9JCA | pdb_00009jca

CalA-like lipase from Ustilago trichophora

PDB DOI: https://doi.org/10.2210/pdb9JCA/pdb

Classification: HYDROLASE
Organism(s): Ustilago trichophora
Expression System: Komagataella pastoris
Mutation(s): No

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: 3.33 Å
R-Value Free:
0.297 (Depositor), 0.300 (DCC)
R-Value Work:
0.221 (Depositor), 0.246 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9JCA

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: 48.58 kDa
Atom Count: 3,337
Modeled Residue Count: 435
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	446	Ustilago trichophora	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C3EAQ1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.33 Å
R-Value Free: 0.297 (Depositor), 0.300 (DCC)
R-Value Work: 0.221 (Depositor), 0.246 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.73	α = 90
b = 96.73	β = 90
c = 207.397	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 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.