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Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion
DOI:10.2210/pdb4j7m/pdb   NDB ID: NA2269
4J7M
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/rna
    Structure Weight: 45499.31
    Molecule: Protein Dom3Z
    Polymer: 1 Type: protein Length: 378
    Chains: A
    EC#: 3.1.13    3.6.1   
    Organism: Mus musculus
    Gene Names: Dxo Dom3z Ng6
    UniProtKB: Protein Feature View | Search PDB | O70348  
    Molecule: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3')
    Polymer: 2 Type: rna Length: 5
    Chains: B
    Details: 5'-end monophosphorylated oligo RNA with Phosphorothioate link between 1-2 U and 2-3 U
    Organism: synthetic construct
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Mus musculus   Taxonomy   Common Name: Mouse Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3FQI   
    3FQJ   
    4J7L   
    4J7N   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    CA Ca
    CALCIUM ION
    UBD
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    UBD C9 H14 N2 O12 P2
    URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)
    UBD:4J7M
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    U37
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    U37 C9 H13 N2 O8 P S U rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2269
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Chang, J.H.,  Tong, L.

    Deposition:   2013-02-13
    Release:   2013-03-27
    Last Modified (REVDAT):   2014-03-12
     
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    2014-03-12
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.70
    R-Value: 0.183 (obs.)
    R-Free: 0.213
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 49.99 α = 90.00 
    b = 87.84 β = 111.69 
    c = 54.36 γ = 90.00