2GFI

Crystal structure of the phytase from D. castellii at 2.3 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Debaryomyces castellii CBS 2923 phytase.

Ragon, M.Hoh, F.Aumelas, A.Chiche, L.Moulin, G.Boze, H.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 321-326

  • DOI: 10.1107/S1744309109008653
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Phytate (myo-inositol hexakisphosphate) is the primary storage form of phosphate in seeds and legumes (Reddy et al., 1982). Phytases are phosphatases that hydrolyze phytate to less phosphorylated myo-inositol derivatives and inorganic phosphate. The ...

    Phytate (myo-inositol hexakisphosphate) is the primary storage form of phosphate in seeds and legumes (Reddy et al., 1982). Phytases are phosphatases that hydrolyze phytate to less phosphorylated myo-inositol derivatives and inorganic phosphate. The crystal structure of phytase from Debaryomyces castellii has been determined at 2.3 A resolution. The crystals belonged to space group P6(5)22, with unit-cell parameters a = 121.65, c = 332.24 A. The structure was solved by molecular replacement and refined to a final R factor of 15.7% (R(free) = 20.9%). The final model consists of a dimer (with two monomers of 458 residues), five NAG molecules and 628 water molecules.


    Organizational Affiliation

    UMR IR2B, Equipe Génie Microbiologique et Enzymatique, ENSAM-INRA, Montpellier, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phytase
A, B
458Debaryomyces castelliiMutation(s): 0 
Gene Names: phyt
EC: 3.1.3.8
Find proteins for A2TBB4 (Debaryomyces castellii)
Go to UniProtKB:  A2TBB4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.154 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.655α = 90
b = 121.655β = 90
c = 332.245γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-03-22 
  • Released Date: 2007-03-27 
  • Deposition Author(s): Hoh, F.

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance