4D59 | pdb_00004d59

Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.291 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Cwp84, a Clostridium Difficile Cysteine Protease, Exhibits Conformational Flexibility in the Absence of its Propeptide

Bradshaw, W.J.Roberts, A.K.Shone, C.C.Acharya, K.R.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 295

  • DOI: https://doi.org/10.1107/S2053230X15001065
  • Primary Citation Related Structures: 
    4D59, 4D5A

  • PubMed Abstract: 

    In recent decades, the global healthcare problems caused by Clostridium difficile have increased at an alarming rate. A greater understanding of this antibiotic-resistant bacterium, particularly with respect to how it interacts with the host, is required for the development of novel strategies for fighting C. difficile infections. The surface layer (S-layer) of C. difficile is likely to be of significant importance to host-pathogen interactions. The mature S-layer is formed by a proteinaceous array consisting of multiple copies of a high-molecular-weight and a low-molecular-weight S-layer protein. These components result from the cleavage of SlpA by Cwp84, a cysteine protease. The structure of a truncated Cwp84 active-site mutant has recently been reported and the key features have been identified, providing the first structural insights into the role of Cwp84 in the formation of the S-layer. Here, two structures of Cwp84 after propeptide cleavage are presented and the three conformational changes that are observed are discussed. These changes result in a reconfiguration of the active site and exposure of the hydrophobic pocket.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.

Macromolecule Content 

  • Total Structure Weight: 91.47 kDa 
  • Atom Count: 6,861 
  • Modeled Residue Count: 812 
  • Deposited Residue Count: 812 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
A, B
406Clostridioides difficile QCD-32g58Mutation(s): 1 
EC: 3.4.22.15

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.291 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.22α = 89.28
b = 58.421β = 77.96
c = 93.1γ = 71.62
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description