5ACN

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1073/pnas.86.10.3639
  • Structures With Same Primary Citation

  • 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 dete ...

    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.


    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

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACONITASE
A
754Sus scrofaMutation(s): 0 
Gene Names: ACO2
EC: 4.2.1.3
Find proteins for P16276 (Sus scrofa)
Go to UniProtKB:  P16276
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

Download CCD File 
A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
TRC
Query on TRC

Download CCD File 
A
TRICARBALLYLIC ACID
C6 H8 O6
KQTIIICEAUMSDG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
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 = 173.6α = 90
b = 72β = 90
c = 72.7γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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