6IVY | pdb_00006ivy

Crystal structure of iron-bound HitA from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6IVY/pdb

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


• Deposited: 2018-12-04 Released: 2019-12-04 
• Deposition Author(s): Zhang, Z.R., Li, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Identification and Characterization of a Metalloprotein Involved in Gallium Internalization in Pseudomonas aeruginosa.

Guo, Y., Li, W., Li, H., Xia, W.

(2019) ACS Infect Dis 5: 1693-1697

• PubMed: 31475514 
• DOI: https://doi.org/10.1021/acsinfecdis.9b00271
• Primary Citation Related Structures: 
  6IVY, 6IWF, 6J2S


• PubMed Abstract: 
  

  Gallium nitrate (Ganite) is a potential drug for the treatment of Pseudomonas aeruginosa infection. CRISPR/Cas9-based gene mutagenesis studies reveal that siderophore pyochelin-facilitated uptake and an ABC transporter are two major Ga ³⁺ internalization pathways in Pseudomonas aeruginosa ( P. aeruginosa ). Crystal structures reveal that Ga ³⁺ and Fe ³⁺ occupy exactly the same metal site of HitA, a periplasmic iron-binding protein of the ABC transporter system. The study provides a molecular basis for Ga ³⁺ internalization by P. aeruginosa and facilitates gallium-based antimicrobial drug development.

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Organizational Affiliation: 
• MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-sen University , Guangzhou , Guangdong 510275 , China.
Guangdong Institute of Applied Biological Resources , Guangdong Key Laboratory of Animal Conservation and Resource Utilization/Guangdong Public Laboratory of Wild Animal Conservation and Utilization , Guangzhou , Guangdong 510260 , China.
Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.72 kDa 
• Atom Count: 4,989 
• Modeled Residue Count: 613 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic Ferric iron-binding Protein HitA	A, B	307	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: hitA, PA4687
UniProt
Find proteins for Q9HVA8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVA8  Go to UniProtKB:  Q9HVA8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	D [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.577	α = 90
b = 104.6	β = 110.192
c = 58.758	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Zhang, Z.R., Li, H.Y.

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description