8GTY

Crystal structure of exopolyphosphatase (PPX) from Zymomonas mobilis in complex with magnesium ions

• PDB DOI: https://doi.org/10.2210/pdb8GTY/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-09-09 Released: 2023-09-13 
• Deposition Author(s): Lu, Z., Wang, J., Zhang, B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 

Literature

Structure of the exopolyphosphatase (PPX) from Zymomonas mobilis reveals a two-magnesium-ions PPX

Lu, Z., Hu, Y., Wang, J., Zhang, B., Zhang, Y., Cui, Z., Zhang, L., Zhang, A.

(2024) Int J Biol Macromol 262: 129796

• DOI: https://doi.org/10.1016/j.ijbiomac.2024.129796

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: SAXS

Macromolecule Content

• Total Structure Weight: 53.52 kDa 
• Atom Count: 3,934 
• Modelled Residue Count: 472 
• Deposited Residue Count: 483 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ppx/GppA phosphatase	A	483	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 1  Gene Names: ZMO0713
UniProt
Find proteins for Q5NPM3 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q5NPM3  Go to UniProtKB:  Q5NPM3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.023	α = 90
b = 47.118	β = 124.45
c = 89.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Lu, Z., Wang, J., Zhang, B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 2.0: 2024-03-27
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary