3EOO | pdb_00003eoo

2.9A crystal structure of methyl-isocitrate lyase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3EOO/pdb

• Classification: LYASE
• Organism(s): Burkholderia pseudomallei 1655
• 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: 2.90 Å
• R-Value Free: 
  0.299 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.240 (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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 512.15 kDa 
• Atom Count: 34,623 
• Modeled Residue Count: 4,596 
• Deposited Residue Count: 4,768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylisocitrate lyase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	298	Burkholderia pseudomallei 1655	Mutation(s): 0  Gene Names: BURPS1655_C0444, BURPS1710B_2458, BURPS1710b_3237, MSRB, prpB EC: 4.1.3.30

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.299 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.807	α = 90
b = 172.404	β = 90
c = 179.277	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: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Refinement description, Structure summary