5T07 | pdb_00005t07

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

• PDB DOI: https://doi.org/10.2210/pdb5T07/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: 1.72 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative acyl-CoA thioesterase EC709/ECK0725 from Escherichia coli in complex with Decanoyl-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: 64.79 kDa 
• Atom Count: 4,932 
• Modeled Residue Count: 520 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFK	E [auth A], F [auth C], G [auth D]	decanoyl-CoA C31 H54 N7 O17 P3 S CNKJPHSEFDPYDB-HSJNEKGZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.923	α = 90
b = 97.12	β = 90
c = 97.696	γ = 90

Software Package:

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

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