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(-) Description

Title :  INSIGHT INTO GROUP II INTRON CATALYSIS FROM REVISED CRYSTAL STRUCTURE
 
Authors :  J. Wang
Date :  09 Feb 09  (Deposition) - 16 Feb 10  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,Z
Keywords :  Revised Crystal Structure, Revision, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang
Inclusion Of Weak High-Resolution X-Ray Data For Improvemen Of A Group Ii Intron Structure.
Acta Crystallogr. , Sect. D V. 66 988 2010
PubMed-ID: 20823550  |  Reference-DOI: 10.1107/S0907444910029938

(-) Compounds

Molecule 1 - GROUP II INTRON
    Chains: A
    Engineered: YES
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710
    Other Details: RNA WAS PEPARED BY IN VITRO TRANSCRIPTION BY T7 RNA POLYMERASE
    Synthetic: YES
 
Molecule 2 - LIGATED EXON PRODUCT
    Chains: Z
    Engineered: YES
    Fragment: UNKNOWN EXON PRODUCT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 77)

Asymmetric/Biological Unit (2, 77)
No.NameCountTypeFull Name
1K26Ligand/IonPOTASSIUM ION
2MG51Ligand/IonMAGNESIUM ION

(-) Sites  (73, 73)

Asymmetric Unit (73, 73)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU A:375 , C A:377 , HOH A:588 , U Z:6 , U Z:7BINDING SITE FOR RESIDUE MG Z 10
02AC2SOFTWAREC A:358 , G A:359 , C A:377 , U Z:7BINDING SITE FOR RESIDUE MG Z 11
03AC3SOFTWAREU Z:6 , U Z:7BINDING SITE FOR RESIDUE MG Z 12
04AC4SOFTWAREG A:5 , A A:287 , A A:380 , HOH A:739BINDING SITE FOR RESIDUE MG A 413
05AC5SOFTWAREG A:3 , U A:4 , HOH A:670BINDING SITE FOR RESIDUE MG A 414
06AC6SOFTWAREG A:14 , G A:15 , U A:256BINDING SITE FOR RESIDUE MG A 415
07AC7SOFTWAREHOH A:752BINDING SITE FOR RESIDUE MG A 417
08AC8SOFTWAREC A:289 , G A:385 , G A:386 , HOH A:704BINDING SITE FOR RESIDUE MG A 418
09AC9SOFTWAREHOH A:549 , HOH A:564BINDING SITE FOR RESIDUE MG A 419
10BC1SOFTWAREA A:290 , HOH A:508 , HOH A:704BINDING SITE FOR RESIDUE MG A 420
11BC2SOFTWAREG A:173BINDING SITE FOR RESIDUE MG A 421
12BC3SOFTWAREA A:50 , HOH A:673BINDING SITE FOR RESIDUE MG A 422
13BC4SOFTWAREC A:360 , G A:374 , HOH A:692 , HOH A:697 , HOH A:747 , HOH A:835BINDING SITE FOR RESIDUE MG A 423
14BC5SOFTWAREA A:260 , HOH A:618BINDING SITE FOR RESIDUE MG A 426
15BC6SOFTWAREG A:142 , A A:144 , C A:145BINDING SITE FOR RESIDUE MG A 427
16BC7SOFTWAREG A:325 , HOH A:492BINDING SITE FOR RESIDUE MG A 428
17BC8SOFTWAREU A:59 , HOH A:593 , HOH A:766 , HOH A:814BINDING SITE FOR RESIDUE MG A 429
18BC9SOFTWAREHOH A:519BINDING SITE FOR RESIDUE MG A 430
19CC1SOFTWAREG A:107 , HOH A:507 , HOH A:597 , HOH A:711BINDING SITE FOR RESIDUE MG A 432
