1HO3 | pdb_00001ho3

CRYSTAL STRUCTURE ANALYSIS OF E. COLI L-ASPARAGINASE II (Y25F MUTANT)

• PDB DOI: https://doi.org/10.2210/pdb1HO3/pdb

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


• Deposited: 2000-12-08 Released: 2001-03-07 
• Deposition Author(s): Jaskolski, M., Kozak, M., Lubkowski, P., Palm, J.G., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 

Starting Model: experimental

Literature

Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.

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

(2001) Acta Crystallogr D Biol Crystallogr 57: 369-377

• PubMed: 11223513 
• DOI: https://doi.org/10.1107/s0907444900020175
• Primary Citation 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.

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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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 69.49 kDa 
• Atom Count: 4,987 
• Modeled Residue Count: 652 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ASPARAGINASE II	A, B	326	Escherichia coli	Mutation(s): 1  EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805  Go to UniProtKB:  P00805

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	C [auth A], D [auth B]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.999	α = 90
b = 80.999	β = 90
c = 341.075	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-07 
Deposition Author(s): Jaskolski, M., Kozak, M., Lubkowski, P., Palm, J.G., Wlodawer, A.

Revision History  

• Version 1.0: 2001-03-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2021-10-27
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.5: 2023-08-09
  Changes: Data collection, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary