9JC9 | pdb_00009jc9

CalA-like lipase from Ustilago trichophora (S200A mutant)

PDB DOI: https://doi.org/10.2210/pdb9JC9/pdb

Classification: HYDROLASE
Organism(s): Ustilago trichophora
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2024-08-29 Released: 2025-04-02
Deposition Author(s): Xue, B., Ling, L.H., Jia, X., Yew, W.S.
Funding Organization(s): National Research Foundation (NRF, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.235 (Depositor), 0.242 (DCC)
R-Value Work:
0.194 (Depositor), 0.206 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Sustainable Biosynthesis of Diverse Fatty Acid Esters of Hydroxy Fatty Acids (FAHFAs) for Industrial Production

Ling, L.H., Chua, E.T., Xue, B., Jia, X., Chow, J.Y., Yang, R.L., Lim, Y.P., Han, P., Xie, H., Tan, C.H., Nguyen, G.K.T., Yew, W.S.

(2025) ACS Sustain Chem Eng 13: 2830-2844

DOI: https://doi.org/10.1021/acssuschemeng.4c08793

Macromolecule Content

Total Structure Weight: 49.03 kDa
Atom Count: 3,544
Modeled Residue Count: 434
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	446	Ustilago trichophora	Mutation(s): 1 Gene Names: UTRI_04204_B EC: 3.1.1.3
UniProt
Find proteins for A0A5C3EAQ1 (Ustilago trichophora) Explore A0A5C3EAQ1 Go to UniProtKB: A0A5C3EAQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5C3EAQ1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM (Subject of Investigation/LOI) Query on PLM 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]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-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: 2.37 Å
R-Value Free: 0.235 (Depositor), 0.242 (DCC)
R-Value Work: 0.194 (Depositor), 0.206 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.358	α = 90
b = 97.358	β = 90
c = 209.686	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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.