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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.P.Roper, D.I.

(2004) Acta Crystallogr.,Sect.D 60: 397

  • DOI: 10.1107/S0907444903027999

  • 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 EPIMERASE
A
274Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Gene Names: dapF
EC: 5.1.1.7
Find proteins for P44859 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44859
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 99.637α = 90.00
b = 113.870β = 90.00
c = 64.481γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance