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)

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
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This is version 1.0 of the entry. See complete history.

Literature

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

Xu, F., Fan, S., Li, Y.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q841S6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.