4ALF

Pseudomonas fluorescens PhoX in complex with phosphate

PDB DOI: https://doi.org/10.2210/pdb4ALF/pdb

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

Deposited: 2012-03-02 Released: 2013-03-13
Deposition Author(s): Yong, S.C., Roversi, P., Lillington, J.E.D., Zeldin, O.B., Garman, E.F., Lea, S.M., Berks, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.164
R-Value Work: 0.133
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1254237
Primary Citation of 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.

Organizational Affiliation

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecule Content

Total Structure Weight: 131.08 kDa
Atom Count: 10,802
Modelled Residue Count: 1,162
Deposited Residue Count: 1,184
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALKALINE PHOSPHATASE PHOX	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3K5N8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FEO Query on FEO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain W [auth B]	G [auth A], W [auth B]	MU-OXO-DIIRON Fe₂ O NPMYUMBHPJGBFA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain W [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B]	C [auth A], S [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] H [auth A] BA [auth B], CA [auth B], DA [auth B], EA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	D [auth A] E [auth A] F [auth A] T [auth B] U [auth B] D [auth A], E [auth A], F [auth A], T [auth B], U [auth B], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain L [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain L [auth A]	AA [auth B], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain L [auth A] Interactions & Density Focus chain AA [auth B] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.164
R-Value Work: 0.133
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.099	α = 90
b = 71.035	β = 90
c = 228.501	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2014-09-10
Changes: Database references
Version 1.2: 2014-09-17
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description