8H5M | pdb_00008h5m

Crystal structure of PETase S121E/D186H/N233C/S242T/N246D/S282C mutant from Ideonella sakaiensis

PDB DOI: https://doi.org/10.2210/pdb8H5M/pdb

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

Deposited: 2022-10-13 Released: 2023-10-25
Deposition Author(s): Lee, S.H., Seo, H., Kim, K.-J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.188 (Depositor), 0.198 (DCC)
R-Value Work:
0.151 (Depositor), 0.162 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

A case of balance engineering exhibits kinetic relationship between mesophilic and thermophilic poly(ethylene terephthalate) depolymerases.

Lee, S.H., Seo, H., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 31.6 kDa
Atom Count: 2,158
Modeled Residue Count: 261
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	300	Piscinibacter sakaiensis	Mutation(s): 6 Gene Names: ISF6_4831 EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Piscinibacter sakaiensis) Explore A0A0K8P6T7 Go to UniProtKB: A0A0K8P6T7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K8P6T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.188 (Depositor), 0.198 (DCC)
R-Value Work: 0.151 (Depositor), 0.162 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.677	α = 90
b = 67.795	β = 90
c = 78.471	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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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.