4AIB

Crystal Structure of Ornithine Decarboxylase from Entamoeba histolytica.

• PDB DOI: https://doi.org/10.2210/pdb4AIB/pdb

• Classification: LYASE
• Organism(s): Entamoeba histolytica HM-1:IMSS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-09 Released: 2013-01-30 
• Deposition Author(s): Preeti, P., Kumar, P., Tomar, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 0.299 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 

Literature

Structural Insight Into Dfmo Resistant Ornithine Decarboxylase from Entamoeba Histolytica: An Inkling to Adaptive Evolution.

Preeti, P., Tapas, S., Kumar, P., Tomar, S.

(2013) PLoS One 8: 53397

• PubMed: 23326423 
• DOI: https://doi.org/10.1371/journal.pone.0053397
• Primary Citation of Related Structures:  
  4AIB


• PubMed Abstract: 
  

  Polyamine biosynthetic pathway is a validated therapeutic target for large number of infectious diseases including cancer, giardiasis and African sleeping sickness, etc. α-Difluoromethylornithine (DFMO), a potent drug used for the treatment of African sleeping sickness is an irreversible inhibitor of ornithine decarboxylase (ODC), the first rate limiting enzyme of polyamine biosynthesis. The enzyme ODC of E. histolytica (EhODC) has been reported to exhibit resistance towards DFMO.

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Organizational Affiliation: 

Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.

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 2  

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

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

Macromolecule Content

• Total Structure Weight: 178.3 kDa 
• Atom Count: 10,585 
• Modelled Residue Count: 1,315 
• Deposited Residue Count: 1,580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORNITHINE DECARBOXYLASE	A, B, C, D	395	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0  EC: 4.1.1.17
UniProt
Find proteins for Q58P26 (Entamoeba histolytica) Explore Q58P26  Go to UniProtKB:  Q58P26

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 0.299 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.671	α = 90
b = 119.283	β = 90
c = 179.292	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Preeti, P., Kumar, P., Tomar, S.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description