3V4D

Crystal structure of RutC protein a member of the YjgF family from E.coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Structure of Escherichia coli RutC, a member of the YjgF family and putative aminoacrylate peracid reductase of the rut operon.

Knapik, A.A., Petkowski, J.J., Otwinowski, Z., Cymborowski, M.T., Cooper, D.R., Chruszcz, M., Krajewska, W.M., Minor, W.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1294-1299

  • DOI: 10.1107/S1744309112041796
  • Primary Citation of Related Structures:  
    3V4D

  • PubMed Abstract: 

    • RutC is the third enzyme in the Escherichia coli rut pathway of uracil degradation. RutC belongs to the highly conserved YjgF family of proteins. The structure of the RutC protein was determined and refined to 1.95 Å resolution. The crystal belonged to space group P2(1)2(1)2 and contained six molecules in the asymmetric unit ...

    RutC is the third enzyme in the Escherichia coli rut pathway of uracil degradation. RutC belongs to the highly conserved YjgF family of proteins. The structure of the RutC protein was determined and refined to 1.95 Å resolution. The crystal belonged to space group P2(1)2(1)2 and contained six molecules in the asymmetric unit. The structure was solved by SAD phasing and was refined to an Rwork of 19.3% (Rfree=21.7%). The final model revealed that this protein has a Bacillus chorismate mutase-like fold and forms a homotrimer with a hydrophobic cavity in the center of the structure and ligand-binding clefts between two subunits. A likely function for RutC is the reduction of peroxy-aminoacrylate to aminoacrylate as a part of a detoxification process.

    Organizational Affiliation: 

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoacrylate peracid reductase RutC134Escherichia coli O6Mutation(s): 0 
Gene Names: c1147, rutC
EC: 1
UniProt
Find proteins for P0AFQ6 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P0AFQ6 
Go to UniProtKB:  P0AFQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFQ6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,
B [auth C],
C [auth F],
D [auth B],
E [auth D],
A,
B [auth C],
C [auth F],
D [auth B],
E [auth D],
F [auth E]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.255α = 90
b = 179.181β = 90
c = 45.217γ = 90
Software Package:
Software NamePurpose
MD2data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
SOLVEphasing
RESOLVEmodel building
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Database references, Structure summary
  • Version 1.2: 2012-11-07
    Changes: Database references
  • Version 1.3: 2012-12-12
    Changes: Database references
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary