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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 :  1.35
Chains :  Asym. Unit :  K,L,M,N  (2x)
Biol. Unit 1:  K,L  (1x)
Biol. Unit 2:  M,N  (1x)
Keywords :  Deouble 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')
    Chains: K, M
    Engineered: YES
    Other Details: THIS SEQUENCE IS A 'SPIEGELMER' AND OCCURS IN 5S RNA FROM THERMUS FLAVUS
    Synthetic: YES
 
Molecule 2 - RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))- 3')
    Chains: L, N
    Engineered: YES
    Other Details: THIS SEQUENCE IS A 'SPIEGELMER' AND OCCURS IN 5S RNA FROM THERMUS FLAVUS
    Synthetic: YES

 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:5 , HOH N:6 , HOH N:26 , HOH N:56 , HOH N:80 , HOH N:98 , HOH N:101 , CA N:304BINDING SITE FOR RESIDUE CA N 302
2AC2SOFTWAREHOH N:5 , HOH N:26 , HOH N:38 , HOH N:56 , 0G N:96 , HOH N:144 , HOH N:167 , CA N:302BINDING SITE FOR RESIDUE CA N 304
3AC3SOFTWAREHOH K:33 , HOH K:51 , HOH N:54 , HOH N:61 , HOH N:87 , 0G N:97 , HOH N:100BINDING SITE FOR RESIDUE CA N 306
4AC4SOFTWAREHOH M:27 , HOH M:30 , HOH M:35 , HOH M:44 , HOH M:73 , 0G M:86 , HOH M:104BINDING SITE FOR RESIDUE CA M 308
5AC5SOFTWAREHOH L:74 , HOH L:88 , 0G L:97 , HOH L:102 , HOH L:110 , HOH M:49 , HOH M:87BINDING SITE FOR RESIDUE CA L 310
6AC6SOFTWAREHOH M:1 , HOH M:21 , HOH M:53 , 0G M:82 , HOH M:246BINDING SITE FOR RESIDUE CA M 311
7AC7SOFTWARE0G K:85 , 0G K:86 , 0C L:91 , 0G M:85 , HOH N:19 , 0G N:92 , 0C N:93BINDING SITE FOR RESIDUE GOL N 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GQ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GQ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 2GQ4)

(-) 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
                                       
                  2gq4 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
                                       
                  2gq4 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
                                       
                  2gq4 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
                                       
                  2gq4 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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  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 2GQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GQ4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2GQ4)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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