2R96

Crystal structure of E. coli WrbA in complex with FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.bbapap.2009.08.001
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases
      Carey, J.,Brynda, J.,Wolfova, J.,Grandori, R.,Gustavsson, T.,Ettrich, R.,Kuta Smatanova, I.
      (2007) Protein Sci. 16: 1
    • Crystallization and preliminary diffraction analysis of Escherichia coli WrbA in complex with its cofactor flavin mononucleotide
      Wolfova, J.,Mesters, J.R.,Brynda, J.,Grandori, R.,Natalello, A.,Carey, J.,Kuta Smatanova, I.
      (2007) Acta Crystallogr.,Sect.F 63: 571


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavoprotein WrbA
A, C
198Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: wrbA
EC: 1.6.5.2
Find proteins for P0A8G6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8G6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, C
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.350α = 90.00
b = 94.350β = 90.00
c = 175.380γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description