6WYY | pdb_00006wyy

Crystal structure of Pseudomonas 7A Glutaminase-Asparaginase in complex with L-Glu at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb6WYY/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: 1.35 Å
• R-Value Free: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.123 (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: 145.84 kDa 
• Atom Count: 11,171 
• Modeled Residue Count: 1,288 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], N [auth D]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], J [auth B], L [auth C], M [auth C], O [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.542	α = 90
b = 130.791	β = 117.82
c = 81.548	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
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