3G05

Crystal structure of N-terminal domain (2-550) of E.coli MnmG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme.

Shi, R., Villarroya, M., Ruiz-Partida, R., Li, Y., Proteau, A., Prado, S., Moukadiri, I., Benitez-Paez, A., Lomas, R., Wagner, J., Matte, A., Velazquez-Campoy, A., Armengod, M.E., Cygler, M.

(2009) J Bacteriol 191: 7614-7619

  • DOI: https://doi.org/10.1128/JB.00650-09
  • Primary Citation of Related Structures:  
    3CES, 3G05

  • PubMed Abstract: 

    The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-A resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

    • Organizational Affiliation: 

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
A, B
576Escherichia coli O157:H7 str. EDL933Mutation(s): 0 
Gene Names: ECs4683, gidA, mnmG, Z5241
UniProt
Find proteins for Q8XAY0 (Escherichia coli O157:H7)
Explore Q8XAY0 
Go to UniProtKB:  Q8XAY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XAY0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.593α = 90
b = 144.593β = 90
c = 271.019γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description