5T06

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb5T06/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-08-15 Released: 2016-09-07 
• Deposition Author(s): Watanabe, N., Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Hexanoyl-CoA

Watanabe, N., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 63.26 kDa 
• Atom Count: 4,791 
• Modelled Residue Count: 515 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA thioester hydrolase YbgC	A, B, C, D	134	Escherichia coli O157:H7	Mutation(s): 1  Gene Names: ybgC, Z0904, ECs0771 EC: 3.1.2
UniProt
Find proteins for P0A8Z3 (Escherichia coli (strain K12)) Explore P0A8Z3  Go to UniProtKB:  P0A8Z3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HXC	H [auth C]	HEXANOYL-COENZYME A C27 H46 N7 O17 P3 S OEXFMSFODMQEPE-HDRQGHTBSA-N
EDO	E [auth A], F [auth B], G [auth B], I [auth C], J [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.213 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.747	α = 90
b = 96.772	β = 90
c = 97.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Watanabe, N., Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary