6RUE | pdb_00006rue

Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-Asp

• PDB DOI: https://doi.org/10.2210/pdb6RUE/pdb

• Classification: HYDROLASE
• Organism(s): Wolinella succinogenes DSM 1740
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2020-07-15 
• Deposition Author(s): Timofeev, V.I., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Features of the Three Dimensional Structure of the Mutant Form of Wolinella succinogenes L-Asparaginase in Complexes with L-Aspartic and L-Glutamic Acids

Timofeev, V.I., Zhukhlistova, N.E., Kuranova, I.P.

(2020) Russ J Bioorg Chem 46

• DOI: https://doi.org/10.1134/S1068162020020168

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 134.71 kDa 
• Atom Count: 10,218 
• Modeled Residue Count: 1,264 
• Deposited Residue Count: 1,264 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	A	318	Wolinella succinogenes DSM 1740	Mutation(s): 0  Gene Names: ansA, ansB, WS0660 EC: 3.5.1.1
UniProt
Find proteins for P50286 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore P50286  Go to UniProtKB:  P50286

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	B	314	Wolinella succinogenes DSM 1740	Mutation(s): 0  Gene Names: ansA, ansB, WS0660 EC: 3.5.1.1
UniProt
Find proteins for P50286 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore P50286  Go to UniProtKB:  P50286

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	C	315	Wolinella succinogenes DSM 1740	Mutation(s): 0  Gene Names: ansA, ansB, WS0660 EC: 3.5.1.1
UniProt
Find proteins for P50286 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore P50286  Go to UniProtKB:  P50286

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase	D	317	Wolinella succinogenes DSM 1740	Mutation(s): 0  Gene Names: ansA, ansB, WS0660 EC: 3.5.1.1
UniProt
Find proteins for P50286 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W)) Explore P50286  Go to UniProtKB:  P50286

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.92	α = 90
b = 134.36	β = 93.7
c = 73.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Timofeev, V.I., Kuranova, I.P.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references