3PYW | pdb_00003pyw

The structure of the SLH domain from B. anthracis surface array protein at 1.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of Surface Layer Homology (SLH) Domains from Bacillus anthracis Surface Array Protein.

Kern, J.Wilton, R.Zhang, R.Binkowski, T.A.Joachimiak, A.Schneewind, O.

(2011) J Biological Chem 286: 26042-26049

  • DOI: https://doi.org/10.1074/jbc.M111.248070
  • Primary Citation Related Structures: 
    3PYW

  • PubMed Abstract: 

    Surface (S)-layers, para-crystalline arrays of protein, are deposited in the envelope of most bacterial species. These surface organelles are retained in the bacterial envelope through the non-covalent association of proteins with cell wall carbohydrates. Bacillus anthracis, a Gram-positive pathogen, produces S-layers of the protein Sap, which uses three consecutive repeats of the surface-layer homology (SLH) domain to engage secondary cell wall polysaccharides (SCWP). Using x-ray crystallography, we reveal here the structure of these SLH domains, which assume the shape of a three-prong spindle. Each SLH domain contributes to a three-helical bundle at the spindle base, whereas another α-helix and its connecting loops generate the three prongs. The inter-prong grooves contain conserved cationic and anionic residues, which are necessary for SLH domains to bind the B. anthracis SCWP. Modeling experiments suggest that the SLH domains of other S-layer proteins also fold into three-prong spindles and capture bacterial envelope carbohydrates by a similar mechanism.


  • Organizational Affiliation
    • Department of Microbiology, University of Chicago, Chicago, Illinois 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 22.01 kDa 
  • Atom Count: 1,606 
  • Modeled Residue Count: 178 
  • Deposited Residue Count: 203 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-layer protein sap203Bacillus anthracisMutation(s): 0 
Gene Names: BAS0841BA_0885GBAA_0885GI:49183865sap
UniProt
Find proteins for P49051 (Bacillus anthracis)
Explore P49051 
Go to UniProtKB:  P49051
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49051
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.767α = 90
b = 77.767β = 90
c = 100.408γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references
  • Version 1.3: 2012-08-08
    Changes: Other
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations