Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 36.91 kDa 
• Atom Count: 2146 
• Residue Count: 269 
• Unique protein chains: 1

6IKI

Crystal structure of YfiB(W55L)

• DOI: 10.2210/pdb6IKI/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-16 Released: 2019-03-13 
• Deposition Author(s): Li, S., Zhang, Q., Bartlam, M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 

Literature

Structural analysis of activating mutants of YfiB from Pseudomonas aeruginosa PAO1.

Li, S., Li, T., Teng, X., Lou, X., Xu, Y., Zhang, Q., Bartlam, M.

(2018) Biochem Biophys Res Commun 506: 997-1003

• PubMed: 30404734 
• DOI: 10.1016/j.bbrc.2018.10.190
• Primary Citation of Related Structures:  
  6IKI, 6IKK, 6IKJ


• PubMed Abstract: 
  

Bacterial cyclic-di-GMP (c-di-GMP) is an important messenger molecule that influences diverse cellular processes including motility, virulence and cytotoxicity systems, polysaccharide synthesis and biofilm formation. The YfiBNR tripartite signalling system in P. aeruginosa modulates the cellular c-di-GMP levels in response to signals received from the periplasm. In this study, we analyse the structures of activating mutants of the outer membrane protein YfiB that give rise to increased surface attachment and biofilm formation. The F48S and W55L mutants of YfiB(27-168) crystallize in the same dimeric arrangement as our previously reported YfiB structures that preclude complex formation with YfiR. The L43P mutant of YfiB(27-168) is monomeric and forms a stable complex with YfiR. The YfiB(L43P)-YfiR crystal structure reveals a dramatic rearrangement of the N-terminal fragment, which is implicated in increased YfiB activation and membrane attachment, upon YfiR binding. Comparison with our previous complex structure between YfiB(59-168) and YfiR reveals extensive interactions between the N-terminal fragment of YfiB (residues 35-55) and YfiR.

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Organizational Affiliation: 

State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China; College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfiB	A, B	168	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: yfiB, PA1119
Find proteins for Q9I4L6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4L6  Go to UniProtKB:  Q9I4L6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.563	α = 90
b = 44.563	β = 90
c = 154.934	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-10-16 
• Released Date: 2019-03-13 
Deposition Author(s): Li, S., Zhang, Q., Bartlam, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570128

Revision History 

• Version 1.0: 2019-03-13
  Type: Initial release