7W1I | pdb_00007w1i

Crystal structure of carboxylesterase mutant from Thermobifida fusca with C8X and C9C

PDB DOI: https://doi.org/10.2210/pdb7W1I/pdb

Classification: HYDROLASE
Organism(s): Thermobifida fusca
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-11-19 Released: 2022-11-23
Deposition Author(s): Han, X., Gerlis, H., Li, Z., Gao, J., Wei, R., Liu, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.208 (Depositor), 0.194 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7W1I

Ligand Structure Quality Assessment

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

Literature

Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization

Von Haugwitz, G., Han, X., Pfaff, L., Li, Q., Wei, H., Gao, J., Methling, K., Ao, Y., Brack, Y., Mican, J., Feiler, C.G., Weiss, M.S., Bednar, D., Palm, G.J., Lalk, M., Lammers, M., Damborsky, J., Weber, G., Liu, W., Bornscheuer, U.T., Wei, R.

(2022) ACS Catal 12: 15259-15270

DOI: https://doi.org/10.1021/acscatal.2c03772

Macromolecule Content

Total Structure Weight: 53.43 kDa
Atom Count: 4,465
Modeled Residue Count: 497
Deposited Residue Count: 497
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase	A	497	Thermobifida fusca	Mutation(s): 1 EC: 3.1.1.1
UniProt
Find proteins for P86325 (Thermobifida fusca) Explore P86325 Go to UniProtKB: P86325
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P86325
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C8X (Subject of Investigation/LOI) Query on C8X 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]	bis(2-hydroxyethyl) benzene-1,4-dicarboxylate C₁₂ H₁₄ O₆ QPKOBORKPHRBPS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
C9C (Subject of Investigation/LOI) Query on C9C Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(2-hydroxyethyloxycarbonyl)benzoic acid C₁₀ H₁₀ O₅ BCBHDSLDGBIFIX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.208 (Depositor), 0.194 (DCC)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.744	α = 90
b = 110.236	β = 106.42
c = 53.418	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2023-06-07
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.