5BOI

Bacillus megaterium YpeB C-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb5BOI/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Priestia megaterium QM B1551
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-27 Released: 2015-08-12 
• Deposition Author(s): Christie, G., Chirgadze, D.Y., Ustok, F.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Crystal structure of the PepSY-containing domain of the YpeB protein involved in germination of bacillus spores.

Ustok, F.I., Chirgadze, D.Y., Christie, G.

(2015) Proteins 83: 1914-1921

• PubMed: 26219275 
• DOI: https://doi.org/10.1002/prot.24868
• Primary Citation of Related Structures:  
  5BOI


• PubMed Abstract: 
  

  The crystal structure of the C-terminal domain of the Bacillus megaterium YpeB protein has been solved by X-ray crystallography to 1.80-Å resolution. The full-length protein is essential in stabilising the SleB cortex lytic enzyme in Bacillus spores, and may have a role in regulating SleB activity during spore germination. The YpeB-C crystal structure comprises three tandemly repeated PepSY domains, which are aligned to form an extended laterally compressed molecule. A predominantly positively charged region located in the second PepSY domain may provide a site for protein interactions that are important in stabilising SleB and YpeB within the spore.

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Organizational Affiliation: 

Department of Chemical Engineering and Biotechnology, Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.4 kDa 
• Atom Count: 1,943 
• Modelled Residue Count: 226 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germination protein YpeB	A	246	Priestia megaterium QM B1551	Mutation(s): 0  Gene Names: ypeB, BMQ_4349
UniProt
Find proteins for D5DRI0 (Priestia megaterium (strain ATCC 12872 / QMB1551)) Explore D5DRI0  Go to UniProtKB:  D5DRI0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [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: 0.227 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.208	α = 90
b = 110.104	β = 90
c = 85.806	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Christie, G., Chirgadze, D.Y., Ustok, F.I.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references