1DKP

CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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This is version 1.5 of the entry. See complete history


Literature

Crystal structures of Escherichia coli phytase and its complex with phytate.

Lim, D.Golovan, S.Forsberg, C.W.Jia, Z.

(2000) Nat Struct Biol 7: 108-113

  • DOI: https://doi.org/10.1038/72371
  • Primary Citation of Related Structures:  
    1DKL, 1DKM, 1DKN, 1DKO, 1DKP, 1DKQ

  • PubMed Abstract: 

    Phytases catalyze the hydrolysis of phytate and are able to improve the nutritional quality of phytate-rich diets. Escherichia coli phytase, a member of the histidine acid phosphatase family has the highest specific activity of all phytases characterized. The crystal structure of E. coli phytase has been determined by a two-wavelength anomalous diffraction method using the exceptionally strong anomalous scattering of tungsten. Despite a lack of sequence similarity, the structure closely resembles the overall fold of other histidine acid phosphatases. The structure of E. coli phytase in complex with phytate, the preferred substrate, reveals the binding mode and substrate recognition. The binding is also accompanied by conformational changes which suggest that substrate binding enhances catalysis by increasing the acidity of the general acid.


  • Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHYTASE410Escherichia coliMutation(s): 2 
EC: 3.1.3.2
UniProt
Find proteins for P07102 (Escherichia coli (strain K12))
Explore P07102 
Go to UniProtKB:  P07102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07102
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.573α = 90
b = 75.127β = 90
c = 90.393γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
XTALVIEWrefinement
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2020-10-14
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2021-11-03
    Changes: Database references