Experimental Data Snapshot

  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

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This is version 1.3 of the entry. See complete history


Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.

Cirilli, M.Zheng, R.Scapin, G.Blanchard, J.S.

(1998) Biochemistry 37: 16452-16458

  • DOI: https://doi.org/10.1021/bi982138o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Haemophilus influenzae diaminopimelate epimerase was cloned, expressed, purified, and crystallized in the C2221 space group (a = 102.1 A, b = 115.4 A, c = 66.3 A, alpha = beta = gamma = 90 degrees). The three-dimensional structure was solved to 2.7 A using a single Pt derivative and the Se-Met-substituted enzyme to a conventional R factor of 19.0% (Rfree = 24.2%). The 274 amino acid enzyme consists of two structurally homologous domains, each containing eight beta-strands and two alpha-helices. Diaminopimelate epimerase is a representative of the PLP-independent amino acid racemases, for which no structure has yet been determined and substantial evidence exists supporting the role of two cysteine residues as the catalytic acid and base. Cys73 of the amino terminal domain is found in disulfide linkage, at the domain interface, with Cys217 of the carboxy terminal domain, and we suggest that these two cysteine residues in the reduced, active enzyme function as the acid and base in the mechanism.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (DIAMINOPIMELATE EPIMERASE)274Haemophilus influenzaeMutation(s): 0 
Gene Names: DAPF
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: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.1α = 90
b = 115.4β = 90
c = 66.3γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description