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 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 68: 1294-1299

  • DOI: 10.1107/S1744309112041796

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoacrylate peracid reductase RutC
A, C, F, B, D, E
134Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Gene Names: rutC
EC: 1.-.-.-
Find proteins for P0AFQ6 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0AFQ6
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 92.255α = 90.00
b = 179.181β = 90.00
c = 45.217γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CCP4model building
MD2data collection
DMmodel building
RESOLVEphasing
CCP4phasing
MLPHAREphasing
SHELXCDphasing
SOLVEphasing
SHELXEmodel building
ARP/wARPmodel building
HKL-3000phasing
REFMACrefinement
DMphasing
HKL-2000data reduction
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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