Crystal Structure Analysis of Bacillus subtilis 168 XepA

Experimental Data Snapshot

  • Resolution: 1.88 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS.

Freitag-Pohl, S.Jasilionis, A.Hakansson, M.Svensson, L.A.Kovacic, R.Welin, M.Watzlawick, H.Wang, L.Altenbuchner, J.Plotka, M.Kaczorowska, A.K.Kaczorowski, T.Nordberg Karlsson, E.Al-Karadaghi, S.Walse, B.Aevarsson, A.Pohl, E.

(2019) Acta Crystallogr D Struct Biol 75: 1028-1039

  • DOI: https://doi.org/10.1107/S2059798319013330
  • Primary Citation of Related Structures:  
    6I56, 6I5O, 6IA5

  • PubMed Abstract: 

    As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.

  • Organizational Affiliation

    Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage-like element PBSX protein XepAA [auth D],
B [auth A],
D [auth B],
279Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: xepAxkdYBSU12780
Find proteins for P39797 (Bacillus subtilis (strain 168))
Explore P39797 
Go to UniProtKB:  P39797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39797
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
F [auth D]
G [auth D]
HA [auth E]
M [auth A]
AA [auth B],
F [auth D],
G [auth D],
HA [auth E],
M [auth A],
N [auth A],
O [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
C3 H8 O3
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
H [auth D],
I [auth D],
IA [auth E],
J [auth D],
JA [auth E],
K [auth D],
KA [auth E],
L [auth D],
LA [auth E],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
Y [auth C],
Z [auth C]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.88 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.612α = 90
b = 126.028β = 90
c = 151.458γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom685778

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references