X-Ray Structure of imidazoleglycerol-phosphate dehydratase

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure and mechanism of imidazoleglycerol-phosphate dehydratase.

Glynn, S.E.Baker, P.J.Sedelnikova, S.E.Davies, C.L.Eadsforth, T.C.Levy, C.W.Rodgers, H.F.Blackburn, G.M.Hawkes, T.R.Viner, R.Rice, D.W.

(2005) Structure 13: 1809-1817

  • DOI: https://doi.org/10.1016/j.str.2005.08.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of A. thaliana imidazoleglycerol-phosphate dehydratase, an enzyme of histidine biosynthesis and a target for the triazole phosphonate herbicides, has been determined to 3.0 A resolution. The structure is composed of 24 identical subunits arranged in 432 symmetry and shows how the formation of a novel dimanganese cluster is crucial to the assembly of the active 24-mer from an inactive trimeric precursor and to the formation of the active site of the enzyme. Molecular modeling suggests that the substrate is bound to the manganese cluster as an imidazolate moiety that subsequently collapses to yield a diazafulvene intermediate. The mode of imidazolate recognition exploits pseudosymmetry at the active site arising from a combination of the assembly of the particle and the pseudosymmetry present in each subunit as a result of gene duplication. This provides an intriguing example of the role of evolution in the design of Nature's catalysts.

  • Organizational Affiliation

    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
207Arabidopsis thalianaMutation(s): 0 
Find proteins for P34047 (Arabidopsis thaliana)
Explore P34047 
Go to UniProtKB:  P34047
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34047
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
CB [auth M]
EA [auth E]
FB [auth N]
HA [auth F]
BA [auth D],
CB [auth M],
EA [auth E],
FB [auth N],
HA [auth F],
IB [auth O],
KA [auth G],
LB [auth P],
NA [auth H],
QA [auth I],
S [auth A],
TA [auth J],
V [auth B],
WA [auth K],
Y [auth C],
ZA [auth L]
O4 S
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth M]
BB [auth M]
CA [auth E]
DA [auth E]
AA [auth D],
AB [auth M],
BB [auth M],
CA [auth E],
DA [auth E],
DB [auth N],
EB [auth N],
FA [auth F],
GA [auth F],
GB [auth O],
HB [auth O],
IA [auth G],
JA [auth G],
JB [auth P],
KB [auth P],
LA [auth H],
MA [auth H],
OA [auth I],
PA [auth I],
Q [auth A],
R [auth A],
RA [auth J],
SA [auth J],
T [auth B],
U [auth B],
UA [auth K],
VA [auth K],
W [auth C],
X [auth C],
XA [auth L],
YA [auth L],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.949α = 90
b = 157.949β = 90
c = 479.965γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description