7VWN | pdb_00007vwn

The structure of an engineered PET hydrolase

• PDB DOI: https://doi.org/10.2210/pdb7VWN/pdb

• Classification: HYDROLASE
• Organism(s): Piscinibacter sakaiensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-11-11 Released: 2022-11-16 
• Deposition Author(s): Xie, W., Jia, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

An engineered PET hydrolase for biodegradation of microplastics in ocean water

Xie, W., Jia, Q.

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: homology

Macromolecule Content 

• Total Structure Weight: 28.62 kDa 
• Atom Count: 2,221 
• Modeled Residue Count: 263 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	270	Piscinibacter sakaiensis	Mutation(s): 9  Gene Names: ISF6_4831 EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Piscinibacter sakaiensis) Explore A0A0K8P6T7  Go to UniProtKB:  A0A0K8P6T7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.588	α = 90
b = 50.536	β = 92.458
c = 41.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Xie, W., Jia, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770075
National Natural Science Foundation of China (NSFC)	China	31870782

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary