Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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This is version 1.5 of the entry. See complete history


The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue.

Meining, W.Mortl, S.Fischer, M.Cushman, M.Bacher, A.Ladenstein, R.

(2000) J Mol Biol 299: 181-197

  • DOI: https://doi.org/10.1006/jmbi.2000.3742
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lumazine synthase of Saccharomyces cerevisiae is a homopentamer with a molecular weight of 90 kDa. Crystals of the recombinant enzyme with a size of up to 1.6 mm were obtained. The space group is P4(1)2(1)2 with lattice dimensions 82.9 A x 82.9 A x 300.2 A. X-ray diffraction data collected under cryogenic conditions were complete to 1.85 A resolution. The structure of the enzyme in complex with the intermediate analogue, 5-(6-D-ribitylamino-2,4-dihydroxypyrimidine-5-yl)-1-pentyl-p hosphonic acid was solved via molecular replacement using the structure of the Bacillus subtilis enzyme as search model and was refined to a final R-factor of 19.8% (Rfree: 22.5%). The conformation of the active site ligand of the enzyme mimicks that of the Schiff base intermediate of the enzyme-catalyzed reaction. The data enable the reconstruction of the reactant topology during the early steps of the catalytic reaction. Structural determinants, which are likely to be responsible for the inability of the S. cerevisiae enzyme to form icosahedral capsids, will be discussed.

  • Organizational Affiliation

    Södertörns Högskola, Huddinge, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
168Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P50861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50861 
Go to UniProtKB:  P50861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50861
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.893α = 90
b = 82.893β = 90
c = 298.842γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-02
    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: 2013-01-16
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.5: 2024-02-07
    Changes: Advisory, Data collection, Database references, Derived calculations