1UPS

GlcNAc[alpha]1-4Gal releasing endo-[beta]-galactosidase from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb1UPS/pdb

• Classification: GLYCOSYL HYDROLASE
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-10 Released: 2004-11-25 
• Deposition Author(s): Tempel, W., Liu, Z.-J., Horanyi, P.S., Deng, L., Lee, D., Newton, M.G., Rose, J.P., Ashida, H., Li, S.-C., Li, Y.-T., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Three-dimensional structure of GlcNAcalpha1-4Gal releasing endo-beta-galactosidase from Clostridium perfringens.

Tempel, W., Liu, Z.J., Horanyi, P.S., Deng, L., Lee, D., Newton, M.G., Rose, J.P., Ashida, H., Li, S.C., Li, Y.T., Wang, B.C.

(2005) Proteins 59: 141-144

• PubMed: 15688452 
• DOI: https://doi.org/10.1002/prot.20363
• Primary Citation of Related Structures:  
  1UPS

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 98.94 kDa 
• Atom Count: 6,991 
• Modelled Residue Count: 799 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLCNAC-ALPHA-1,4-GAL-RELEASING ENDO-BETA-GALACTOSIDASE	A, B	420	Clostridium perfringens	Mutation(s): 0
UniProt
Find proteins for Q934G8 (Clostridium perfringens) Explore Q934G8  Go to UniProtKB:  Q934G8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.43	α = 90
b = 160.43	β = 90
c = 86.14	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE/RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-25 
Deposition Author(s): Tempel, W., Liu, Z.-J., Horanyi, P.S., Deng, L., Lee, D., Newton, M.G., Rose, J.P., Ashida, H., Li, S.-C., Li, Y.-T., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-11-25
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary