1GQZ

Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A

• PDB DOI: https://doi.org/10.2210/pdb1GQZ/pdb

• Classification: ISOMERASE
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-12-07 Released: 2003-06-12 
• Deposition Author(s): Roper, D.I., Huyton, T., Turkenburg, J.P.

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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 

Starting Model: experimental

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

• PubMed: 14747737 
• DOI: https://doi.org/10.1107/S0907444903027999
• Primary Citation of Related Structures:  
  1GQZ


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 30.28 kDa 
• Atom Count: 2,436 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIAMINOPIMELATE EPIMERASE	A	274	Haemophilus influenzae Rd KW20	Mutation(s): 0  EC: 5.1.1.7
UniProt
Find proteins for P44859 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44859  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 
• R-Value Observed: 0.167 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.637	α = 90
b = 113.87	β = 90
c = 64.481	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-12 
Deposition Author(s): Roper, D.I., Huyton, T., Turkenburg, J.P.

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
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description