1HFJ

Asparaginase from Erwinia chrysanthemi, hexagonal form with sulfate

• PDB DOI: https://doi.org/10.2210/pdb1HFJ/pdb

• Classification: HYDROLASE
• Organism(s): Dickeya chrysanthemi
• Mutation(s): Yes 


• Deposited: 2000-12-05 Released: 2000-12-07 
• Deposition Author(s): Palm, G.J., Lubkowski, J., Kozak, M., Jaskolski, M., Wlodawer, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 

Literature

Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups

Jaskolski, M., Kozak, M., Lubkowski, J., Palm, G.J., Wlodawer, A.

(2001) Acta Crystallogr D Biol Crystallogr 57: 369

• PubMed: 11223513 
• DOI: https://doi.org/10.1107/s0907444900020175
• Primary Citation of Related Structures:  
  1HFJ, 1HFK, 1HO3


• PubMed Abstract: 
  

  Quasi-enantiomorphic crystals of the Y25F mutant of Escherichia coli L-asparaginase and of the native Erwinia chrysanthemi L-asparaginase were obtained in the hexagonal space groups P6(5)22 and P6(1)22, respectively. The structures of these highly homologous enzymes were solved by molecular replacement and were refined with data extending to 2.2-2.5 A. These structures were compared with each other, as well as with other L-asparaginase structures previously observed with different crystal packing. It is concluded that the observed phenomenon, which is rare, was most likely to have arisen by chance.

---

Organizational Affiliation: 

Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.44 kDa 
• Atom Count: 5,429 
• Modelled Residue Count: 650 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ASPARAGINE AMIDOHYDROLASE	A, B [auth C]	327	Dickeya chrysanthemi	Mutation(s): 4  EC: 3.5.1.1
UniProt
Find proteins for P06608 (Dickeya chrysanthemi) Explore P06608  Go to UniProtKB:  P06608

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.4	α = 90
b = 91.4	β = 90
c = 346.6	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
X-PLOR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-07 
Deposition Author(s): Palm, G.J., Lubkowski, J., Kozak, M., Jaskolski, M., Wlodawer, A.

Revision History  

• Version 1.0: 2000-12-07
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other