1EXP | pdb_00001exp

BETA-1,4-GLYCANASE CEX-CD

• PDB DOI: https://doi.org/10.2210/pdb1EXP/pdb

• Classification: HYDROLASE
• Organism(s): Cellulomonas fimi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-01-11 Released: 1997-01-27 
• Deposition Author(s): White, A., Tull, D., Johns, K.L., Withers, S.G., Rose, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.283 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.

White, A., Tull, D., Johns, K., Withers, S.G., Rose, D.R.

(1996) Nat Struct Biol 3: 149-154

• PubMed: 8564541 
• DOI: https://doi.org/10.1038/nsb0296-149
• Primary Citation Related Structures: 
  1EXP


• PubMed Abstract: 
  

  The three-dimensional structure of a catalytically competent glycosyl-enzyme intermediate of a retaining beta-1,4-glycanase has been determined at a resolution of 1.8 A by X-ray diffraction. A fluorinated slow substrate forms an alpha-D-glycopyranosyl linkage to one of the two invariant carboxylates, Glu 233, as supported in solution by 19F-NMR studies. The resulting ester linkage is coplanar with the cyclic oxygen of the proximal saccharide and is inferred to form a strong hydrogen bond with the 2-hydroxyl of that saccharide unit in natural substrates. The active-site architecture of this covalent intermediate gives insights into both the classical double-displacement catalytic mechanism and the basis for the enzyme's specificity.

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Organizational Affiliation: 
• Protein Engineering Network of Centres of Excellence, Ontario Cancer Institute, Toronto, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.4 kDa 
• Atom Count: 2,607 
• Modeled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-1,4-D-GLYCANASE CEX-CD	A	312	Cellulomonas fimi	Mutation(s): 0  EC: 3.2.1.91 (PDB Primary Data), 3.2.1.8 (PDB Primary Data)
UniProt
Find proteins for P07986 (Cellulomonas fimi) Explore P07986  Go to UniProtKB:  P07986
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G29564OM GlyCosmos: G29564OM

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900050	B	2-deoxy-2-fluoro-beta-cellobiose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.283 (Depositor) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.172	α = 90
b = 88.172	β = 90
c = 81.097	γ = 90

Software Package:

Software Name	Purpose
SDMW	data collection
X-PLOR	model building
X-PLOR	refinement
SDMS	data reduction
XENGEN	data reduction
NIELSEN	data reduction
XUONG)	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-27 
Deposition Author(s): White, A., Tull, D., Johns, K.L., Withers, S.G., Rose, D.R.

Revision History  

• Version 1.0: 1997-01-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary