Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 59.60 kDa 
• Atom Count: 4608 
• Modelled Residue Count: 538 
• Deposited Residue Count: 540 
• Unique protein chains: 1

3JS8

Solvent-stable cholesterol oxidase

• PDB DOI: 10.2210/pdb3JS8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Chromobacterium sp. DS-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-09 Released: 2010-02-09 
• Deposition Author(s): Sagermann, M., Ohtaki, A., Newton, K., Doukyu, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.196 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Structural characterization of the organic solvent-stable cholesterol oxidase from Chromobacterium sp. DS-1.

Sagermann, M., Ohtaki, A., Newton, K., Doukyu, N.

(2010) J Struct Biol 170: 32-40

• PubMed: 20102741 
• DOI: 10.1016/j.jsb.2010.01.012
• Primary Citation of Related Structures:  
  3JS8


• PubMed Abstract: 
  

Cholesterol oxidase is of significant commercial interest as it is widely used as a biosensor for the detection of cholesterol in clinical samples, blood serum and food. Increased stability of this enzyme with regards to temperature and different solvent conditions are of great importance to the reliability and versatility of its applications. We here report the crystal structure of the cholesterol oxidase of Chromobacterium sp. DS-1 (CHOLOX). In contrast to other previously characterized cholesterol oxidases, this enzyme retains high activity in organic solvents and detergents at temperatures above 85 degrees C despite its mesophilic origin. With the availability of one other homologous oxidase of known three-dimensional structure, a detailed comparison of its sequence and structure was performed to elucidate the mechanisms of stabilization. In contrast to factors that typically contribute to the stability of thermophilic proteins, the structure of CHOLOX exhibits a larger overall cavity volume, less charged residues and less salt bridge interactions. Moreover, the vast majority of residue substitutions were found on or near the protein's solvent exposed surface. We propose that the engineering of enhanced stability may also be accomplished through selective engineering of the protein periphery rather than by redesigning its entire core.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholesterol oxidase	A	540	Chromobacterium sp. DS-1	Mutation(s): 0  Gene Names: cho EC: 1.1.3.6
UniProt
Find proteins for B5MGF8 (Chromobacterium sp. DS-1) Explore B5MGF8  Go to UniProtKB:  B5MGF8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.196 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.227	α = 90
b = 90.38	β = 90
c = 124.198	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-09 
• Released Date: 2010-02-09 
Deposition Author(s): Sagermann, M., Ohtaki, A., Newton, K., Doukyu, N.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary