8ZU4 | pdb_00008zu4

Crystal Structure of Methyl parathion hydrolase mutant A127L/I145L/Q272D/S279A/S304P

• PDB DOI: https://doi.org/10.2210/pdb8ZU4/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. WBC-3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-06-07 Released: 2025-06-11 
• Deposition Author(s): Xu, F., Fan, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Methyl parathion hydrolase mutant A127L/I145L/Q272D/S279A/S304P

Xu, F., Fan, S., Li, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.03 kDa 
• Atom Count: 5,066 
• Modeled Residue Count: 590 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl parathion hydrolase	A, B	296	Pseudomonas sp. WBC-3	Mutation(s): 5  Gene Names: mpd
UniProt
Find proteins for Q841S6 (Pseudomonas sp. (strain WBC-3)) Explore Q841S6  Go to UniProtKB:  Q841S6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.233	α = 90
b = 86.32	β = 112.81
c = 58.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Xu, F., Fan, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22078129

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release