Equivalence class NR_4.0_35054.4 Current
| # | IFE | Compound(s) | RNA source organism | Title | Method | Resolution | Date |
|---|---|---|---|---|---|---|---|
| 1 | 3IGI|1|A (rep) | Group IIC intron, 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3' | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 2009-12-22 | |
| 2 | 5J02|1|A | GROUP II INTRON LARIAT, 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3') | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC Intron Ribozyme | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron, 5'-R(*CP*G*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 intron, domain 1 | Oceanobacillus iheyensis | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 2015-10-14 |
| 12 | 4Y1O|1|B | group II intron, domain 1 | Oceanobacillus iheyensis | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 2015-10-14 |
| 13 | 6T3N|1|A | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron, 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | 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 intron lariat | Oceanobacillus iheyensis | 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 IIC intron, 5'-R(*A*UP*UP*UP*AP*UP*UP*A)-3' | Oceanobacillus iheyensis | 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 IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | Refined group II intron structure | X-RAY DIFFRACTION | 3.12 | 2008-10-28 | |
| 19 | 6T3R|1|A | Group IIC Intron Ribozyme | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 IIC intron | Oceanobacillus iheyensis | 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 intron, domain 1 | Oceanobacillus iheyensis | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 2015-10-14 |
| 23 | 3G78|1|A | Group II intron, Ligated EXON product | Oceanobacillus iheyensis | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 2010-02-16 |
| 24 | 4E8M|1|A | Group IIC intron | Oceanobacillus iheyensis | 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 IIC Intron Ribozyme | Oceanobacillus iheyensis | 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 intron, domain 1 | Oceanobacillus iheyensis | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 2015-10-14 |
| 27 | 4DS6|1|A | Mutant Group IIC Intron | Oceanobacillus iheyensis | 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 IIC intron, 5'-R(*UP*UP*AP*UP*UP*A)-3' | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 2008-10-28 | |
| 29 | 3BWP|1|A | Group IIC intron | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 2008-04-15 | |
| 30 | 4E8V|1|A | Group IIC intron | Oceanobacillus iheyensis | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_35054.4 | NR_4.0_35054.3 | 3.127 | (26) 4FB0|1|A, 3G78|1|A, 4E8R|1|A, 4FAX|1|A, 3EOH|1|A, 4E8Q|1|A, 4FAW|1|A, 3EOG|1|A, 5J02|1|A, 4E8P|1|A, 4FAU|1|A, 3BWP|1|A, 5J01|1|A, 4E8N|1|A, 4FAR|1|A, 4Y1O|1|B, 4E8M|1|A, 4FAQ|1|A, 4Y1O|1|A, 4E8K|1|A, 4E8V|1|A, 4Y1N|1|B, 4DS6|1|A, 4E8T|1|A, 4Y1N|1|A, 3IGI|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 | 3EOG|1|A | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 388 |
| 4 | 3BWP|1|A | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 356 |
| 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 | 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 |
| 12 | 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 |
| 13 | 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 |
| 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 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 |
| 30 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |