5YHP | pdb_00005yhp

Proline iminopeptidase from Psychrophilic yeast glaciozyma antarctica

• PDB DOI: https://doi.org/10.2210/pdb5YHP/pdb

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


• Deposited: 2017-09-29 Released: 2017-10-25 
• Deposition Author(s): Rodzli, N.A., Kamaruddin, S., Jonet, A., Seman, W.M.K.W., Tab, M.M., Minor, N., Jaafar, N.R., Mahadi, N.M., Murad, A.M.A., Bakar, F.D.A., Illias, R.M.D.
• Funding Organization(s): MINISTRY OF SCIENCE, TECHNOLOGY AND INNOVATION MALAYSIA

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Biochemical Characterisation and Structure Determination of a Novel Cold-Active Proline Iminopeptidase from the Psychrophilic Yeast, Glaciozyma antarctica PI12

Kamaruddin, S., Ahmad Redzuan, R., Minor, N., Seman, W.M., Md Tab, M., Jaafar, N.R., Ahmad Rodzli, N., Jonet, M.A., Bharudin, I., Yusof, N.A., Xia, D.Q., Mahadi, N.M., Abdul Murad, A.M., Abu Bakar, F.D.

(2022) Catalysts 12

• DOI: https://doi.org/10.3390/catal12070722

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 79.71 kDa 
• Atom Count: 5,177 
• Modeled Residue Count: 637 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold active proline iminopeptidase	A, B	355	Glaciozyma antarctica	Mutation(s): 0  EC: 3.4.11.5
UniProt
Find proteins for A0A2H4A311 (Glaciozyma antarctica) Explore A0A2H4A311  Go to UniProtKB:  A0A2H4A311

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A], D [auth A], E [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.388	α = 90
b = 82.269	β = 90
c = 171.005	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Rodzli, N.A., Kamaruddin, S., Jonet, A., Seman, W.M.K.W., Tab, M.M., Minor, N., Jaafar, N.R., Mahadi, N.M., Murad, A.M.A., Bakar, F.D.A., Illias, R.M.D.

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Funding Organization	Location	Grant Number
MINISTRY OF SCIENCE, TECHNOLOGY AND INNOVATION MALAYSIA	Malaysia	02-05-20-SF0007

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Database references, Structure summary