Crystal structure of YckF from Bacillus subtilis

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.5 of the entry. See complete history


Crystal structure of Bacillus subtilis YckF: structural and functional evolution.

Sanishvili, R.Wu, R.Kim, D.E.Watson, J.D.Collart, F.Joachimiak, A.

(2004) J Struct Biol 148: 98-109

  • DOI: https://doi.org/10.1016/j.jsb.2004.04.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the YckF protein from Bacillus subtilis was determined with MAD phasing and refined at 1.95A resolution. YckF forms a tight tetramer both in crystals and in solution. Conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. The structure of YckF was compared to with its ortholog from Methanococcus jannaschii, MJ1247. Both of these proteins have phosphate hexulose isomerase activity, although neither of the organisms can utilize methane or methanol as source of energy and/or carbon. Extensive sequence and structural similarities with MJ1247 and with the isomerase domain of glucosamine-6-phosphate synthase from Escherichia coli allowed us to group residues contributing to substrate binding or catalysis. Few notable differences among these structures suggest possible cooperativity of the four active sites of the tetramer. Phylogenetic relationships between obligatory and facultative methylotrophs along with B. subtilis and E. coli provide clues about the possible evolution of genes as they loose their physiological importance.

  • Organizational Affiliation

    Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, IL 60439, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein yckf
A, B
186Bacillus subtilisMutation(s): 0 
Gene Names: YckF
Find proteins for P42404 (Bacillus subtilis (strain 168))
Explore P42404 
Go to UniProtKB:  P42404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42404
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.08α = 90
b = 72.08β = 90
c = 245.56γ = 120
Software Package:
Software NamePurpose
dtDisplaydata collection
HKL-2000data reduction
d*TREKdata scaling
d*TREKdata reduction
DTDISPLAYdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references