46 n 46 ASN 46 A LEU 47 n 47 LEU 47 A ILE 48 n 48 ILE 48 A LYS 49 n 49 LYS 49 A GLN 50 n 50 GLN 50 A HIS 51 n 51 HIS 51 A ILE 52 n 52 ILE 52 A ALA 53 n 53 ALA 53 A PRO 54 n 54 PRO 54 A LEU 55 n 55 LEU 55 A MSE 56 n 56 MSE 56 A GLN 57 n 57 GLN 57 A PHE 58 n 58 PHE 58 A LEU 59 n 59 LEU 59 A ILE 60 n 60 ILE 60 A ASP 61 n 61 ASP 61 A GLU 62 n 62 GLU 62 A LEU 63 n 63 LEU 63 A ASN 64 n 64 ASN 64 A VAL 65 n 65 VAL 65 A LYS 66 n 66 LYS 66 A SER 67 n 67 SER 67 A LYS 68 n 68 LYS 68 A ILE 69 n 69 ILE 69 A GLN 70 n 70 GLN 70 A ILE 71 n 71 ILE 71 A VAL 72 n 72 VAL 72 A LYS 73 n 73 LYS 73 A GLY 74 n 74 GLY 74 A ASP 75 n 75 ASP 75 A THR 76 n 76 THR 76 A ARG 77 n 77 ARG 77 A TYR 78 n 78 TYR 78 A GLU 79 n 79 GLU 79 A LEU 80 n 80 LEU 80 A ARG 81 n 81 ARG 81 A VAL 82 n 82 VAL 82 A SER 83 n 83 SER 83 A SER 84 n 84 SER 84 A LYS 85 n 85 LYS 85 A LYS 86 n 86 LYS 86 A LEU 87 n 87 LEU 87 A TYR 88 n 88 TYR 88 A TYR 89 n 89 TYR 89 A TYR 90 n 90 TYR 90 A PHE 91 n 91 PHE 91 A ALA 92 n 92 ALA 92 A ASN 93 n 93 ASN 93 A MSE 94 n 94 MSE 94 A LEU 95 n 95 LEU 95 A GLU 96 n 96 GLU 96 A ARG 97 n 97 ARG 97 A ILE 98 n 98 ILE 98 A ARG 99 n 99 ARG 99 A LEU 100 n 100 LEU 100 A PHE 101 n 101 PHE 101 A ASN 102 n 102 ASN 102 A MSE 103 n 103 MSE 103 A ARG 104 n 104 ARG 104 A GLU 105 n 105 GLU 105 A GLN 106 n 106 GLN 106 A ILE 107 n 107 ILE 107 A ALA 108 n 108 ALA 108 A PHE 109 n 109 PHE 109 A ILE 110 n 110 ILE 110 A LYS 111 n 111 LYS 111 A GLY 112 n 112 GLY 112 A LEU 113 n 113 LEU 113 A TYR 114 n 114 TYR 114 A VAL 115 n 115 VAL 115 A ALA 116 n 116 ALA 116 A GLU 117 n 117 GLU 117 A GLY 118 n 118 GLY 118 A ASP 119 n 119 ASP 119 A LYS 120 n 120 LYS 120 A THR 121 n 121 THR 121 A LEU 122 n 122 LEU 122 A LYS 123 n 123 LYS 123 A ARG 124 n 124 ARG 124 A LEU 125 n 125 LEU 125 A ARG 126 n 126 ARG 126 A ILE 127 n 127 ILE 127 A TRP 128 n 128 TRP 128 A ASN 129 n 129 ASN 129 A LYS 130 n 130 LYS 130 A ASN 131 n 131 ASN 131 A LYS 132 n 132 LYS 132 A ALA 133 n 133 ALA 133 A LEU 134 n 134 LEU 134 A LEU 135 n 135 LEU 135 A GLU 136 n 136 GLU 136 A ILE 137 n 137 ILE 137 A VAL 138 n 138 VAL 138 A SER 139 n 139 SER 139 A ARG 140 n 140 ARG 140 A TRP 141 n 141 TRP 141 A LEU 142 n 142 LEU 142 A ASN 143 n 143 ASN 143 A ASN 144 n 144 ASN 144 A LEU 145 n 145 LEU 145 A GLY 146 n 146 GLY 146 A VAL 147 n 147 VAL 147 A ARG 148 n 148 ARG 148 A ASN 149 n 149 ASN 149 A THR 150 n 150 THR 150 A ILE 151 n 151 ILE 151 A HIS 152 n 152 HIS 152 A LEU 153 n 153 LEU 153 A ASP 154 n 154 ASP 154 A ASP 155 n 155 ASP 155 A HIS 156 n 156 HIS 156 A ARG 157 n 157 ARG 157 A HIS 158 n 158 HIS 158 A GLY 159 n 159 GLY 159 A VAL 160 n 160 VAL 160 A TYR 161 n 161 TYR 161 A VAL 162 n 162 VAL 162 A LEU 163 n 163 LEU 163 A ASN 164 n 164 ASN 164 A ILE 165 n 165 ILE 165 A SER 166 n 166 SER 166 A LEU 167 n 167 LEU 167 A ARG 168 n 168 ARG 168 A ASP 169 n 169 ASP 169 A ARG 170 n 170 ARG 170 A ILE 171 n 171 ILE 171 A LYS 172 n 172 LYS 172 A PHE 173 n 173 PHE 173 A VAL 174 n 174 VAL 174 A HIS 175 n 175 HIS 175 A THR 176 n 176 THR 176 A ILE 177 n 177 ILE 177 A LEU 178 n 178 LEU 178 A SER 179 n 179 SER 179 A n 180 180 A n 181 181 A n 182 182 A n 183 183 A n 184 184 A n 185 185 A n 186 186 A n 187 