1M3S

Crystal structure of YckF from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1016/j.jsb.2004.04.006

  • 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 su ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein yckf
A, B
186Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: hxlB (yckF)
EC: 5.3.1.27
Find proteins for P42404 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42404
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.080α = 90.00
b = 72.080β = 90.00
c = 245.560γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
CNSphasing
dtDisplaydata collection
DTDISPLAYdata reduction
HKL-2000data scaling
d*TREKdata reduction
d*TREKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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