1B0J

CRYSTAL STRUCTURE OF ACONITASE WITH ISOCITRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex

Lloyd, S.J.Lauble, H.Prasad, G.S.Stout, C.D.

(1999) Protein Sci 8: 2655-2662

  • DOI: https://doi.org/10.1110/ps.8.12.2655
  • Primary Citation of Related Structures:  
    1B0J, 1B0K, 1B0M, 1C96, 1C97

  • PubMed Abstract: 

    The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.


  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACONITATE HYDRATASE754Sus scrofaMutation(s): 1 
EC: 4.2.1.3
UniProt
Find proteins for P16276 (Sus scrofa)
Explore P16276 
Go to UniProtKB:  P16276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16276
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ICT
Query on ICT

Download Ideal Coordinates CCD File 
C [auth A]ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: B 1 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.4α = 90
b = 72.1β = 90
c = 73.9γ = 77.7
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 2.0: 2019-02-06
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 2.2: 2023-08-09
    Changes: Data collection, Refinement description