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(-) Description

Title :  TERTIARY ARCHITECTURE OF THE OCEANOBACILLUS IHEYENSIS GROUP II INTRON
 
Authors :  N. Toor, K. S. Keating, O. Fedorova, K. Rajashankar, J. Wang, A. M. Pyle
Date :  27 Jul 09  (Deposition) - 22 Dec 09  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna, Ribonucleic Acid, Intron, Group Ii, Exon (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Toor, K. S. Keating, O. Fedorova, K. Rajashankar, J. Wang, A. M. Pyle
Tertiary Architecture Of The Oceanobacillus Iheyensis Group Ii Intron.
Rna V. 16 57 2010
PubMed-ID: 19952115  |  Reference-DOI: 10.1261/RNA.1844010

(-) Compounds

Molecule 1 - GROUP IIC INTRON
    Chains: A
    Engineered: YES
    Other Details: SEQUENCE MODIFIED FROM GROUP IIC INTRON FOUND NATURALLY IN OCEANOBACILLUS IHEYENSIS
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3'
    Chains: B
    Engineered: YES
    Other Details: EXON-LIKE OLIGONUCLEOTIDE
    Other Details - Source: PRODUCT OF INTRON SELF-CLEAVAGE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 66)

Asymmetric/Biological Unit (2, 66)
No.NameCountTypeFull Name
1K22Ligand/IonPOTASSIUM ION
2MG44Ligand/IonMAGNESIUM ION

(-) Sites  (62, 62)

