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RIP-Radiation-damage Induced Phasing
DOI:10.2210/pdb1n7a/pdb   NDB ID: UH0003
1N7A
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: DNA , RNA
    Structure Weight: 16717.45
    Molecule: RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
    Polymer: 1 Type: hybrid Length: 6
    Chains: A, B, C, D, E, F, G, H
    Details: The RNA hexamer UGAGGU where the 2nd G was replaced by a C8-brominated Gd was phased using radiation damage on the highly susceptible Br-C8 bond.
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1N6X  Trypsin model refined against data collected before "X-ray burn" 
    1N6Y  Trypsin model refined against data collected after "X-ray burn" 
    1N7B  RNA/DNA model refined against data collected after "X-ray burn" 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    K
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    K K
    POTASSIUM ION
    SPM
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    SPM C10 H26 N4
    SPERMINE
    SPM:1N7A
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    BGM
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    BGM C10 H13 Br N5 O7 P DG dnaLinking
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: UH0003
     
 
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:   Ravelli, R.B.G.,  Leiros, H.-K.S.,  Pan, B.,  Caffrey, M.,  McSweeney, S.

    Deposition:   2002-11-13
    Release:   2003-03-04
    Last Modified (REVDAT):   2009-02-24
     
  •   Revision History    Hide
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    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
    N/A
    Resolution[Å]:   1.20
    R-Value: 0.125 (obs.)
    R-Free: 0.156
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 31.23 α = 90.00 
    b = 51.10 β = 90.00 
    c = 70.65 γ = 90.00