9JCB | pdb_00009jcb

CalA-like lipase from Kalmanozyma brasiliensis

• PDB DOI: https://doi.org/10.2210/pdb9JCB/pdb

• Classification: HYDROLASE
• Organism(s): Kalmanozyma brasiliensis GHG001
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.46 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 286.26 kDa 
• Atom Count: 19,440 
• Modeled Residue Count: 2,544 
• Deposited Residue Count: 2,634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B, C, D, E, F	439	Kalmanozyma brasiliensis GHG001	Mutation(s): 0  Gene Names: PSEUBRA_SCAF1g00196 EC: 3.1.1.3
UniProt
Find proteins for V5F2U3 (Kalmanozyma brasiliensis (strain GHG001)) Explore V5F2U3  Go to UniProtKB:  V5F2U3
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.46 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.372	α = 90
b = 178.309	β = 119.24
c = 105.386	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Xue, B., Ling, L.H., Jia, X., Yew, W.S.

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

Revision History  

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