1NNS | pdb_00001nns

L-asparaginase of E. coli in C2 space group and 1.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1NNS/pdb

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


• Deposited: 2003-01-14 Released: 2003-03-11 
• Deposition Author(s): Sanches, M., Barbosa, J.A.R.G., de Oliveira, R.T., Neto, J.A.A., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.171 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Structural comparison of Escherichia coli L-asparaginase in two monoclinic space groups.

Sanches, M., Barbosa, J.A.R.G., de Oliveira, R.T., Abrahao Neto, J., Polikarpov, I.

(2003) Acta Crystallogr D Biol Crystallogr 59: 416-422

• PubMed: 12595697 
• DOI: https://doi.org/10.1107/s0907444902021200
• Primary Citation Related Structures: 
  1NNS


• PubMed Abstract: 
  

  The functional L-asparaginase from Escherichia coli is a homotetramer with a molecular weight of about 142 kDa. The X-ray structure of the enzyme, crystallized in a new form (space group C2) and refined to 1.95 A resolution, is compared with that of the previously determined crystal form (space group P2(1)). The asymmetric unit of the new crystal form contains an L-asparaginase dimer instead of the tetramer found in the previous crystal form. It is found that crystal contacts practically do not affect the conformation of the protein. It is shown that subunit C of the tetrameric form is in a conformation which is systematically different from that of all other subunits in both crystal forms. Major conformational differences are confined to the lid loop (residues 14-27). In addition, the stability of this globular protein is analyzed in terms of the interactions between hydrophobic parts of the subunits.

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Organizational Affiliation: 
• Grupo de Cristalografia, Departamento de Física em Sã;o Carlos, USP, Av. Trabalhador SãoCarlense 400, CEP 13560-970, São Carlos/SP, Brazil.

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: 69.52 kDa 
• Atom Count: 5,209 
• Modeled Residue Count: 652 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase II	A, B	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	C [auth A], D [auth B]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.171 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.296	α = 90
b = 134.617	β = 110.51
c = 64.867	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-11 
Deposition Author(s): Sanches, M., Barbosa, J.A.R.G., de Oliveira, R.T., Neto, J.A.A., Polikarpov, I.

Revision History  

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-07-05
  Changes: Database references
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary