Equivalence class NR_all_35054.4 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3IGI|1|A (rep) | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3' | RF01998 | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-ray diffraction | 3.12 | 2009-12-22 | ||
| 2 | 5J02|1|A | Group II catalytic intron D1-D4-1 | GROUP II INTRON LARIAT, 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3') | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-ray diffraction | 3.49 | 2016-12-14 |
| 3 | 4FAX|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-ray diffraction | 3.1 | 2012-11-14 |
| 4 | 4FAR|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 2.86 | 2012-11-14 |
| 5 | 4E8N|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-ray diffraction | 2.96 | 2012-11-14 |
| 6 | 6T3S|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.28 | 2020-05-13 |
| 7 | 4FAU|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-ray diffraction | 2.87 | 2012-11-14 |
| 8 | 4FB0|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.22 | 2012-11-14 |
| 9 | 4E8K|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*CP*G*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-ray diffraction | 3.03 | 2012-11-14 |
| 10 | 4E8Q|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-ray diffraction | 2.84 | 2012-11-14 |
| 11 | 4Y1O|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 2015-10-14 |
| 12 | 4Y1O|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 | X-ray diffraction | 2.95 | 2015-10-14 |
| 13 | 6T3N|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-ray diffraction | 3.22 | 2020-05-13 |
| 14 | 4E8P|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-ray diffraction | 3.28 | 2012-11-14 |
| 15 | 4E8T|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-ray diffraction | 3.34 | 2012-11-14 |
| 16 | 5J01|1|A | Group II catalytic intron D1-D4-1 | group II intron lariat | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-ray diffraction | 3.39 | 2016-12-14 |
| 17 | 4FAW|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*A*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-ray diffraction | 2.7 | 2012-11-14 |
| 18 | 3EOH|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | RF01998 | Refined group II intron structure | X-ray diffraction | 3.12 | 2008-10-28 | ||
| 19 | 6T3R|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 3.57 | 2020-05-13 |
| 20 | 4FAQ|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-ray diffraction | 3.11 | 2012-11-14 |
| 21 | 4E8R|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-ray diffraction | 3.36 | 2012-11-14 |
| 22 | 4Y1N|1|B | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 2015-10-14 |
| 23 | 3G78|1|A | Group II catalytic intron D1-D4-1 | Group II intron, Ligated EXON product | Oceanobacillus iheyensis | Bacteria | RF01998 | Insight into group II intron catalysis from revised crystal structure | X-ray diffraction | 2.8 | 2010-02-16 |
| 24 | 4E8M|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-ray diffraction | 3.5 | 2012-11-14 |
| 25 | 6T3K|1|A | Group II catalytic intron D1-D4-1 | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-ray diffraction | 3.44 | 2020-05-13 |
| 26 | 4Y1N|1|A | Group II catalytic intron D1-D4-3 | group II intron, domain 1 | Oceanobacillus iheyensis | Bacteria | RF02001 | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-ray diffraction | 3 | 2015-10-14 |
| 27 | 4DS6|1|A | Group II catalytic intron D1-D4-1 | Mutant Group IIC Intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Crystal structure of a group II intron in the pre-catalytic state | X-ray diffraction | 3.64 | 2012-04-18 |
| 28 | 3EOG|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | RF01998 | Co-crystallization showing exon recognition by a group II intron | X-ray diffraction | 3.39 | 2008-10-28 | ||
| 29 | 3BWP|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | RF01998 | Crystal structure of a self-spliced group II intron | X-ray diffraction | 3.1 | 2008-04-15 | ||
| 30 | 4E8V|1|A | Group II catalytic intron D1-D4-1 | Group IIC intron | Oceanobacillus iheyensis | Bacteria | RF01998 | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+ | X-ray diffraction | 3.99 | 2012-11-14 |
Release history
| Release | 3.127 | 3.128 | 3.129 | 3.130 | 3.131 | 3.132 | 3.133 | 3.134 | 3.135 | 3.136 | 3.137 | 3.138 | 3.139 | 3.140 | 3.141 | 3.142 | 3.143 | 3.144 | 3.145 | 3.146 | 3.147 | 3.148 | 3.149 | 3.150 | 3.151 | 3.152 | 3.153 | 3.154 | 3.155 | 3.156 | 3.157 | 3.158 | 3.159 | 3.160 | 3.161 | 3.162 | 3.163 | 3.164 | 3.165 | 3.166 | 3.167 | 3.168 | 3.169 | 3.170 | 3.171 | 3.172 | 3.173 | 3.174 | 3.175 | 3.176 | 3.177 | 3.178 | 3.179 | 3.180 | 3.181 | 3.182 | 3.183 | 3.184 | 3.185 | 3.186 | 3.187 | 3.188 | 3.189 | 3.190 | 3.191 | 3.192 | 3.193 | 3.194 | 3.195 | 3.196 | 3.197 | 3.198 | 3.199 | 3.200 | 3.201 | 3.202 | 3.203 | 3.204 | 3.205 | 3.206 | 3.207 | 3.208 | 3.209 | 3.210 | 3.211 | 3.212 | 3.213 | 3.214 | 3.215 | 3.216 | 3.217 | 3.218 | 3.219 | 3.220 | 3.221 | 3.222 | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 | 3.285 | 3.286 | 3.287 | 3.288 | 3.289 | 3.290 | 3.291 | 3.292 | 3.293 | 3.294 | 3.295 | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 | 3.301 |
