8J5N | pdb_00008j5n

Crystal structure of a PETase variant V20 from Ideonella sakaiensis

• PDB DOI: https://doi.org/10.2210/pdb8J5N/pdb

• Classification: HYDROLASE
• Organism(s): Piscinibacter sakaiensis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-04-23 Released: 2024-04-24 
• Deposition Author(s): Wei, H.L., Gao, S.F., Li, Q., Liu, W.D., Zhu, L.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

beta-sheet Engineering of IsPETase for PET Depolymerization

Gao, S., Shi, L., Wei, H., Liu, P., Zhao, W., Gong, L., Tan, Z., Zhai, H., Liu, W., Liu, H., Zhu, L.

(2024) Engineering (beijing) 

• DOI: https://doi.org/10.1016/j.eng.2024.10.015

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.75 kDa 
• Atom Count: 4,043 
• Modeled Residue Count: 522 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A, B [auth D]	298	Piscinibacter sakaiensis	Mutation(s): 10  Gene Names: ISF6_4831 EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Piscinibacter sakaiensis) Explore A0A0K8P6T7  Go to UniProtKB:  A0A0K8P6T7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.279	α = 90
b = 77.925	β = 90
c = 125.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Wei, H.L., Gao, S.F., Li, Q., Liu, W.D., Zhu, L.L.

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

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2025-02-12
  Changes: Database references