Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.85 kDa 
• Atom Count: 2667 
• Modelled Residue Count: 311 
• Deposited Residue Count: 314 
• Unique protein chains: 1

1PGS

THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM

• PDB DOI: 10.2210/pdb1PGS/pdb

• Classification: ENDOGLYCOSIDASE
• Organism(s): Elizabethkingia meningoseptica
• Mutation(s): No 


• Deposited: 1994-10-06 Released: 1995-01-26 
• Deposition Author(s): Norris, G.E., Stillman, T.J., Anderson, B.F., Baker, E.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.168 

Literature

The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.

Norris, G.E., Stillman, T.J., Anderson, B.F., Baker, E.N.

(1994) Structure 2: 1049-1059

• PubMed: 7881905 
• DOI: 10.1016/s0969-2126(94)00108-1
• Primary Citation of Related Structures:  
  1PGS


• PubMed Abstract: 
  

Peptide:N-glycosidase F (PNGase F) is an enzyme that catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. Often called an endoglycosidase, it is more correctly termed an amidase or glycosylasparaginase as cleavage is at the asparagine-sugar amide linkage. The enzyme is widely used in structure-function studies of glycoproteins.

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Related Citations: 

• Crystal Structure of Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase F at 2.2 Angstroms Resolution
  Kuhn, P., Tarantino, A.L., Plummer Junior, T.H., Van Roey, P.
  () To be published --: --

• Purification and Crystallization of the Endoglycosidase Pgnase F, a Peptide:N-Glycosidase from Flavobacterium Meningosepticum
  Norris, G.E., Flaus, A.J., Moore, C.H., Baker, E.N.
  (1994) J Biol Chem 241: 624

• Cloning and Expression of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase F in Escherichia Coli
  Barsomian, G.D., Johnson, T.L., Borowski, M., Denman, J., Ollington, J.F., Hirani, S., Mcneilly, D.S., Rasmussen, J.R.
  (1990) J Biol Chem 265: 6967

• Molecular Cloning and Amino Acid Sequence of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase from Flavobacterium Meningosepticum
  Tarentino, A.L., Quinones, G., Trumble, A., Changchien, L.M., Duceman, B., Maley, F., Plummer Junior, T.H.
  (1990) J Biol Chem 265: 6961

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F	A	314	Elizabethkingia meningoseptica	Mutation(s): 0  EC: 3.5.1.52
UniProt
Find proteins for P21163 (Elizabethkingia miricola) Explore P21163  Go to UniProtKB:  P21163

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.07	α = 90
b = 85.14	β = 90
c = 48.5	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-10-06 
• Released Date: 1995-01-26 
Deposition Author(s): Norris, G.E., Stillman, T.J., Anderson, B.F., Baker, E.N.

Revision History  

• Version 1.0: 1995-01-26
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance