3B72

Crystal structure of lysozyme folded in SDS and 2-methyl-2,4-pentanediol

• PDB DOI: https://doi.org/10.2210/pdb3B72/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2007-10-30 Released: 2008-09-09 
• Deposition Author(s): Michaux, C., Pouyez, J., Wouters, J., Prive, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.241 
• R-Value Observed: 0.204 

Literature

Protecting role of cosolvents in protein denaturation by SDS: a structural study.

Michaux, C., Pouyez, J., Wouters, J., Prive, G.G.

(2008) BMC Struct Biol 8: 29-29

• PubMed: 18522744 
• DOI: https://doi.org/10.1186/1472-6807-8-29
• Primary Citation of Related Structures:  
  3B6L, 3B72


• PubMed Abstract: 
  

  Recently, we reported a unique approach to preserve the activity of some proteins in the presence of the denaturing agent, Sodium Dodecyl Sulfate (SDS). This was made possible by addition of the amphipathic solvent 2,4-Methyl-2-PentaneDiol (MPD), used as protecting but also as refolding agent for these proteins. Although the persistence of the protein activity in the SDS/MPD mixture was clearly established, preservation of their structure was only speculative until now.

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Organizational Affiliation: 

Chemistry department, CBS lab, CPTS group, 61 rue de Bruxelles, B-5000 Namur, Belgium. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.59 kDa 
• Atom Count: 1,137 
• Modelled Residue Count: 129 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.241 
• R-Value Observed: 0.204 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.9	α = 90
b = 77.9	β = 90
c = 37.53	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Michaux, C., Pouyez, J., Wouters, J., Prive, G.G.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2018-06-06
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description