6V5F | pdb_00006v5f

L-asparaginase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6V5F/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-04 Released: 2021-02-03 
• Deposition Author(s): Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

L-asparaginase from Escherichia coli: Novel insights about the behavior of flexible part of the active site

Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 139.01 kDa 
• Atom Count: 9,423 
• Modeled Residue Count: 1,227 
• Deposited Residue Count: 1,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase 2	A, B, C, D	326	Escherichia coli	Mutation(s): 0  EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805  Go to UniProtKB:  P00805

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP (Subject of Investigation/LOI)	E [auth A], H [auth D]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
SIN (Subject of Investigation/LOI)	F [auth B], G [auth C]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.917	α = 90
b = 125.435	β = 106.94
c = 68.816	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary