8GTZ | pdb_00008gtz

Crystal structure of exopolyphosphatase (PPX) mutant E137A from Zymomonas mobilis in complex with magnesium ions

• PDB DOI: https://doi.org/10.2210/pdb8GTZ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Zymomonas mobilis
• Expression System: Escherichia coli
• 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: 1.56 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

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

Aili, Z., Lu, Z.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.62 kDa 
• Atom Count: 4,297 
• Modeled Residue Count: 462 
• 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	Mutation(s): 2  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.74	α = 90
b = 47.901	β = 126.53
c = 94.892	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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 1.1: 2026-03-04
  Changes: Refinement description, Structure summary