6PAE

Dickeya chrysanthemi complex with L-Asp at pH 5.6

• PDB DOI: https://doi.org/10.2210/pdb6PAE/pdb

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


• Deposited: 2019-06-11 Released: 2019-09-04 
• Deposition Author(s): Lubkowski, J., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.176 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Literature

Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.

Lubkowski, J., Wlodawer, A.

(2019) Protein Sci 28: 1850-1864

• PubMed: 31423681 
• DOI: https://doi.org/10.1002/pro.3709
• Primary Citation of Related Structures:  
  6PA2, 6PA3, 6PA4, 6PA5, 6PA6, 6PA8, 6PA9, 6PAA, 6PAB, 6PAC, 6PAE


• PubMed Abstract: 
  

  Twenty crystal structures of the complexes of l-asparaginase with l-Asn, l-Asp, and succinic acid that are currently available in the Protein Data Bank, as well as 11 additional structures determined in the course of this project, were analyzed in order to establish the level of conservation of the geometric parameters describing interactions between the substrates and the active site of the enzymes. We found that such stereochemical relationships are highly conserved, regardless of the organism from which the enzyme was isolated, specific crystallization conditions, or the nature of the ligands. Analysis of the geometry of the interactions, including Bürgi-Dunitz and Flippin-Lodge angles, indicated that Thr12 (Escherichia coli asparaginase II numbering) is optimally placed to be the primary nucleophile in the most likely scenario utilizing a double-displacement mechanism, whereas catalysis through a single-displacement mechanism appears to be the least likely.

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Organizational Affiliation: 

Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland.

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)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 141.43 kDa 
• Atom Count: 11,140 
• Modelled Residue Count: 1,248 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	A, B, C, D	327	Dickeya chrysanthemi	Mutation(s): 0  Gene Names: ansB, asn EC: 3.5.1.1
UniProt
Find proteins for P06608 (Dickeya chrysanthemi) Go to UniProtKB:  P06608

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP (Subject of Investigation/LOI)	E [auth A], K [auth B], L [auth C], N [auth D]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
GOL	M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.176 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.159	α = 90
b = 90.4	β = 91.88
c = 127.359	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Lubkowski, J., Wlodawer, A.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references