8XM1

Phytase mutant APPAmut4

• PDB DOI: https://doi.org/10.2210/pdb8XM1/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia intermedia
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-12-27 Released: 2024-07-03 
• Deposition Author(s): Tu, T., Wang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

The mutant crystal structure of phytase APPAmut4 from Yersinia intermedia

Tu, T., Wang, Q.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.74 kDa 
• Atom Count: 3,687 
• Modelled Residue Count: 409 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytase	A	418	Yersinia intermedia	Mutation(s): 4  EC: 3.1.3.26
UniProt
Find proteins for Q000T0 (Yersinia intermedia) Explore Q000T0  Go to UniProtKB:  Q000T0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS (Subject of Investigation/LOI)	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.514	α = 90
b = 46.016	β = 90
c = 192.797	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Tu, T., Wang, Q.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32222082

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release