Experimental Data Snapshot

  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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This is version 1.3 of the entry. See complete history


X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex.

Walsh, M.A.McCarthy, A.O'Farrell, P.A.McArdle, P.Cunningham, P.D.Mayhew, S.G.Higgins, T.M.

(1998) Eur J Biochem 258: 362-371

  • DOI: https://doi.org/10.1046/j.1432-1327.1998.2580362.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex with riboflavin. The ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of FMN for flavin binding. The redox potential of the semiquinone/hydroquinone couple of the bound riboflavin is 180 mV less negative than the corresponding complex with FMN. To elucidate the binding of riboflavin, the complex has been crystallized and the crystal structure solved by molecular replacement using native flavodoxin as a search model to a resolution of 0.183 nm. Compared to the FMN complex, the hydrogen-bonding network at the isoalloxazine sub-site of the riboflavin complex is severely disrupted by movement of the loop residues Ser58-Ile64 (60-loop) which contact the isoalloxazine by over 0.35 nm, and by a small displacement of the isoalloxazine moiety. The 60-loop movement away from the flavin increases the solvent exposure of the flavin-binding site. The conformation of the site at which 5'-phosphate of FMN normally binds is similar in the two complexes, but in the riboflavin complex a sulphate or phosphate ion from the crystallization buffer occupies the space. This causes small structural perturbations in the phosphate-binding site. The flexibility of the 60-loop in D. vulgaris flavodoxin appears to be a contributing factor to the binding of riboflavin by the apoprotein, and a feature that distinguishes the protein from other 'short chain' flavodoxins. In the absence of the terminal phosphate group, free movement at the 5'-OH group of the ribityl chain can occur. Thus, the 5'-phosphate of FMN secures the cofactor at the binding site and positions it optimally. The structural changes which occur in the 60-loop in the riboflavin complex probably account for most of the positive shift that is observed in the midpoint potential of the semiquinone/hydroquinone couple of the riboflavin complex compared to that of the FMN complex.

  • Organizational Affiliation

    Department of Chemistry, University College, Galway, Ireland. walsh@anl.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
147Nitratidesulfovibrio vulgarisMutation(s): 0 
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00323
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.38α = 90
b = 62.31β = 127.26
c = 77.42γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations