6IJ4 | pdb_00006ij4

Crystal structure of PETase S121E, D186H mutant from Ideonella sakaiensis

• PDB DOI: https://doi.org/10.2210/pdb6IJ4/pdb

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


• Deposited: 2018-10-08 Released: 2019-09-04 
• Deposition Author(s): Joo, S., Kim, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.247 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation

Son, H.F., Cho, I.J., Joo, S., Seo, H., Sagong, H.Y., Choi, S.Y., Lee, S.Y., Kim, K.J.

(2019) ACS Catal 9: 3519-3526

• DOI: https://doi.org/10.1021/acscatal.9b00568

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.58 kDa 
• Atom Count: 2,027 
• Modeled Residue Count: 262 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	300	Piscinibacter sakaiensis	Mutation(s): 2  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: 1.86 Å
• R-Value Free:  0.247 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.198	α = 90
b = 50.864	β = 92.7
c = 41.486	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection
Coot	model building
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Joo, S., Kim, K.J.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary