1DKL

CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)

• PDB DOI: https://doi.org/10.2210/pdb1DKL/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-12-08 Released: 2000-08-03 
• Deposition Author(s): Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.202 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 

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

• PubMed: 10655611 
• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.47 kDa 
• Atom Count: 6,508 
• Modelled Residue Count: 806 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYTASE	A, B	410	Escherichia coli	Mutation(s): 0  EC: 3.1.3.2
UniProt
Find proteins for P07102 (Escherichia coli (strain K12)) Explore P07102  Go to UniProtKB:  P07102

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.202 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.802	α = 90
b = 72.126	β = 92.04
c = 82.434	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-03 
Deposition Author(s): Lim, D., Golovan, S., Forsberg, C.W., Jia, Z.

Revision History  

• 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