3EOL | pdb_00003eol

2.0A crystal structure of isocitrate lyase from Brucella melitensis (P43212)

• PDB DOI: https://doi.org/10.2210/pdb3EOL/pdb

• Classification: LYASE
• Organism(s): Brucella melitensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-28 Released: 2008-10-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structures of isocitrate lyase from Brucella melitensis

SSGCID

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: 94.72 kDa 
• Atom Count: 5,848 
• Modeled Residue Count: 724 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isocitrate lyase	A, B	433	Brucella melitensis	Mutation(s): 0  Gene Names: BMEI0409 EC: 4.1.3.1
UniProt
Find proteins for Q2YQA0 (Brucella abortus (strain 2308)) Explore Q2YQA0  Go to UniProtKB:  Q2YQA0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth B], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.702	α = 90
b = 79.702	β = 90
c = 281.595	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations