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): Pseudideonella 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)

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
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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

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

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A, B [auth D]	298	Pseudideonella 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K8P6T7
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

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

Revision History (Full details and data files)

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