Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87698.55 
• Atom Count: 5665 
• Residue Count: 804 
• Unique protein chains: 1

3V4D

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

• DOI: 10.2210/pdb3V4D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-12-14 Released: 2012-01-04 
• Deposition Author(s): Knapik, A.A., Petkowski, J.J., Otwinowski, Z., Cymborowski, M.T., Cooper, D.R., Chruszcz, M., Porebski, P.J., Niedzialkowska, E., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

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

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

• PubMed: 23143235 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Aminoacrylate peracid reductase RutC	A, C, F, B, D, E	134	Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)	Mutation(s): 0  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
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.217 
• R-Value Work: 0.193 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data DOI: 
  10.18430/M3TG6G Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 92.255	α = 90.00
b = 179.181	β = 90.00
c = 45.217	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CCP4	model building
MD2	data collection
DM	model building
RESOLVE	phasing
CCP4	phasing
MLPHARE	phasing
SHELXCD	phasing
SOLVE	phasing
SHELXE	model building
ARP/wARP	model building
HKL-3000	phasing
REFMAC	refinement
DM	phasing
HKL-2000	data reduction
RESOLVE	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-14 
• Released Date: 2012-01-04 
• Deposition Author(s): Knapik, A.A., Petkowski, J.J., Otwinowski, Z., Cymborowski, M.T., Cooper, D.R., Chruszcz, M., Porebski, P.J., Niedzialkowska, E., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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