5KL9

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

• PDB DOI: https://doi.org/10.2210/pdb5KL9/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-23 Released: 2016-07-06 
• Deposition Author(s): 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: 2.22 Å
• R-Value Free: 0.239 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

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

Stogios, P.J.

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: 64.62 kDa 
• Atom Count: 4,758 
• Modelled Residue Count: 522 
• 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): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	E [auth A], L [auth D]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	F [auth A], I [auth B], J [auth B], K [auth C], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], N [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.239 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m35kl9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.702	α = 90
b = 97.195	β = 90
c = 96.114	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): 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: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Other
• Version 1.2: 2016-08-31
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description