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 

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This is version 1.3 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
  • Primary Citation of Related Structures:  
    2GFI

  • 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 crystal structure of phytase from Debaryomyces castellii has been determined at 2 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phytaseA, B458Debaryomyces castelliiMutation(s): 0 
Gene Names: phyt
EC: 3.1.3.8 (PDB Primary Data), 3.1.3.2 (UniProt)
UniProt
Find proteins for A2TBB4 (Debaryomyces castellii)
Explore A2TBB4 
Go to UniProtKB:  A2TBB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2TBB4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B],
G [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary