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(-) Description

Title :  CRYSTAL STRUCTURE OF AN RNA RACEMATE
 
Authors :  W. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, C. Betzel, V. A.
Date :  20 Apr 06  (Deposition) - 27 Jun 06  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  K,L,M,N  (2x)
Biol. Unit 1:  K,L  (1x)
Biol. Unit 2:  M,N  (1x)
Keywords :  Double Helix, Racemate, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, L. J. Delucas, C. Betzel, V. A. Erdmann
The First Crystal Structure Of An Rna Racemate.
Acta Crystallogr. , Sect. D V. 62 659 2006
PubMed-ID: 16699193  |  Reference-DOI: 10.1107/S090744490601359X

(-) Compounds

Molecule 1 - RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))- 3')
    ChainsK, M
    EngineeredYES
    Other DetailsTHIS SEQUENCE IS A 'SPIEGELMER' AND OCCURS IN 5S RNA FROM THERMUS FLAVUS
    SyntheticYES
 
Molecule 2 - RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))- 3')
    ChainsL, N
    EngineeredYES
    Other DetailsTHIS IS A 'SPIEGELMER' OF A SEQUENCE FROM 5S RNA FROM THERMUS FLAVUS
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit (2x)KLMN
Biological Unit 1 (1x)KL  
Biological Unit 2 (1x)  MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 45)

Asymmetric Unit (5, 45)
No.NameCountTypeFull Name
10C12Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
20G16Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
30U4Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
4CA12Ligand/IonCALCIUM ION
5GOL1Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
10C-1Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
20G-1Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
30U-1Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
4CA-1Ligand/IonCALCIUM ION
5GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10C-1Mod. ResidueL-CYTIDINE-5'-MONOPHOSPHATE
20G-1Mod. ResidueL-GUANOSINE-5'-MONOPHOSPHATE
30U-1Mod. ResidueL-URIDINE-5'-MONOPHOSPHATE
4CA-1Ligand/IonCALCIUM ION
5GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH N:4 , HOH N:5 , HOH N:24 , HOH N:31 , HOH N:63 , HOH N:122 , HOH N:125 , CA N:304BINDING SITE FOR RESIDUE CA N 302
2AC2SOFTWAREHOH N:5 , HOH N:17 , HOH N:24 , HOH N:63 , HOH N:84 , 0G N:96 , HOH N:111 , CA N:302BINDING SITE FOR RESIDUE CA N 304
3AC3SOFTWAREHOH K:59 , HOH N:45 , HOH N:53 , HOH N:60 , HOH N:65 , HOH N:73 , 0G N:97BINDING SITE FOR RESIDUE CA N 306
4AC4SOFTWAREHOH M:29 , HOH M:36 , HOH M:43 , HOH M:46 , HOH M:62 , 0G M:86 , HOH M:136BINDING SITE FOR RESIDUE CA M 308
5AC5SOFTWARE0G L:97 , HOH L:101 , HOH L:115 , HOH L:168 , HOH L:205 , HOH M:117BINDING SITE FOR RESIDUE CA L 310
6AC6SOFTWAREHOH M:8 , HOH M:74 , 0G M:82 , HOH M:91BINDING SITE FOR RESIDUE CA M 311
7AC7SOFTWARE0G K:85 , 0C L:91 , 0G L:92 , HOH N:80 , 0G N:92 , 0C N:93BINDING SITE FOR RESIDUE GOL N 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GQ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GQ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 2GQ6)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain K from PDB  Type:OTHER  Length:8
                                       
                  2gq6 K 79 xxxxxxxx 86
                            ||||||||
                            ||||||||
                           79-0C||||
                            80-0U|||
                             81-0G||
                              82-0G|
                               83-0G
                                84-0C
                                 85-0G
                                  86-0G

Chain L from PDB  Type:OTHER  Length:8
                                       
                  2gq6 L 90 xxxxxxxx 97
                            ||||||||
                            ||||||||
                           90-0C||||
                            91-0C|||
                             92-0G||
                              93-0C|
                               94-0C
                                95-0U
                                 96-0G
                                  97-0G

Chain M from PDB  Type:OTHER  Length:8
                                       
                  2gq6 M 79 xxxxxxxx 86
                            ||||||||
                            ||||||||
                           79-0C||||
                            80-0U|||
                             81-0G||
                              82-0G|
                               83-0G
                                84-0C
                                 85-0G
                                  86-0G

Chain N from PDB  Type:OTHER  Length:8
                                       
                  2gq6 N 90 xxxxxxxx 97
                            ||||||||
                            ||||||||
                           90-0C||||
                            91-0C|||
                             92-0G||
                              93-0C|
                               94-0C
                                95-0U
                                 96-0G
                                  97-0G

   Legend:   → Mismatch (orange background)
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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 2GQ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GQ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GQ6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2GQ6)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2GQ6)

(-) Related Entries Specified in the PDB File

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2gq7