8U0I

Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb8U0I/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-29 Released: 2024-09-04 
• Deposition Author(s): Hammons, N.A., Schnicker, N.J., Fuentes, E.J.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.210 
• R-Value Work: 0.173 

Starting Model: in silico

Literature

Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa

Hammons, N.A., Schnicker, N.J., Fuentes, E.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 11.63 kDa 
• Atom Count: 874 
• Modelled Residue Count: 86 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PilZ domain-containing protein	A	90	Pseudomonas aeruginosa PA14	Mutation(s): 0  Gene Names: PA0012
UniProt
Find proteins for Q9I7B4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I7B4  Go to UniProtKB:  Q9I7B4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E (Subject of Investigation/LOI)	B [auth A], C [auth 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
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.210 
• R-Value Work: 0.173 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.317	α = 90
b = 50.317	β = 90
c = 90.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Hammons, N.A., Schnicker, N.J., Fuentes, E.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	1R01AI170557-01A1

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release