6L6S

The structure of the UdgX mutant H109E crosslinked to single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report



Literature

Structure of a covalent complex-forming UdgX mutant

Xie, W.Tu, J.Zeng, H.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phage SPO1 DNA polymerase-related proteinAB212Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: MSMEI_0259
EC: 2.7.7.7 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for I7F541 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7F541 
Go to UniProtKB:  I7F541
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')C, D16synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SF4
    Query on SF4

    Download CCD File 
    A, B
    IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.06 Å
    • R-Value Free: 0.261 
    • R-Value Work: 0.209 
    • R-Value Observed: 0.212 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.265α = 90
    b = 82.348β = 94.927
    c = 122.444γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2019-10-29 
    • Released Date: 2020-11-04 
    • Deposition Author(s): Xie, W., Tu, J., Zeng, H.

    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina31870782

    Revision History 

    • Version 1.0: 2020-11-04
      Type: Initial release