Asymmetric Unit (62, 62)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:374 , U A:375 , C A:377 , U B:6 , A B:7BINDING SITE FOR RESIDUE MG A 413
02AC2SOFTWAREC A:358 , G A:359 , C A:377 , A B:7BINDING SITE FOR RESIDUE MG A 414
03AC3SOFTWAREG A:3 , U A:4 , HOH A:533BINDING SITE FOR RESIDUE MG A 415
04AC4SOFTWAREG A:14 , G A:15 , U A:256BINDING SITE FOR RESIDUE MG A 416
05AC5SOFTWAREG A:244BINDING SITE FOR RESIDUE MG A 417
06AC6SOFTWAREHOH A:546BINDING SITE FOR RESIDUE MG A 418
07AC7SOFTWAREG A:385 , G A:386 , MG A:421BINDING SITE FOR RESIDUE MG A 419
08AC8SOFTWAREHOH A:501BINDING SITE FOR RESIDUE MG A 420
09AC9SOFTWAREA A:290 , G A:386 , MG A:419BINDING SITE FOR RESIDUE MG A 421
10BC1SOFTWAREC A:360 , G A:374 , HOH A:536BINDING SITE FOR RESIDUE MG A 422
11BC2SOFTWAREA A:260 , HOH A:519BINDING SITE FOR RESIDUE MG A 423
12BC3SOFTWAREG A:324 , G A:325 , HOH A:480 , HOH A:483BINDING SITE FOR RESIDUE MG A 424
13BC4SOFTWAREG A:46 , U A:47 , U A:59 , HOH A:511 , HOH A:549 , HOH A:558BINDING SITE FOR RESIDUE MG A 425
14BC5SOFTWAREHOH A:490BINDING SITE FOR RESIDUE MG A 426
15BC6SOFTWAREG A:107 , HOH A:486 , HOH A:513 , HOH A:539BINDING SITE FOR RESIDUE MG A 427
16BC7SOFTWAREC A:372 , G A:373 , HOH A:482 , HOH A:502 , HOH A:562BINDING SITE FOR RESIDUE MG A 428
17BC8SOFTWAREU A:379 , HOH A:527 , HOH A:563BINDING SITE FOR RESIDUE MG A 429
18BC9SOFTWAREC A:119 , A A:174 , G A:239 , HOH A:479 , HOH A:528 , HOH A:564BINDING SITE FOR RESIDUE MG A 430
19CC1SOFTWAREA A:186 , HOH A:506 , HOH A:548BINDING SITE FOR RESIDUE MG A 431
20CC2SOFTWAREG A:269 , G A:270 , HOH A:485 , HOH A:508 , HOH A:517BINDING SITE FOR RESIDUE MG A 432
21CC3SOFTWAREG A:275 , K A:459 , HOH A:504BINDING SITE FOR RESIDUE MG A 433
22CC4SOFTWAREA A:105BINDING SITE FOR RESIDUE MG A 434
23CC5SOFTWAREG A:136 , A A:137 , U A:225 , HOH A:494 , HOH A:523BINDING SITE FOR RESIDUE MG A 435
24CC6SOFTWAREU A:66 , A A:67 , HOH A:487 , HOH A:540BINDING SITE FOR RESIDUE MG A 436
25CC7SOFTWAREG A:284 , HOH A:498BINDING SITE FOR RESIDUE MG A 437
26CC8SOFTWAREA A:181 , A A:223BINDING SITE FOR RESIDUE MG A 438
27CC9SOFTWAREG A:111 , C A:112 , HOH A:522BINDING SITE FOR RESIDUE MG A 439
28DC1SOFTWAREHOH A:537 , HOH A:567BINDING SITE FOR RESIDUE MG A 440
29DC2SOFTWAREG A:266BINDING SITE FOR RESIDUE MG A 441
30DC3SOFTWAREC A:119 , G A:173BINDING SITE FOR RESIDUE MG A 442
31DC4SOFTWAREC A:6BINDING SITE FOR RESIDUE MG A 443
32DC5SOFTWAREG A:169 , G A:170BINDING SITE FOR RESIDUE MG A 444
33DC6SOFTWAREA A:61 , HOH A:557BINDING SITE FOR RESIDUE MG A 445
34DC7SOFTWAREC A:145 , U A:146BINDING SITE FOR RESIDUE MG A 446
35DC8SOFTWAREA A:184BINDING SITE FOR RESIDUE MG A 447
36DC9SOFTWAREA A:67 , G A:68BINDING SITE FOR RESIDUE MG A 448
37EC1SOFTWAREA A:154 , G A:155 , HOH A:503BINDING SITE FOR RESIDUE MG A 449
38EC2SOFTWAREG A:320BINDING SITE FOR RESIDUE MG A 450
39EC3SOFTWAREU A:285BINDING SITE FOR RESIDUE MG A 451
40EC4SOFTWAREA A:355 , A A:356BINDING SITE FOR RESIDUE MG A 452
41EC5SOFTWAREG A:170 , HOH A:555BINDING SITE FOR RESIDUE MG A 453
42EC6SOFTWAREC A:286 , A A:287 , G A:288BINDING SITE FOR RESIDUE MG A 454
43EC7SOFTWAREG A:382 , HOH A:552BINDING SITE FOR RESIDUE MG A 455
44EC8SOFTWAREA A:333 , U A:334 , G A:335BINDING SITE FOR RESIDUE MG A 456
45EC9SOFTWAREU A:4 , G A:107 , U A:375 , A A:376BINDING SITE FOR RESIDUE K A 457
46FC1SOFTWAREC A:116 , G A:117BINDING SITE FOR RESIDUE K A 458
47FC2SOFTWAREMG A:433BINDING SITE FOR RESIDUE K A 459
48FC3SOFTWAREG A:28BINDING SITE FOR RESIDUE K A 460
49FC4SOFTWAREG A:264 , G A:265BINDING SITE FOR RESIDUE K A 462
50FC5SOFTWAREA A:283 , G A:284BINDING SITE FOR RESIDUE K A 463
51FC6SOFTWAREG A:194BINDING SITE FOR RESIDUE K A 464
52FC7SOFTWAREC A:86 , G A:87 , A A:95 , U A:96 , G A:97BINDING SITE FOR RESIDUE K A 466
53FC8SOFTWAREU A:4 , G A:5 , A A:376BINDING SITE FOR RESIDUE K A 467
54FC9SOFTWAREG A:80BINDING SITE FOR RESIDUE K A 468
55GC1SOFTWAREG A:32 , G A:34BINDING SITE FOR RESIDUE K A 469
56GC2SOFTWAREG A:229BINDING SITE FOR RESIDUE K A 470
57GC3SOFTWAREA A:370BINDING SITE FOR RESIDUE K A 471
58GC4SOFTWAREG A:288 , C A:358 , G A:359 , C A:377BINDING SITE FOR RESIDUE K A 472
59GC5SOFTWAREG A:331 , U A:332BINDING SITE FOR RESIDUE K A 473
60GC6SOFTWAREA A:348 , A A:349 , G A:350 , C A:351BINDING SITE FOR RESIDUE K A 474
61GC7SOFTWAREA A:120BINDING SITE FOR RESIDUE K A 475
62GC8SOFTWAREG A:90BINDING SITE FOR RESIDUE K A 476

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IGI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IGI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IGI)

(-) Exons   (0, 0)

(no "Exon" information available for 3IGI)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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Chain A from PDB  Type:DNA/RNA  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
                 3igi A   2 UGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUG 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         


Chain B from PDB  Type:DNA/RNA  Length:9
                                         
                 3igi B   2 GCUCUACUC  10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3IGI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IGI)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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