6WYX | pdb_00006wyx

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Asp at pH 5.0

• PDB DOI: https://doi.org/10.2210/pdb6WYX/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-13 Released: 2020-10-14 
• Deposition Author(s): Strzelczyk, P., Zhang, D., Wlodawer, A., Lubkowski, J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.120 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.088 (Depositor), 0.090 (DCC) 
• R-Value Observed: 
  0.088 (Depositor) 

Starting Model: experimental

Literature

Generalized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria.

Strzelczyk, P., Zhang, D., Dyba, M., Wlodawer, A., Lubkowski, J.

(2020) Sci Rep 10: 17516

• DOI: https://doi.org/10.1038/s41598-020-74480-4

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: equilibrium centrifugation, gel filtration, homology

Macromolecule Content 

• Total Structure Weight: 145.41 kDa 
• Atom Count: 10,945 
• Modeled Residue Count: 1,273 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminase-asparaginase	A, B, C, D	337	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: ansB, PP_2453 EC: 3.5.1.38
UniProt
Find proteins for Q88K39 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88K39  Go to UniProtKB:  Q88K39

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP (Subject of Investigation/LOI)	E [auth A], F [auth B], H [auth C], I [auth D]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.120 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.088 (Depositor), 0.090 (DCC) 
• R-Value Observed: 0.088 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.958	α = 90
b = 80.958	β = 90
c = 176.819	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Strzelczyk, P., Zhang, D., Wlodawer, A., Lubkowski, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description