Crystal structure of E. coli WrbA in complex with FMN

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural organization of WrbA in apo- and holoprotein crystals.

Wolfova, J.Smatanova, I.K.Brynda, J.Mesters, J.R.Lapkouski, M.Kuty, M.Natalello, A.Chatterjee, N.Chern, S.Y.Ebbel, E.Ricci, A.Grandori, R.Ettrich, R.Carey, J.

(2009) Biochim Biophys Acta 1794: 1288-1298

  • DOI: https://doi.org/10.1016/j.bbapap.2009.08.001
  • Primary Citation of Related Structures:  
    2R96, 2R97, 2RG1

  • PubMed Abstract: 

    Two previously reported holoprotein crystal forms of the flavodoxin-like E. coli protein WrbA, diffracting to 2.6 and 2.0 A resolution, and new crystals of WrbA apoprotein diffracting to 1.85 A, are refined and analysed comparatively through the lens of flavodoxin structures. The results indicate that differences between apo- and holoWrbA crystal structures are manifested on many levels of protein organization as well as in the FMN-binding sites. Evaluation of the influence of crystal contacts by comparison of lattice packing reveals the protein's global response to FMN binding. Structural changes upon cofactor binding are compared with the monomeric flavodoxins. Topologically non-equivalent residues undergo remarkably similar local structural changes upon FMN binding to WrbA or to flavodoxin, despite differences in multimeric organization and residue types at the binding sites. Analysis of the three crystal structures described here, together with flavodoxin structures, rationalizes functional similarities and differences of the WrbAs relative to flavodoxins, leading to a new understanding of the defining features of WrbAs. The results suggest that WrbAs are not a remote and unusual branch of the flavodoxin family as previously thought but rather a central member with unifying structural features.

  • Organizational Affiliation

    Institute of Physical Biology, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavoprotein WrbAA,
B [auth C]
198Escherichia coliMutation(s): 0 
Gene Names: wrbA
Find proteins for P0A8G6 (Escherichia coli (strain K12))
Explore P0A8G6 
Go to UniProtKB:  P0A8G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8G6
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.13α = 90
b = 61.13β = 90
c = 168.38γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description