3I4E | pdb_00003i4e

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3I4E/pdb

• Classification: LYASE
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-01 Released: 2009-07-14 
• Deposition Author(s): Staker, B.L., Arakaki, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei

Staker, B.L., Arakaki, T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 192.51 kDa 
• Atom Count: 12,730 
• Modeled Residue Count: 1,648 
• Deposited Residue Count: 1,756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B, C, D	439	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: aceA, BPSL2188 EC: 4.1.3.1
UniProt
Find proteins for Q63SY3 (Burkholderia pseudomallei (strain K96243)) Explore Q63SY3  Go to UniProtKB:  Q63SY3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.666	α = 90
b = 137.025	β = 90
c = 160.162	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Staker, B.L., Arakaki, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2025-10-22
  Changes: Structure summary