187 A n 188 188 A author_defined_assembly 1 monomeric A MSE 56 modified residue A MSE 56 MET A MSE 94 modified residue A MSE 94 MET A MSE 103 modified residue A MSE 103 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 O GLY 23 A O GLY 23 A N VAL 39 A N VAL 39 A O VAL 38 A O VAL 38 A N VAL 82 A N VAL 82 A O GLU 79 A O GLU 79 A N VAL 72 A N VAL 72 A O ILE 127 A O ILE 127 A N LEU 163 A N LEU 163 A O VAL 160 A O VAL 160 A N ASP 155 A N ASP 155 1 A CA SER 179 A CA SER 179 1 Y 1 A C SER 179 A C SER 179 1 Y 1 A O SER 179 A O SER 179 1 Y 1 A CB SER 179 A CB SER 179 1 Y 1 A OG SER 179 A OG SER 179 1 Y 1 A MET 1 A MET 1 1 Y 1 A HIS 2 A HIS 2 1 Y 1 A ASN 3 A ASN 3 1 Y 1 A ASN 4 A ASN 4 1 Y 1 A GLU 5 A GLU 5 1 Y 1 A ASN 6 A ASN 6 1 Y 1 A SER 180 A SER 180 1 Y 1 A HIS 181 A HIS 181 1 Y 1 A LEU 182 A LEU 182 1 Y 1 A ASN 183 A ASN 183 1 Y 1 A PRO 184 A PRO 184 1 Y 1 A LEU 185 A LEU 185 1 Y 1 A PRO 186 A PRO 186 1 Y 1 A PRO 187 A PRO 187 1 Y 1 A GLU 188 A GLU 188 1 Y 1 A A O O HOH HOH 210 255 1.86 1 A A O O HOH HOH 229 234 1.88 1 A A O O HOH HOH 237 257 1.95 1 A A O O HOH HOH 203 230 2.03 1 A A O O HOH HOH 230 255 2.19 1 A ASP 21 -158.15 88.02 1 A TYR 29 -91.46 -77.37 1 A HIS 51 -130.99 -62.66 1 A THR 76 84.47 -38.74 1 A ARG 97 -96.58 42.29 PROTEIN_REP.PARAM TOPHCSDX.PRO PARAM19.SOL TOPH19.SOL TOPH19.PEP PARHCSDX.PRO 0.3240000 0.2180000 2.2 10.0 887 8878 10.0 98.7 RANDOM 1 THROUGHOUT 0.0 MAD 2.2 10.0 78 1505 0 0 1427 0.007 1.285 26.23 0.609 0.3613000 0.2996000 2.30 80 737 8 10.0 98.7 2.2 20.0 1B24 8884 0.0 0.059 1 32.3 11.1 98.5 2.20 2.28 24.7 0.070 6 97.4 phasing PHASES refinement X-PLOR 3.851 data reduction DENZO data scaling SCALEPACK I-DMOI, INTRON-ENCODED ENDONUCLEASE 1 N N 2 N N A SER 8 A SER 8 HELX_P A GLY 20 A GLY 20 1 1 13 A GLU 45 A GLU 45 HELX_P A GLN 50 A GLN 50 1 2 6 A PRO 54 A PRO 54 HELX_P A GLU 62 A GLU 62 5 3 9 A LYS 85 A LYS 85 HELX_P A ALA 92 A ALA 92 1 4 8 A ILE 98 A ILE 98 HELX_P A LEU 100 A LEU 100 5 5 3 A GLU 105 A GLU 105 HELX_P A GLU 117 A GLU 117 1 6 13 A LYS 132 A LYS 132 HELX_P A LEU 145 A LEU 145 1 7 14 A LEU 167 A LEU 167 HELX_P A THR 176 A THR 176 5 8 10 covale 1.330 both A LEU 55 A C LEU 55 1_555 A MSE 56 A N MSE 56 1_555 covale 1.330 both A MSE 56 A C MSE 56 1_555 A GLN 57 A N GLN 57 1_555 covale 1.335 both A ASN 93 A C ASN 93 1_555 A MSE 94 A N MSE 94 1_555 covale 1.327 both A MSE 94 A C MSE 94 1_555 A LEU 95 A N LEU 95 1_555 covale 1.323 both A ASN 102 A C ASN 102 1_555 A MSE 103 A N MSE 103 1_555 covale 1.328 both A MSE 103 A C MSE 103 1_555 A ARG 104 A N ARG 104 1_555 INTRON-ENCODED INTRON-ENCODED, ENDONUCLEASE, HOMING, THERMOSTABLE DMO1_DESMO UNP 1 1 P21505 MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYEL RVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGV YVLNISLRDRIKFVHTILSSHLNPLPPE 1 188 1B24 1 188 P21505 A 1 1 188 4 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A GLY 22 A GLY 22 A LYS 28 A LYS 28 A SER 34 A SER 34 A GLN 42 A GLN 42 A TYR 78 A TYR 78 A SER 83 A SER 83 A GLN 70 A GLN 70 A LYS 73 A LYS 73 A ARG 126 A ARG 126 A ASN 129 A ASN 129 A VAL 160 A VAL 160 A ILE 165 A ILE 165 A ASN 149 A ASN 149 A ASP 155 A ASP 155 5 C 1 2 1