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(-) Description

Title :  CRYSTALLIZATION OF THE THERMOTOGA MARITIMA LYSINE RIBOSWITCH BOUND TO L-4-OXALYSINE
 
Authors :  A. A. Serganov
Date :  21 Jun 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Lysine Ribsowitch, Oxalysine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Serganov, L. Huang, D. J. Patel
Structural Insights Into Amino Acid Binding And Gene Contro By A Lysine Riboswitch.
Nature V. 455 1263 2008
PubMed-ID: 18784651  |  Reference-DOI: 10.1038/NATURE07326

(-) Compounds

Molecule 1 - RNA (174-MER)
    ChainsA
    EngineeredYES
    Other DetailsIN VITRO TRANSCRIBED RNA FROM THE THERMOTOGA MARITIMA MSB8 ASD GENE
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2K1Ligand/IonPOTASSIUM ION
3NA17Ligand/IonSODIUM ION
4OLZ1Ligand/IonO-(2-AMINOETHYL)-L-SERINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:221BINDING SITE FOR RESIDUE K A 200
2AC2SOFTWAREHOH A:239 , HOH A:272BINDING SITE FOR RESIDUE NA A 201
3AC3SOFTWAREHOH A:228 , HOH A:245 , HOH A:258BINDING SITE FOR RESIDUE NA A 202
4AC7SOFTWAREHOH A:249 , HOH A:294BINDING SITE FOR RESIDUE NA A 209
5AC8SOFTWAREHOH A:256BINDING SITE FOR RESIDUE NA A 210
6AC9SOFTWAREHOH A:274 , HOH A:292BINDING SITE FOR RESIDUE NA A 212
7BC1SOFTWAREHOH A:252BINDING SITE FOR RESIDUE NA A 213
8BC4SOFTWAREHOH A:225BINDING SITE FOR RESIDUE OLZ A 175

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DJ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DJ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 3DJ0)

(-) 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:RNA  Length:174
                                                                                                                                                                                                              
                 3dj0 A   1 GGCCGACGGAGGCGCGCCCGAGAUGAGUAGGCUGUCCCAUCAGGGGAGGAAUCGGGGACGGCUGAAAGGCGAGGGCGCCGAAGGGUGCAGAGUUCCUCCCGCUCUGCAUGCCUGGGGGUAUGGGGAAUACCCAUACCACUGUCACGGAGGUCUCUCCGUGGAGAGCCGUCGGUc 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |
                                                                                                                                                                                                       174-CCC

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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 3DJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DJ0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3DJ0)

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(-) Related Entries Specified in the PDB File

3dig 3dil 3dim 3dio 3diq 3dir 3dis 3dix 3diy 3diz 3dj2