Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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This is version 1.4 of the entry. See complete history


Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.

Lloyd, A.J.Huyton, T.Turkenburg, J.Roper, D.I.

(2004) Acta Crystallogr D Biol Crystallogr 60: 397-400

  • DOI: https://doi.org/10.1107/S0907444903027999
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Diaminopimelate (DAP) epimerase (DapF) is central to the biosynthesis of both lysine and cell-wall peptidoglycan in many bacteria species. The peptidoglycan layer provides great potential for the development of novel antimicrobials as it is a uniquely prokaryotic feature. Crystals of recombinant Haemophilus influenzae DapF that diffract to beyond 2 A resolution have been obtained which facilitated the solution of the structure by molecular replacement at a resolution approximately 1 A higher than that previously determined. An analysis of the structure (i) in comparison to other PLP-independent racemaces and (ii) in relation to the catalytic mechanism and stereospecificity of DapF is presented.

  • Organizational Affiliation

    Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIAMINOPIMELATE EPIMERASE274Haemophilus influenzae Rd KW20Mutation(s): 0 
Find proteins for P44859 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44859 
Go to UniProtKB:  P44859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44859
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.637α = 90
b = 113.87β = 90
c = 64.481γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description