4JEI | pdb_00004jei

Nonglycosylated Yarrowia lipolytica LIP2 lipase

• PDB DOI: https://doi.org/10.2210/pdb4JEI/pdb

• Classification: HYDROLASE
• Organism(s): Yarrowia lipolytica
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2013-02-27 Released: 2013-03-13 
• Deposition Author(s): Aloulou, A., Benarouche, A., Puccinelli, D., Spinelli, S., Cavalier, J.-F., Cambillau, C., Carriere, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.250 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Biochemical and structural characterization of non-glycosylated Yarrowia lipolytica LIP2 lipase

Aloulou, A., Benarouche, A., Puccinelli, D., Spinelli, S., Cavalier, J.-F., Cambillau, C., Carriere, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 33.44 kDa 
• Atom Count: 2,444 
• Modeled Residue Count: 299 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase 2	A	301	Yarrowia lipolytica	Mutation(s): 2  Gene Names: LIP2 EC: 3.1.1.3
UniProt
Find proteins for E0A7J0 (Yarrowia lipolytica) Explore E0A7J0  Go to UniProtKB:  E0A7J0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.250 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.693	α = 90
b = 116.693	β = 90
c = 170.272	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Aloulou, A., Benarouche, A., Puccinelli, D., Spinelli, S., Cavalier, J.-F., Cambillau, C., Carriere, F.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary