2XC8 | pdb_00002xc8

Crystal structure of the gene 22 product of the Bacillus subtilis SPP1 phage

• PDB DOI: https://doi.org/10.2210/pdb2XC8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bacillus phage SPP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-19 Released: 2010-06-09 
• Deposition Author(s): Veesler, D., Blangy, S., Tavares, P., Campanacci, V., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal Structure of Bacillus Subtilis Spp1 Phage Gp22 Shares Fold Similarity with a Domain of Lactococcal Phage P2 Rbp.

Veesler, D., Blangy, S., Spinelli, S., Tavares, P., Campanacci, V., Cambillau, C.

(2010) Protein Sci 19: 1439

• PubMed: 20506290 
• DOI: https://doi.org/10.1002/pro.416
• Primary Citation of Related Structures:  
  2XC8


• PubMed Abstract: 
  

  SPP1 is a siphophage infecting the gram-positive bacterium Bacillus subtilis. It is constituted by an icosahedric head and a long non-contractile tail formed by gene products (gp) 17-21. A group of 5 small genes (gp 22-24.1) follows in the genome those coding for the main tail components. However, the belonging of the corresponding gp to the tail or to other parts of the phage is not documented. Among these, gp22 lacks sequence identity to any known protein. We report here the gp22 structure solved by X-ray crystallography at 2.35 A resolution. We found that gp22 is a monomer in solution and possesses a significant structural similarity with lactococcal phage p2 ORF 18 N-terminal "shoulder" domain.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I and II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 50.47 kDa 
• Atom Count: 2,213 
• Modelled Residue Count: 260 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GENE 22 PRODUCT	A, B, C	146	Bacillus phage SPP1	Mutation(s): 0
UniProt
Find proteins for O48465 (Bacillus phage SPP1) Explore O48465  Go to UniProtKB:  O48465

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.911	α = 90
b = 64.116	β = 90
c = 101.053	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Veesler, D., Blangy, S., Tavares, P., Campanacci, V., Cambillau, C.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary