Equivalence class NR_4.0_35054.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4FAU|1|A (rep) | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 3IGI|1|A | 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 | ||
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 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 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 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 | ||
| 18 | 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 |
| 19 | 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 |
| 20 | 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 |
| 21 | 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 | ||
| 22 | 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 |
| 23 | 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 | ||
| 24 | 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 | 2.45 | 2.46 | 2.47 | 2.48 | 2.49 | 2.50 | 2.51 | 2.52 | 2.53 | 2.54 | 2.55 | 2.56 | 2.57 | 2.58 | 2.59 | 2.60 | 2.61 | 2.62 | 2.63 | 2.64 | 2.65 | 2.66 | 2.67 | 2.68 | 2.69 | 2.70 | 2.71 | 2.72 | 2.73 | 2.74 | 2.75 | 2.76 | 2.77 | 2.78 | 2.79 | 2.80 | 2.81 | 2.82 | 2.83 | 2.84 | 2.85 | 2.86 | 2.87 | 2.88 | 2.89 | 2.90 | 2.91 | 2.92 | 2.93 | 2.94 | 2.95 | 2.96 | 2.97 | 2.98 | 2.99 | 2.100 | 2.101 | 2.102 | 2.103 | 2.104 | 2.105 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2015-10-16 | 2015-10-23 | 2015-10-30 | 2015-11-06 | 2015-11-13 | 2015-11-20 | 2015-11-27 | 2015-12-04 | 2015-12-11 | 2015-12-18 | 2015-12-25 | 2016-01-01 | 2016-01-08 | 2016-01-15 | 2016-01-22 | 2016-01-29 | 2016-02-05 | 2016-02-12 | 2016-02-19 | 2016-02-26 | 2016-03-04 | 2016-03-11 | 2016-03-18 | 2016-03-25 | 2016-04-01 | 2016-04-08 | 2016-04-15 | 2016-04-22 | 2016-04-29 | 2016-05-06 | 2016-05-13 | 2016-05-20 | 2016-05-27 | 2016-06-03 | 2016-06-10 | 2016-06-17 | 2016-06-24 | 2016-07-01 | 2016-07-08 | 2016-07-15 | 2016-07-22 | 2016-07-29 | 2016-08-05 | 2016-08-12 | 2016-08-19 | 2016-08-26 | 2016-09-02 | 2016-09-09 | 2016-09-16 | 2016-09-23 | 2016-09-30 | 2016-10-07 | 2016-10-14 | 2016-10-21 | 2016-10-28 | 2016-11-04 | 2016-11-11 | 2016-11-18 | 2016-11-25 | 2016-12-02 | 2016-12-09 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_35054.2 | NR_all_35054.1 | 2.45 | (20) 4FAX|1|A, 3EOH|1|A, 4E8Q|1|A, 4FAW|1|A, 3EOG|1|A, 4E8P|1|A, 4FAU|1|A, 3BWP|1|A, 4E8N|1|A, 4FAR|1|A, 4E8M|1|A, 4FAQ|1|A, 4E8K|1|A, 4DS6|1|A, 4E8V|1|A, 3IGI|1|A, 4E8T|1|A, 4FB0|1|A, 3G78|1|A, 4E8R|1|A | (4) 4Y1O|1|A, 4Y1N|1|B, 4Y1N|1|A, 4Y1O|1|B | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_35054.2 | NR_4.0_35054.3 | 2.106 | (24) 4Y1N|1|A, 3IGI|1|A, 4E8T|1|A, 4FB0|1|A, 3G78|1|A, 4E8R|1|A, 4FAX|1|A, 3EOH|1|A, 4E8Q|1|A, 4FAW|1|A, 3EOG|1|A, 4E8P|1|A, 4FAU|1|A, 3BWP|1|A, 4E8N|1|A, 4FAR|1|A, 4Y1O|1|B, 4E8M|1|A, 4FAQ|1|A, 4Y1O|1|A, 4E8K|1|A, 4Y1N|1|B, 4DS6|1|A, 4E8V|1|A | (0) | (2) 5J01|1|A, 5J02|1|A |
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 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 3G78|1|A | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 389 |
| 12 | 3IGI|1|A | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 389 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 4DS6|1|A | Crystal structure of a group II intron in the pre-catalytic state | X-RAY DIFFRACTION | 3.64 | 393 |
| 18 | 3BWP|1|A | Crystal structure of a self-spliced group II intron | X-RAY DIFFRACTION | 3.1 | 356 |
| 19 | 3EOH|1|A | Refined group II intron structure | X-RAY DIFFRACTION | 3.12 | 381 |
| 20 | 3EOG|1|A | Co-crystallization showing exon recognition by a group II intron | X-RAY DIFFRACTION | 3.39 | 388 |
| 21 | 4Y1O|1|B | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 256 |
| 22 | 4Y1N|1|A | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 249 |
| 23 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |
| 24 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 |