Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 30.01 kDa 
• Atom Count: 2340 
• Residue Count: 242 
• Unique protein chains: 1

3HV8

Crystal structure of FimX EAL domain from Pseudomonas aeruginosa bound to c-di-GMP

• DOI: 10.2210/pdb3HV8/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-15 Released: 2009-08-18 
• Deposition Author(s): Navarro, M.V.A.S., De, N., Bae, N., Sondermann, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX.

Navarro, M.V., De, N., Bae, N., Wang, Q., Sondermann, H.

(2009) Structure 17: 1104-1116

• PubMed: 19679088 
• DOI: 10.1016/j.str.2009.06.010
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Bacterial pathogenesis involves social behavior including biofilm formation and swarming, processes that are regulated by the bacterially unique second messenger cyclic di-GMP (c-di-GMP). Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding signal transmission and the targets of c-di-GMP. FimX, a protein from Pseudomonas aeruginosa that governs twitching motility, belongs to a large subfamily containing both GGDEF and EAL domains. Biochemical and structural analyses reveals its function as a high-affinity receptor for c-di-GMP. A model for full-length FimX was generated combining solution scattering data and crystal structures of the degenerate GGDEF and EAL domains. Although FimX forms a dimer in solution via the N-terminal domains, a crystallographic EAL domain dimer suggests modes for the regulation of FimX by c-di-GMP binding. The results provide the structural basis for c-di-GMP sensing via degenerate phosphodiesterases.

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Organizational Affiliation: 

Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein FimX	A	268	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: fimX, PA4959 EC: 3.1.4.52
Find proteins for Q9HUK6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Go to UniProtKB:  Q9HUK6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	A	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C2E	Kd:  104.19999694824219   nM  PDBBind
C2E	Kd:  104.19999694824219   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.95	α = 90
b = 93.95	β = 90
c = 68.45	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-15 
• Released Date: 2009-08-18 
Deposition Author(s): Navarro, M.V.A.S., De, N., Bae, N., Sondermann, H.

Revision History 

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references