5J72

Cwp6 from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6.

Usenik, A.Renko, M.Mihelic, M.Lindic, N.Borisek, J.Perdih, A.Pretnar, G.Muller, U.Turk, D.

(2017) Structure 25: 514-521

  • DOI: 10.1016/j.str.2016.12.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial cell wall proteins play crucial roles in cell survival, growth, and environmental interactions. In Gram-positive bacteria, cell wall proteins include several types that are non-covalently attached via cell wall binding domains. Of the two c ...

    Bacterial cell wall proteins play crucial roles in cell survival, growth, and environmental interactions. In Gram-positive bacteria, cell wall proteins include several types that are non-covalently attached via cell wall binding domains. Of the two conserved surface-layer (S-layer)-anchoring modules composed of three tandem SLH or CWB2 domains, the latter have so far eluded structural insight. The crystal structures of Cwp8 and Cwp6 reveal multi-domain proteins, each containing an embedded CWB2 module. It consists of a triangular trimer of Rossmann-fold CWB2 domains, a feature common to 29 cell wall proteins in Clostridium difficile 630. The structural basis of the intact module fold necessary for its binding to the cell wall is revealed. A comparison with previously reported atomic force microscopy data of S-layers suggests that C. difficile S-layers are complex oligomeric structures, likely composed of several different proteins.


    Organizational Affiliation

    Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
A, B
638Peptoclostridium difficile (strain 630)Mutation(s): 0 
Gene Names: cwp6
EC: 3.5.1.28
Find proteins for Q183L9 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q183L9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.357α = 90.00
b = 212.916β = 90.00
c = 84.931γ = 90.00
Software Package:
Software NamePurpose
ARPmodel building
XDSdata reduction
XDSdata scaling
REFMACrefinement
SHELXDEmodel building
PHASERphasing
MAINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0048
Centre of Excellence CIPKeBiPSloveniaOP13.1.1.2.02.0005

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Refinement description
  • Version 1.2: 2017-03-22
    Type: Data collection, Database references
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations