8IBM | pdb_00008ibm

Sulfate bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation

PDB DOI: https://doi.org/10.2210/pdb8IBM/pdb

Classification: HYDROLASE
Organism(s): Saccharomonospora viridis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-10 Released: 2023-03-15
Deposition Author(s): Emori, M., Numoto, N., Kamiya, N., Oda, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.267 (Depositor), 0.270 (DCC)
R-Value Work:
0.234 (Depositor), 0.230 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.

Numoto, N., Kamiya, N., Oda, M.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.02.26.529345

Macromolecule Content

Total Structure Weight: 58.05 kDa
Atom Count: 4,135
Modeled Residue Count: 524
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase family protein	A, B	263	Saccharomonospora viridis	Mutation(s): 8 Gene Names: Cut190, SAMN02982918_2340 EC: 3.1.1.74
UniProt
Find proteins for W0TJ64 (Saccharomonospora viridis) Explore W0TJ64 Go to UniProtKB: W0TJ64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W0TJ64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267 (Depositor), 0.270 (DCC)
R-Value Work: 0.234 (Depositor), 0.230 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.755	α = 90
b = 83.755	β = 90
c = 64.752	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary

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.