Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.16 kDa 
• Atom Count: 3408 
• Modelled Residue Count: 410 
• Deposited Residue Count: 410 
• Unique protein chains: 1

1DKQ

CRYSTAL STRUCTURE OF PHYTATE COMPLEX ESCHERICHIA COLI PHYTASE AT PH 5.0. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE

• PDB DOI: 10.2210/pdb1DKQ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

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: 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.

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Related Citations: 

• Purification, Crystallization and Preliminary X-ray Analysis of the Escherichia coli Phytase
  Jia, Z., Golovan, S., Ye, Q., Forsberg, C.W.
  (1998) Acta Crystallogr D Biol Crystallogr 54: 647

• The Complete Nucleotide Sequence of the Escherichia coli Gene appA Reveals Significant Homology Between pH 2.5 Acid Phosphatase and Glucose-1-phosphatase
  Dassa, J., Marck, C., Boquet, P.L.
  (1990) J Bacteriol 172: 5497

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYTASE	A	410	Escherichia coli	Mutation(s): 2  EC: 3.1.3.2 (PDB Primary Data), 3.1.3.26 (UniProt)
UniProt
Find proteins for P07102 (Escherichia coli (strain K12)) Explore P07102  Go to UniProtKB:  P07102

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	F [auth A]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
HG	B [auth A], C [auth A], D [auth A], E [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.257 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.445	α = 90
b = 75.141	β = 90
c = 89.957	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
XTALVIEW	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-08 
• 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
• 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