3LG3

1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb3LG3/pdb

• Classification: LYASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-19 Released: 2010-04-14 
• Deposition Author(s): Sharma, S.S., Brunzelle, J.S., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.165 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 

Literature

1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92

Sharma, S.S., Brunzelle, J.S., Wawrzak, Z., Skarina, T., Gordon, E., Savchenko, A., Anderson, W.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 96.37 kDa 
• Atom Count: 7,874 
• Modelled Residue Count: 833 
• Deposited Residue Count: 870 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B	435	Yersinia pestis	Mutation(s): 0  Gene Names: aceA, y0016, YPO3725, YP_3087 EC: 4.1.3.1
UniProt
Find proteins for A0A2S9PCG6 (Yersinia pestis) Explore A0A2S9PCG6  Go to UniProtKB:  A0A2S9PCG6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.165 
• R-Value Work: 0.131 
• R-Value Observed: 0.133 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/m33lg3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.163	α = 90
b = 115.133	β = 90
c = 174.835	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
CRANK	phasing
ARP/wARP	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Sharma, S.S., Brunzelle, J.S., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-14
  Changes: Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary