3C8D | pdb_00003c8d

Crystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of 2,3-Di-hydroxy-N-benzoyl-glycine

• PDB DOI: https://doi.org/10.2210/pdb3C8D/pdb

• Classification: HYDROLASE
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-11 Released: 2008-02-26 
• Deposition Author(s): Kim, Y., Maltseva, N., Abergel, R., Holzle, D., Raymond, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.194 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.153 (DCC) 

Starting Model: experimental

Literature

Siderophore Mediated Iron Acquisition: Structure and Specificity of Enterobactin Esterase from Shigella flexneri.

Kim, Y., Maltseva, N., Abergel, R., Holzle, D., Raymond, K., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 184.48 kDa 
• Atom Count: 13,727 
• Modeled Residue Count: 1,514 
• Deposited Residue Count: 1,612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterochelin esterase	A, B, C, D	403	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: fes, S0503, SF0497 EC: 3.1.1.108
UniProt
Find proteins for A0A0H2VTI6 (Shigella flexneri) Explore A0A0H2VTI6  Go to UniProtKB:  A0A0H2VTI6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], F [auth B], G [auth C], H [auth C]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.194 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.153 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.297	α = 90
b = 155.972	β = 90.01
c = 48.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Kim, Y., Maltseva, N., Abergel, R., Holzle, D., Raymond, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description