3B6L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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: 29-35

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Chemistry department, CBS lab, CPTS group, 61 rue de Bruxelles, B-5000 Namur, Belgium. catherine.michaux@fundp.ac.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA147Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SDS
Query on SDS

Download Ideal Coordinates CCD File 
B [auth A]DODECYL SULFATE
C12 H26 O4 S
MOTZDAYCYVMXPC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.595α = 90
b = 77.595β = 90
c = 37.567γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SHELXL-97refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
SHELXphasing
SHELXmodel building

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection, Refinement description