Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.36 kDa 
• Atom Count: 6,254 
• Modelled Residue Count: 754 
• Deposited Residue Count: 754 
• Unique protein chains: 1

 5ACN

STRUCTURE OF ACTIVATED ACONITASE. FORMATION OF THE (4FE-4S) CLUSTER IN THE CRYSTAL

• PDB DOI:  https://doi.org/10.2210/pdb5ACN/pdb

• Classification: LYASE(CARBON-OXYGEN)
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1990-01-16 Released: 1990-07-15 
• Deposition Author(s): Robbins, A.H., Stout, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.215 

Literature

Structure of activated aconitase: formation of the [4Fe-4S] cluster in the crystal.

Robbins, A.H., Stout, C.D.

(1989) Proc Natl Acad Sci U S A 86: 3639-3643

• PubMed: 2726740 
• DOI: https://doi.org/10.1073/pnas.86.10.3639
• Primary Citation of Related Structures:  
  5ACN, 6ACN


• PubMed Abstract: 
  

The structure of activated pig heart aconitase [citrate(isocitrate) hydro-lyase, EC 4.2.1.3] containing a [4Fe-4S] cluster has been refined at 2.5-A resolution to a crystallographic residual of 18.2%. Comparison of this structure to the recently determined 2.1-A resolution structure of the inactive enzyme containing a [3Fe-4S] cluster, by difference Fourier analysis, shows that upon activation iron is inserted into the structure isomorphously. The common atoms of the [3Fe-4S] and [4Fe-4S] cores agree within 0.1 A; the three common cysteinyl S gamma ligand atoms agree within 0.25 A. The fourth ligand of the Fe inserted into the [3Fe-4S] cluster is a water or hydroxyl from solvent, consistent with the absence of a free cysteine ligand in the enzyme active site cleft and the isomorphism of the two structures. A water molecule occupies a similar site in the crystal structure of the inactive enzyme.

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Related Citations: 

• The Structure of Aconitase
  Robbins, A.H., Stout, C.D.
  (1989) Proteins 5: 289

• Iron-Sulfur Cluster in Aconitase. Crystallographic Evidence for a Three-Iron Center
  Robbins, A.H., Stout, C.D.
  (1985) J Biol Chem 260: 2328

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Organizational Affiliation: 

Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACONITASE	A	754	Sus scrofa	Mutation(s): 0  Gene Names: ACO2 EC: 4.2.1.3
UniProt
Find proteins for P16276 (Sus scrofa) Explore P16276  Go to UniProtKB:  P16276

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3S	C [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-MZMDZPPWAW
TRC	D [auth A]	TRICARBALLYLIC ACID C6 H8 O6 KQTIIICEAUMSDG-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.6	α = 90
b = 72	β = 90
c = 72.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1990-07-15 
Deposition Author(s): Robbins, A.H., Stout, C.D.

Revision History  

• Version 1.0: 1990-07-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence