1GQZ

Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1107/S0907444903027999
  • Structures With Same Primary Citation

  • 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 uniquel ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIAMINOPIMELATE EPIMERASEA274Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: dapFHI_0750
EC: 5.1.1.7
Find proteins for P44859 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44859 
Go to UniProtKB:  P44859
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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