POP-OUT | CLOSE
 
DNA binding and cleavage by the HNH homing endonuclease I-HmuI
DOI:10.2210/pdb1u3e/pdb   NDB ID: PD0575
1U3E
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: DNA Binding Protein/dna
    Structure Weight: 42874.31
    Molecule: 36-MER
    Polymer: 1 Type: dna Length: 36
    Chains: A
    Molecule: 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3'
    Polymer: 2 Type: dna Length: 21
    Chains: B
    Molecule: 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'
    Polymer: 3 Type: dna Length: 15
    Chains: C
    Molecule: HNH homing endonuclease
    Polymer: 4 Type: protein Length: 174
    Chains: M
    EC#: 3.1   
    Organism: Bacillus phage SPO1
    UniProtKB: Protein Feature View | Search PDB | P34081  
     
  •   Structure Validation Hide

    Download full validation report    

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 4
    Scientific Name: Bacillus phage spo1   Taxonomy   Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1A73  Intron-encoded endonuclease I-Ppo1 complexed with DNA (His-Cys box) 
    1FSJ  Crystal structure of the E9 Dnase domain (non-specific HNH nuclease) 
    1I3J  DNA-binding domain of Intron endonuclease I-Tevi with substrate 
    1PT3  crystal structure of Nuclease-Cole& complexed with Octamer DNA (non-specific HNH nuclease) 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    EDO
    Search 
    Download 
    EDO C2 H6 O2
    1,2-ETHANEDIOL
    MN
    Search 
    Download 
    MN Mn
    MANGANESE (II) ION
    SR
    Search 
    Download 
    SR Sr
    STRONTIUM ION
    TRS
    Search 
    Download 
    TRS C4 H12 N O3
    2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    TRS:1U3E
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PD0575
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Shen, B.W.,  Landthaler, M.,  Shub, D.A.,  Stoddard, B.L.

    Deposition:   2004-07-21
    Release:   2004-08-31
    Last Modified (REVDAT):   2011-11-16
     
  •   Revision History    Hide
    Mouse over text for details
    2011-11-16
    Atom occupancy
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.92
    R-Value: 0.220 (obs.)
    R-Free: 0.247
    Space Group: I 2 2 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 45.00 α = 90.00 
    b = 108.30 β = 90.00 
    c = 248.10 γ = 90.00