4AG0 | pdb_00004ag0

Crystal structure of FimX EAL domain

• PDB DOI: https://doi.org/10.2210/pdb4AG0/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-01-23 Released: 2013-01-09 
• Deposition Author(s): Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.284 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of an Eal Domain in Complex with Reaction Product 5'-Pgpg

Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

(2012) PLoS One 7: 52424

• PubMed: 23285035 
• DOI: https://doi.org/10.1371/journal.pone.0052424
• Primary Citation Related Structures: 
  4AFY, 4AG0


• PubMed Abstract: 
  

  FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686): one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

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Organizational Affiliation: 
• Laboratoire de Cristallographie et RMN biologiques, UMR 8015-Cente National de la Recherche Scientifique, Paris, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 60.91 kDa 
• Atom Count: 4,031 
• Modeled Residue Count: 499 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIMX	A, B	274	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA4959 EC: 3.1.4.52
UniProt
Find proteins for Q9HUK6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUK6  Go to UniProtKB:  Q9HUK6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.284 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.53	α = 90
b = 87.66	β = 90
c = 108.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description