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| Date | 2020-05-20 | 2020-05-27 | 2020-06-03 | 2020-06-10 | 2020-06-17 | 2020-06-24 | 2020-07-01 | 2020-07-08 | 2020-07-15 | 2020-07-22 | 2020-07-29 | 2020-08-05 | 2020-08-12 | 2020-08-19 | 2020-08-26 | 2020-09-02 | 2020-09-09 | 2020-09-16 | 2020-09-23 | 2020-09-30 | 2020-10-07 | 2020-10-14 | 2020-10-21 | 2020-10-28 | 2020-11-04 | 2020-11-11 | 2020-11-18 | 2020-11-25 | 2020-12-02 | 2020-12-09 | 2020-12-16 | 2020-12-23 | 2020-12-30 | 2021-01-06 | 2021-01-13 | 2021-01-20 | 2021-01-27 | 2021-02-03 | 2021-02-10 | 2021-02-17 | 2021-02-24 | 2021-03-03 | 2021-03-10 | 2021-03-17 | 2021-03-24 | 2021-03-31 | 2021-04-07 | 2021-04-14 | 2021-04-21 | 2021-04-28 | 2021-05-05 | 2021-05-12 | 2021-05-19 | 2021-05-26 | 2021-06-02 | 2021-06-09 | 2021-06-16 | 2021-06-23 | 2021-06-30 | 2021-07-07 | 2021-07-14 | 2021-07-21 | 2021-07-28 | 2021-08-04 | 2021-08-11 | 2021-08-18 | 2021-08-25 | 2021-09-01 | 2021-09-08 | 2021-09-15 | 2021-09-22 | 2021-09-29 | 2021-10-06 | 2021-10-13 | 2021-10-20 | 2021-10-27 | 2021-11-03 | 2021-11-10 | 2021-11-17 | 2021-11-24 | 2021-12-01 | 2021-12-08 | 2021-12-15 | 2021-12-22 | 2021-12-29 | 2022-01-05 | 2022-01-12 | 2022-01-19 | 2022-01-26 | 2022-02-02 | 2022-02-09 | 2022-02-16 | 2022-02-23 | 2022-03-02 | 2022-03-09 | 2022-03-16 | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 | 2023-05-31 | 2023-06-07 | 2023-06-14 | 2023-06-21 | 2023-06-28 | 2023-07-05 | 2023-07-12 | 2023-07-19 | 2023-07-26 | 2023-08-02 | 2023-08-09 | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 | 2023-09-20 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_35054.4 | NR_all_35054.3 | 3.127 | (26) 3BWP|1|A, 5J01|1|A, 4E8N|1|A, 4FAU|1|A, 4Y1O|1|B, 4E8M|1|A, 4FAR|1|A, 4Y1O|1|A, 4E8K|1|A, 4FAQ|1|A, 4Y1N|1|B, 4DS6|1|A, 4E8V|1|A, 4Y1N|1|A, 3IGI|1|A, 4E8T|1|A, 4FB0|1|A, 3G78|1|A, 4E8R|1|A, 3EOH|1|A, 4E8Q|1|A, 4FAX|1|A, 3EOG|1|A, 5J02|1|A, 4E8P|1|A, 4FAW|1|A | (4) 6T3K|1|A, 6T3S|1|A, 6T3R|1|A, 6T3N|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 5J01|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+. | X-RAY DIFFRACTION | 3.39 | 414 |
| 2 | 5J02|1|A | Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon. | X-RAY DIFFRACTION | 3.49 | 414 |
| 3 | 3BWP|1|A | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 356 |
| 4 | 3EOG|1|A | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 388 |
| 5 | 3EOH|1|A | Refined group II intron structure | X-RAY DIFFRACTION | 3.12 | 381 |
| 6 | 4DS6|1|A | Crystal structure of a group II intron in the pre-catalytic state | X-RAY DIFFRACTION | 3.64 | 393 |
| 7 | 6T3N|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.22 | 394 |
| 8 | 6T3S|1|A | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.28 | 393 |
| 9 | 4FAX|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Na+ and Mg2+ | X-RAY DIFFRACTION | 3.1 | 392 |
| 10 | 4E8R|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+ | X-RAY DIFFRACTION | 3.36 | 393 |
| 11 | 4E8Q|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Tl+ and Mg2+ | X-RAY DIFFRACTION | 2.84 | 393 |
| 12 | 4E8N|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+ | X-RAY DIFFRACTION | 2.96 | 393 |
| 13 | 4E8P|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Rb+ and Mg2+ | X-RAY DIFFRACTION | 3.28 | 393 |
| 14 | 4FB0|1|A | Structure of Oceanobacillus iheyensis group II intron C377G mutant in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.22 | 393 |
| 15 | 4E8M|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Mg2+ | X-RAY DIFFRACTION | 3.5 | 394 |
| 16 | 4FAW|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and a hydrolyzed oligonucleotide fragment | X-RAY DIFFRACTION | 2.7 | 390 |
| 17 | 4FAU|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.87 | 395 |
| 18 | 4FAR|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 2.86 | 390 |
| 19 | 6T3K|1|A | Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.44 | 390 |
| 20 | 6T3R|1|A | Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of K+, Mg2+ and 5'-exon | X-RAY DIFFRACTION | 3.57 | 389 |
| 21 | 3G78|1|A | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 389 |
| 22 | 3IGI|1|A | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 389 |
| 23 | 4E8T|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset) | X-RAY DIFFRACTION | 3.34 | 388 |
| 24 | 4E8K|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and a non-hydrolyzed oligonucleotide substrate | X-RAY DIFFRACTION | 3.03 | 388 |
| 25 | 4FAQ|1|A | Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and 5'-exon | X-RAY DIFFRACTION | 3.11 | 396 |
| 26 | 4E8V|1|A | Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and Ba2+ | X-RAY DIFFRACTION | 3.99 | 389 |
| 27 | 4Y1O|1|B | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 256 |
| 28 | 4Y1N|1|A | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 249 |
| 29 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |
| 30 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 |