Equivalence class NR_4.0_35054.3 Obsolete
# | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 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 | 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 |
7 | 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 |
8 | 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 |
9 | 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 |
10 | 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 |
11 | 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 |
12 | 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 |
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 | 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 |
15 | 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 |
16 | 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 | ||||
17 | 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 |
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 | 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 |
20 | 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 |
21 | 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 |
22 | 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 |
23 | 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 |
24 | 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 | ||||
25 | 3BWP|1|A | Group IIC intron | Crystal structure of a self-spliced group II intron | X-ray diffraction | 3.1 | 2008-04-15 | ||||
26 | 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 | 2.106 | 2.107 | 2.108 | 2.109 | 2.110 | 2.111 | 2.112 | 2.113 | 2.114 | 2.115 | 2.116 | 2.117 | 2.118 | 2.119 | 2.120 | 2.121 | 2.122 | 2.123 | 2.124 | 2.125 | 2.126 | 2.127 | 2.128 | 2.129 | 2.130 | 2.131 | 2.132 | 2.133 | 2.134 | 2.135 | 2.136 | 2.137 | 2.138 | 2.139 | 2.140 | 2.141 | 2.142 | 2.143 | 2.144 | 2.145 | 2.146 | 2.147 | 2.148 | 2.149 | 2.150 | 2.151 | 2.152 | 2.153 | 2.154 | 2.155 | 2.156 | 2.157 | 2.158 | 3.0 | 3.1 | 3.2 | 3.3 | 3.4 | 3.5 | 3.6 | 3.7 | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | 3.14 | 3.15 | 3.16 | 3.17 | 3.18 | 3.19 | 3.20 | 3.21 | 3.22 | 3.23 | 3.24 | 3.25 | 3.26 | 3.27 | 3.28 | 3.29 | 3.30 | 3.31 | 3.32 | 3.33 | 3.34 | 3.35 | 3.36 | 3.37 | 3.38 | 3.39 | 3.40 | 3.41 | 3.42 | 3.43 | 3.44 | 3.45 | 3.46 | 3.47 | 3.48 | 3.49 | 3.50 | 3.51 | 3.52 | 3.53 | 3.54 | 3.55 | 3.56 | 3.57 | 3.58 | 3.59 | 3.60 | 3.61 | 3.62 | 3.63 | 3.64 | 3.65 | 3.66 | 3.67 | 3.68 | 3.69 | 3.70 | 3.71 | 3.72 | 3.73 | 3.74 | 3.75 | 3.76 | 3.77 | 3.78 | 3.79 | 3.80 | 3.81 | 3.82 | 3.83 | 3.84 | 3.85 | 3.86 | 3.87 | 3.88 | 3.89 | 3.90 | 3.91 | 3.92 | 3.93 | 3.94 | 3.95 | 3.96 | 3.97 | 3.98 | 3.99 | 3.100 | 3.101 | 3.102 | 3.103 | 3.104 | 3.105 | 3.106 | 3.107 | 3.108 | 3.109 | 3.110 | 3.111 | 3.112 | 3.113 | 3.114 | 3.115 | 3.116 | 3.117 | 3.118 | 3.119 | 3.120 | 3.121 | 3.122 | 3.123 | 3.124 | 3.125 | 3.126 |
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Date | 2016-12-16 | 2016-12-23 | 2016-12-30 | 2017-01-06 | 2017-01-13 | 2017-01-20 | 2017-01-27 | 2017-02-03 | 2017-02-10 | 2017-02-17 | 2017-02-24 | 2017-03-03 | 2017-03-10 | 2017-03-17 | 2017-03-24 | 2017-03-31 | 2017-04-11 | 2017-04-15 | 2017-04-26 | 2017-04-29 | 2017-05-09 | 2017-05-15 | 2017-05-20 | 2017-05-27 | 2017-06-07 | 2017-06-11 | 2017-06-21 | 2017-06-24 | 2017-06-28 | 2017-07-04 | 2017-07-10 | 2017-07-15 | 2017-07-26 | 2017-07-31 | 2017-08-05 | 2017-08-12 | 2017-08-19 | 2017-08-26 | 2017-09-03 | 2017-09-09 | 2017-09-16 | 2017-09-23 | 2017-09-30 | 2017-10-07 | 2017-10-14 | 2017-10-21 | 2017-10-28 | 2017-11-03 | 2017-11-10 | 2017-11-17 | 2017-11-24 | 2017-12-01 | 2017-12-08 | 2017-12-15 | 2017-12-22 | 2017-12-29 | 2018-01-05 | 2018-01-12 | 2018-01-19 | 2018-01-26 | 2018-02-02 | 2018-02-09 | 2018-02-16 | 2018-02-23 | 2018-03-01 | 2018-03-08 | 2018-03-15 | 2018-03-22 | 2018-03-29 | 2018-04-06 | 2018-04-13 | 2018-04-20 | 2018-04-27 | 2018-05-04 | 2018-05-11 | 2018-05-18 | 2018-05-25 | 2018-06-01 | 2018-06-08 | 2018-06-15 | 2018-06-22 | 2018-06-29 | 2018-07-06 | 2018-07-13 | 2018-07-20 | 2018-07-27 | 2018-08-03 | 2018-08-10 | 2018-08-17 | 2018-08-24 | 2018-08-31 | 2018-09-07 | 2018-09-14 | 2018-09-21 | 2018-09-28 | 2018-10-05 | 2018-10-12 | 2018-10-19 | 2018-10-26 | 2018-11-02 | 2018-11-09 | 2018-11-16 | 2018-11-23 | 2018-11-30 | 2018-12-07 | 2018-12-14 | 2018-12-21 | 2018-12-28 | 2019-01-04 | 2019-01-11 | 2019-01-18 | 2019-01-25 | 2019-02-01 | 2019-02-08 | 2019-02-15 | 2019-02-22 | 2019-03-01 | 2019-03-08 | 2019-03-15 | 2019-03-22 | 2019-03-29 | 2019-04-05 | 2019-04-12 | 2019-04-19 | 2019-04-26 | 2019-05-03 | 2019-05-10 | 2019-05-17 | 2019-05-24 | 2019-05-31 | 2019-06-07 | 2019-06-14 | 2019-06-21 | 2019-06-28 | 2019-07-05 | 2019-07-12 | 2019-07-19 | 2019-07-26 | 2019-08-02 | 2019-08-09 | 2019-08-16 | 2019-08-23 | 2019-08-28 | 2019-09-04 | 2019-09-11 | 2019-09-19 | 2019-09-25 | 2019-10-03 | 2019-10-09 | 2019-10-16 | 2019-10-23 | 2019-10-30 | 2019-11-06 | 2019-11-13 | 2019-11-20 | 2019-11-27 | 2019-12-04 | 2019-12-11 | 2019-12-18 | 2019-12-25 | 2020-01-01 | 2020-01-08 | 2020-01-15 | 2020-01-22 | 2020-01-29 | 2020-02-05 | 2020-02-12 | 2020-02-19 | 2020-02-26 | 2020-03-04 | 2020-03-11 | 2020-03-18 | 2020-03-25 | 2020-04-01 | 2020-04-08 | 2020-04-15 | 2020-04-22 | 2020-04-29 | 2020-05-06 | 2020-05-13 |
Parents
This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
---|---|---|---|---|---|
NR_4.0_35054.3 | NR_4.0_35054.2 | 2.106 | (24) 4E8R|1|A, 4E8Q|1|A, 4E8P|1|A, 4E8N|1|A, 4Y1O|1|B, 4E8M|1|A, 4Y1O|1|A, 4E8K|1|A, 4Y1N|1|B, 4DS6|1|A, 4Y1N|1|A, 3IGI|1|A, 4FB0|1|A, 3G78|1|A, 4FAX|1|A, 3EOH|1|A, 3EOG|1|A, 4FAW|1|A, 3BWP|1|A, 4FAU|1|A, 4FAR|1|A, 4FAQ|1|A, 4E8V|1|A, 4E8T|1|A | (2) 5J01|1|A, 5J02|1|A | (0) |
Children
This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
---|---|---|---|---|---|
NR_4.0_35054.3 | NR_4.0_35054.4 | 3.127 | (26) 4Y1O|1|B, 3G78|1|A, 4E8M|1|A, 4E8R|1|A, 4FAR|1|A, 4FB0|1|A, 4Y1O|1|A, 3EOH|1|A, 4E8K|1|A, 4E8Q|1|A, 4FAQ|1|A, 4FAX|1|A, 4Y1N|1|B, 3EOG|1|A, 5J02|1|A, 4DS6|1|A, 4E8P|1|A, 4E8V|1|A, 4FAW|1|A, 4Y1N|1|A, 3BWP|1|A, 5J01|1|A, 3IGI|1|A, 4E8N|1|A, 4E8T|1|A, 4FAU|1|A | (0) | (4) 6T3K|1|A, 6T3S|1|A, 6T3R|1|A, 6T3N|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 | 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 | 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 |
8 | 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 |
9 | 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 |
10 | 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 |
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 | 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 |
13 | 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 |
14 | 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 |
15 | 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 |
16 | 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 |
17 | 3G78|1|A | Insight into group II intron catalysis from revised crystal structure | X-RAY DIFFRACTION | 2.8 | 389 |
18 | 3IGI|1|A | Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron | X-RAY DIFFRACTION | 3.12 | 389 |
19 | 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 |
20 | 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 |
21 | 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 |
22 | 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 |
23 | 4Y1O|1|B | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 256 |
24 | 4Y1N|1|A | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 249 |
25 | 4Y1N|1|B | Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine | X-RAY DIFFRACTION | 3 | 259 |
26 | 4Y1O|1|A | Oceanobacillus iheyensis group II intron domain 1 | X-RAY DIFFRACTION | 2.95 | 258 |
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