2FU2

Crystal structure of protein SPy2152 from Streptococcus pyogenes

• PDB DOI: https://doi.org/10.2210/pdb2FU2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-25 Released: 2006-03-07 
• Deposition Author(s): Chang, C., Cymborowski, M., Otwinowski, Z., Minor, W., Lezondra, L.-E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.254 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 

Literature

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes.

Chang, C., Coggill, P., Bateman, A., Finn, R.D., Cymborowski, M., Otwinowski, Z., Minor, W., Volkart, L., Joachimiak, A.

(2009) BMC Struct Biol 9: 75-75

• PubMed: 20017931 
• DOI: https://doi.org/10.1186/1472-6807-9-75
• Primary Citation of Related Structures:  
  2FU2


• PubMed Abstract: 
  

  Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable.

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Organizational Affiliation: 

Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.47 kDa 
• Atom Count: 694 
• Modelled Residue Count: 78 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein SPy2152	A	102	Streptococcus pyogenes	Mutation(s): 3
UniProt
Find proteins for Q48QT2 (Streptococcus pyogenes serotype M28 (strain MGAS6180)) Explore Q48QT2  Go to UniProtKB:  Q48QT2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.254 
• R-Value Work: 0.157 
• R-Value Observed: 0.161 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.087	α = 90
b = 30.28	β = 113.26
c = 35.855	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Chang, C., Cymborowski, M., Otwinowski, Z., Minor, W., Lezondra, L.-E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary