5FBP

CRYSTAL STRUCTURE OF THE NEUTRAL FORM OF FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH THE PRODUCT FRUCTOSE 6-PHOSPHATE AT 2.1-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the neutral form of fructose-1,6-bisphosphatase complexed with the product fructose 6-phosphate at 2.1-A resolution.

Ke, H.M.Zhang, Y.P.Liang, J.Y.Lipscomb, W.N.

(1991) Proc.Natl.Acad.Sci.USA 88: 2989-2993

  • DOI: 10.1073/pnas.88.8.2989

  • PubMed Abstract: 
  • The crystal structure of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with the product fructose 6-phosphate (F6P) has been refined at 2.1-A resolution to an R factor of 0.177 with root-mean-square deviations of 0.014 A and 2.9 degrees from the ...

    The crystal structure of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with the product fructose 6-phosphate (F6P) has been refined at 2.1-A resolution to an R factor of 0.177 with root-mean-square deviations of 0.014 A and 2.9 degrees from the ideal geometries of bond lengths and bond angles, respectively. The secondary structures but not the trace of the unligated enzyme have been slightly revised in the F6P complex at this higher resolution. Helix H4 in the unligated structure has been refined to a helix-like coil, and two very short 3(10) helices have been found, one in H4 and one in H5. F6P at 10 mM concentration in the absence of divalent metals in our study shows major binding at the active site and minor binding at the AMP site. The major site has almost equal full occupancy in the C1 and C2 chains of the crystallographic asymmetric unit, while the minor site shows occupancy only in the C1 chain at about 50%. The electron density in both (2Fo - Fc) and (Fo - Fc) maps calculated by omitting F6P slightly favors the beta anomer of D-F6P over the alpha anomer. Possible functions of the active-site residues are discussed, and candidates are suggested for site-directed mutagenesis.


    Related Citations: 
    • Conformational Transition of Fructose-1,6-Bisphosphatase: Structure Comparison between the AMP Complex (T Form) and the Fructose 6-Phosphate Complex (R Form)
      Ke, H.,Liang, J.-Y.,Zhang, Y.,Lipscomb, W.N.
      (1991) Biochemistry 30: 4412


    Organizational Affiliation

    Gibbs Chemical Laboratory, Harvard University, Cambridge, MA 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FRUCTOSE 1,6-BISPHOSPHATASE
A, B
335Sus scrofaMutation(s): 0 
Gene Names: FBP1 (FBP)
EC: 3.1.3.11
Find proteins for P00636 (Sus scrofa)
Go to Gene View: FBP1
Go to UniProtKB:  P00636
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F6P
Query on F6P

Download SDF File 
Download CCD File 
A, B
FRUCTOSE-6-PHOSPHATE
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.177 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.100α = 90.00
b = 131.100β = 90.00
c = 69.700γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other