4A9V | pdb_00004a9v

Pseudomonas fluorescens PhoX

• PDB DOI: https://doi.org/10.2210/pdb4A9V/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas fluorescens Pf0-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-28 Released: 2012-12-05 
• Deposition Author(s): Yong, S.C., Roversi, P., Lillington, J.E.D., Zeldin, O.B., Garman, E.F., Lea, S.M., Berks, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.117 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Starting Model: experimental

Literature

A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry

Yong, S.C., Roversi, P., Lillington, J., Rodriguez, F., Krehenbrink, M., Zeldin, O.B., Garman, E.F., Lea, S.M., Berks, B.C.

(2014) Science 345: 1170

• PubMed: 25190793 
• DOI: https://doi.org/10.1126/science.1254237
• Primary Citation Related Structures: 
  3ZWU, 4A9V, 4A9X, 4ALF, 4AMF


• PubMed Abstract: 
  

  Alkaline phosphatases play a crucial role in phosphate acquisition by microorganisms. To expand our understanding of catalysis by this class of enzymes, we have determined the structure of the widely occurring microbial alkaline phosphatase PhoX. The enzyme contains a complex active-site cofactor comprising two antiferromagnetically coupled ferric iron ions (Fe(3+)), three calcium ions (Ca(2+)), and an oxo group bridging three of the metal ions. Notably, the main part of the cofactor resembles synthetic oxide-centered triangular metal complexes. Structures of PhoX-ligand complexes reveal how the active-site metal ions bind substrate and implicate the cofactor oxo group in the catalytic mechanism. The presence of iron in PhoX raises the possibility that iron bioavailability limits microbial phosphate acquisition.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom.

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: 65.5 kDa 
• Atom Count: 5,585 
• Modeled Residue Count: 581 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOX	A	592	Pseudomonas fluorescens Pf0-1	Mutation(s): 0  EC: 3.1.3.1
UniProt
Find proteins for Q3K5N8 (Pseudomonas fluorescens (strain Pf0-1)) Explore Q3K5N8  Go to UniProtKB:  Q3K5N8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEO	S [auth A]	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	Q [auth A], R [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
LI	C [auth A], D [auth A], G [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.117 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.82	α = 90
b = 75.98	β = 90
c = 114.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Yong, S.C., Roversi, P., Lillington, J.E.D., Zeldin, O.B., Garman, E.F., Lea, S.M., Berks, B.C.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Database references
• Version 1.2: 2014-09-17
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description