7M11 | pdb_00007m11

L-asparaginase from Escherichia coli with bound Aspartic acid

• PDB DOI: https://doi.org/10.2210/pdb7M11/pdb

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


• Deposited: 2021-03-11 Released: 2022-03-16 
• 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: 1.83 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 139.04 kDa 
• Atom Count: 9,779 
• Modeled Residue Count: 1,231 
• 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 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: 1.83 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.838	α = 90
b = 126.545	β = 107.36
c = 68.903	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Souza, T.A.C.B., Morais, S.B., Morini, F.S., Meissner, G.O.

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary