5YNL | pdb_00005ynl

Structure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site

• PDB DOI: https://doi.org/10.2210/pdb5YNL/pdb

• Classification: HYDROLASE
• Organism(s): Glaciozyma antarctica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-24 Released: 2018-01-31 
• Deposition Author(s): Quay, D.H.X., Yusof, N.Y., Illias, R.M., Firdaus-Raih, M., Abu-Bakar, F.D., Mahadi, N.M., Murad, A.M.A.
• Funding Organization(s): Ministry of Science, Technology and Innovation (MOSTI, Malaysia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 

Starting Model: in silico

Literature

Structure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site

Quay, D.H.X., Yusof, N.Y., Illias, R.M., Abu-Bakar, F.D., Mahadi, N.M., Firdaus-Raih, M., Murad, A.M.A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.78 kDa 
• Atom Count: 2,226 
• Modeled Residue Count: 292 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase	A	362	Glaciozyma antarctica	Mutation(s): 0  EC: 3.5.3.1
UniProt
Find proteins for A0A2R2JFW7 (Glaciozyma antarctica (strain PI12)) Explore A0A2R2JFW7  Go to UniProtKB:  A0A2R2JFW7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.193	α = 90
b = 91.193	β = 90
c = 107.779	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Quay, D.H.X., Yusof, N.Y., Illias, R.M., Firdaus-Raih, M., Abu-Bakar, F.D., Mahadi, N.M., Murad, A.M.A.

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Funding Organization	Location	Grant Number
Ministry of Science, Technology and Innovation (MOSTI, Malaysia)	Malaysia	02-05-20-SF0007

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2025-12-31
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Structure summary