20CC2SOFTWAREC A:372 , HOH A:499 , HOH A:554 , HOH A:836BINDING SITE FOR RESIDUE MG A 433
21CC3SOFTWAREG A:378 , HOH A:652 , HOH A:838BINDING SITE FOR RESIDUE MG A 434
22CC4SOFTWAREC A:119 , A A:174 , G A:239 , HOH A:488 , HOH A:653 , HOH A:839BINDING SITE FOR RESIDUE MG A 435
23CC5SOFTWAREU A:285 , HOH A:563 , HOH A:598 , HOH A:693BINDING SITE FOR RESIDUE MG A 436
24CC6SOFTWAREA A:186 , HOH A:569 , HOH A:762BINDING SITE FOR RESIDUE MG A 437
25CC7SOFTWAREG A:269 , HOH A:505 , HOH A:573 , HOH A:608BINDING SITE FOR RESIDUE MG A 438
26CC8SOFTWAREA A:355 , A A:356 , HOH A:576 , HOH A:577 , HOH A:793BINDING SITE FOR RESIDUE MG A 439
27CC9SOFTWAREG A:275 , HOH A:524 , HOH A:560 , HOH A:601 , HOH A:679BINDING SITE FOR RESIDUE MG A 440
28DC1SOFTWAREA A:105 , HOH A:645 , HOH A:717BINDING SITE FOR RESIDUE MG A 441
29DC2SOFTWAREG A:136 , U A:225 , HOH A:526 , HOH A:634BINDING SITE FOR RESIDUE MG A 442
30DC3SOFTWAREU A:66 , A A:67 , HOH A:510 , HOH A:713BINDING SITE FOR RESIDUE MG A 443
31DC4SOFTWAREHOH A:540BINDING SITE FOR RESIDUE MG A 444
32DC5SOFTWAREA A:181 , A A:222 , A A:223BINDING SITE FOR RESIDUE MG A 445
33DC6SOFTWAREG A:111 , HOH A:631BINDING SITE FOR RESIDUE MG A 446
34DC7SOFTWAREHOH A:699 , HOH A:864 , HOH A:886BINDING SITE FOR RESIDUE MG A 447
35DC8SOFTWAREG A:266 , G A:267 , HOH A:591 , HOH A:695 , HOH A:798BINDING SITE FOR RESIDUE MG A 448
36DC9SOFTWAREG A:118 , C A:119 , HOH A:794BINDING SITE FOR RESIDUE MG A 449
37EC1SOFTWAREC A:6BINDING SITE FOR RESIDUE MG A 450
38EC2SOFTWAREHOH A:702BINDING SITE FOR RESIDUE MG A 451
39EC3SOFTWAREG A:275 , A A:276BINDING SITE FOR RESIDUE MG A 452
40EC4SOFTWAREG A:52 , HOH A:531 , HOH A:582BINDING SITE FOR RESIDUE MG A 453
41EC5SOFTWAREG A:169 , HOH A:650 , HOH A:764BINDING SITE FOR RESIDUE MG A 454
42EC6SOFTWAREA A:60 , C A:197 , U A:198BINDING SITE FOR RESIDUE MG A 455
43EC7SOFTWAREA A:290 , G A:354 , G A:388BINDING SITE FOR RESIDUE MG A 456
44EC8SOFTWAREC A:201BINDING SITE FOR RESIDUE MG A 457
45EC9SOFTWAREC A:40 , G A:41BINDING SITE FOR RESIDUE MG A 458
46FC1SOFTWAREA A:61 , C A:62 , HOH A:615BINDING SITE FOR RESIDUE MG A 459
47FC2SOFTWAREHOH A:800BINDING SITE FOR RESIDUE MG A 460
48FC3SOFTWAREU A:4 , G A:107 , U A:375 , A A:376BINDING SITE FOR RESIDUE K A 461
49FC4SOFTWAREA A:67 , G A:68 , HOH A:506 , HOH A:509 , HOH A:614BINDING SITE FOR RESIDUE K A 462
50FC5SOFTWAREC A:116 , G A:117 , HOH A:635 , HOH A:708 , HOH A:746BINDING SITE FOR RESIDUE K A 463
51FC6SOFTWAREG A:275 , HOH A:524 , HOH A:725 , HOH A:776 , HOH A:786BINDING SITE FOR RESIDUE K A 464
52FC7SOFTWAREA A:27 , G A:28 , HOH A:489BINDING SITE FOR RESIDUE K A 465
53FC8SOFTWAREU A:251 , G A:252BINDING SITE FOR RESIDUE K A 466
54FC9SOFTWAREA A:184 , HOH A:497 , HOH A:561BINDING SITE FOR RESIDUE K A 467
55GC1SOFTWAREA A:333 , U A:334 , G A:335BINDING SITE FOR RESIDUE K A 468
56GC2SOFTWAREG A:264 , HOH A:525 , HOH A:559 , HOH A:916BINDING SITE FOR RESIDUE K A 469
57GC3SOFTWAREA A:297 , G A:320 , HOH A:558 , HOH A:785BINDING SITE FOR RESIDUE K A 470
58GC4SOFTWAREA A:283 , HOH A:592 , HOH A:728BINDING SITE FOR RESIDUE K A 471
59GC5SOFTWAREA A:192 , A A:193 , G A:194 , HOH A:545 , HOH A:623BINDING SITE FOR RESIDUE K A 472
60GC6SOFTWAREG A:142BINDING SITE FOR RESIDUE K A 473
61GC7SOFTWAREC A:86 , G A:87 , A A:95 , U A:96 , G A:97BINDING SITE FOR RESIDUE K A 474
62GC8SOFTWAREG A:3 , U A:4 , G A:5 , A A:376BINDING SITE FOR RESIDUE K A 475
63GC9SOFTWAREG A:79 , G A:80BINDING SITE FOR RESIDUE K A 476
64HC1SOFTWAREG A:32 , A A:33 , G A:34 , A A:50 , HOH A:496BINDING SITE FOR RESIDUE K A 477
65HC2SOFTWAREG A:229 , HOH A:641BINDING SITE FOR RESIDUE K A 478
66HC3SOFTWAREA A:370 , HOH A:648 , HOH A:774 , HOH A:789BINDING SITE FOR RESIDUE K A 479
67HC4SOFTWAREG A:288 , C A:358 , G A:359 , C A:377BINDING SITE FOR RESIDUE K A 480
68HC5SOFTWAREG A:331 , U A:332 , HOH A:490 , HOH A:494 , HOH A:570 , HOH A:722BINDING SITE FOR RESIDUE K A 481
69HC6SOFTWAREA A:348 , A A:349 , G A:350 , HOH A:571 , HOH A:751BINDING SITE FOR RESIDUE K A 482
70HC7SOFTWAREA A:120 , A A:121 , HOH A:705BINDING SITE FOR RESIDUE K A 483
71HC8SOFTWAREA A:154 , G A:155 , HOH A:556BINDING SITE FOR RESIDUE K A 484
72HC9SOFTWAREG A:89 , HOH A:682 , HOH A:843BINDING SITE FOR RESIDUE K A 485
73IC1SOFTWAREG A:58 , HOH A:775 , HOH A:797BINDING SITE FOR RESIDUE K A 486

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G78)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G78)

(-) Exons   (0, 0)

(no "Exon" information available for 3G78)

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:RNA  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
                 3g78 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 Z from PDB  Type:RNA  Length:9
                                         
                 3g78 Z   1 UGUUAUUUU   9
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3G78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G78)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3G78)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3bwp ORIGINAL ENTRY OF THIS STRUCTURE
3eoh FIRST ATTEMPT OF REVISION OF THE ORIGINAL STRUCTURE 3BWP. THE CURRENT ENTRY IS THE SECOND ATTEMPT OF THE REVISION