2VLI

Structure of Deinococcus radiodurans tunicamycin resistance protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Deinococcus Radiodurans Tunicamycin-Resistance Protein (Tmrd), a Phosphotransferase.

Kapp, U.Macedo, S.Hall, D.R.Leiros, I.Mcsweeney, S.M.Mitchell, E.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 479

  • DOI: https://doi.org/10.1107/S1744309108011822
  • Primary Citation of Related Structures:  
    2VLI

  • PubMed Abstract: 

    The open-reading frame (ORF) DR_1419 in the Deinococcus radiodurans genome is annotated as a representative of the wide family of tunicamycin-resistance proteins as identified in a range of bacterial genomes. The D. radiodurans ORF DR_1419 was cloned and expressed; the protein TmrD was crystallized and its X-ray crystal structure was determined to 1.95 A resolution. The structure was determined using single-wavelength anomalous diffraction with selenomethionine-derivatized protein. The refined structure is the first to be reported for a member of the tunicamycin-resistance family. It reveals strong structural similarity to the family of nucleoside monophosphate kinases and to the chloramphenicol phosphotransferase of Streptomyces venezuelae, suggesting that the mode of action is possibly by phosphorylation of tunicamycin.


  • Organizational Affiliation

    European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP-220, 38043 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBIOTIC RESISTANCE PROTEIN
A, B
183Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RUG7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RUG7 
Go to UniProtKB:  Q9RUG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RUG7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.36α = 90
b = 118.16β = 90
c = 81.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary