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(-) Description

Title :  CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING
 
Authors :  J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech, J. A. Doudna
Date :  22 Aug 96  (Deposition) - 31 Dec 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna, P4-P6 Ribozyme Domain Of The Tetrahymena Group I Intron (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech, J. A. Doudna
Crystal Structure Of A Group I Ribozyme Domain: Principles Of Rna Packing.
Science V. 273 1678 1996
PubMed-ID: 8781224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P4-P6 RNA RIBOZYME DOMAIN
    ChainsA, B
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsT7 TRANSCRIPT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MG24Ligand/IonMAGNESIUM ION
2NCO4Ligand/IonCOBALT HEXAMMINE(III)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NCO2Ligand/IonCOBALT HEXAMMINE(III)
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NCO2Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:188BINDING SITE FOR RESIDUE MG A 265
02AC2SOFTWAREG B:188BINDING SITE FOR RESIDUE MG B 266
03AC3SOFTWAREA A:183 , A A:184 , A A:186BINDING SITE FOR RESIDUE MG A 267
04AC4SOFTWAREA A:183 , A A:184 , A A:186 , A A:187BINDING SITE FOR RESIDUE MG A 268
05AC5SOFTWAREA B:183 , A B:184 , A B:186BINDING SITE FOR RESIDUE MG B 269
06AC6SOFTWAREA B:183 , A B:184 , A B:186 , A B:187BINDING SITE FOR RESIDUE MG B 270
07AC7SOFTWAREG B:163 , G B:164BINDING SITE FOR RESIDUE MG B 271
08AC8SOFTWAREG A:163 , G A:164BINDING SITE FOR RESIDUE MG A 272
09AC9SOFTWAREA A:171BINDING SITE FOR RESIDUE MG A 274
10BC1SOFTWAREA B:171BINDING SITE FOR RESIDUE MG B 275
11BC2SOFTWAREA A:173BINDING SITE FOR RESIDUE MG A 276
12BC3SOFTWAREC A:213 , C A:255BINDING SITE FOR RESIDUE MG A 277
13BC4SOFTWAREG B:112BINDING SITE FOR RESIDUE MG B 279
14BC5SOFTWAREA B:173BINDING SITE FOR RESIDUE MG B 280
15BC6SOFTWAREA B:248 , U B:249 , G B:250BINDING SITE FOR RESIDUE MG B 281
16BC7SOFTWAREA A:248 , U A:249 , G A:250BINDING SITE FOR RESIDUE MG A 282
17BC8SOFTWAREU A:155BINDING SITE FOR RESIDUE MG A 284
18BC9SOFTWAREG A:112BINDING SITE FOR RESIDUE MG A 285
19CC1SOFTWAREU B:205BINDING SITE FOR RESIDUE MG B 286
20CC2SOFTWAREU A:120BINDING SITE FOR RESIDUE MG A 287
21CC3SOFTWAREU B:120BINDING SITE FOR RESIDUE MG B 288
22CC4SOFTWAREA A:146 , G A:147 , G A:148 , G A:149 , U A:155 , U A:156BINDING SITE FOR RESIDUE NCO A 261
23CC5SOFTWAREG A:174 , G A:175 , G A:176 , U A:177BINDING SITE FOR RESIDUE NCO A 262
24CC6SOFTWAREA B:146 , G B:147 , G B:148 , G B:149 , U B:155 , U B:156BINDING SITE FOR RESIDUE NCO B 263
25CC7SOFTWAREG B:174 , G B:175 , G B:176 , U B:177BINDING SITE FOR RESIDUE NCO B 264

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GID)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GID)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GID)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GID)

(-) Exons   (0, 0)

(no "Exon" information available for 1GID)

(-) Sequences/Alignments

Asymmetric 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
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Chain A from PDB  Type:RNA  Length:158
                                                                                                                                                                                              
                 1gid A 103 GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUC 260
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        

Chain B from PDB  Type:RNA  Length:158
                                                                                                                                                                                              
                 1gid B 103 GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUC 260
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        

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  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 1GID)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1GID)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GID)

(-) Gene Ontology  (0, 0)

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Distance Plot
  representative atom O3*, chain A
  representative atom O3*

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