5XFZ

Crystal structure of a novel PET hydrolase R103G/S131A mutant from Ideonella sakaiensis 201-F6

• PDB DOI: https://doi.org/10.2210/pdb5XFZ/pdb

• Classification: HYDROLASE
• Organism(s): Piscinibacter sakaiensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-04-11 Released: 2017-12-20 
• Deposition Author(s): Han, X., Liu, W.D., Zheng, Y.Y., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.170 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Literature

Structural insight into catalytic mechanism of PET hydrolase

Han, X., Liu, W., Huang, J.W., Ma, J., Zheng, Y., Ko, T.P., Xu, L., Cheng, Y.S., Chen, C.C., Guo, R.T.

(2017) Nat Commun 8: 2106-2106

• PubMed: 29235460 
• DOI: https://doi.org/10.1038/s41467-017-02255-z
• Primary Citation of Related Structures:  
  5XFY, 5XFZ, 5XG0, 5XH2, 5XH3


• PubMed Abstract: 
  

  PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated.

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Organizational Affiliation: 

Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 28.03 kDa 
• Atom Count: 2,208 
• Modelled Residue Count: 262 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	262	Piscinibacter sakaiensis	Mutation(s): 2  Gene Names: ISF6_4831 EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6)) Explore A0A0K8P6T7  Go to UniProtKB:  A0A0K8P6T7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.170 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.945	α = 90
b = 51.618	β = 90
c = 84.59	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Han, X., Liu, W.D., Zheng, Y.Y., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description