3TOC

Crystal structure of Streptococcus pyogenes Csn2

• PDB DOI: https://doi.org/10.2210/pdb3TOC/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-05 Released: 2012-05-30 
• Deposition Author(s): Bae, E., Jung, D.K., Koo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure

Koo, Y., Jung, D.K., Bae, E.

(2012) PLoS One 7: e33401-e33401

• PubMed: 22479393 
• DOI: https://doi.org/10.1371/journal.pone.0033401
• Primary Citation of Related Structures:  
  3TOC, 3V7F


• PubMed Abstract: 
  

  Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute a microbial immune system against invading genetic elements, such as plasmids and phages. Csn2 is an Nmeni subtype-specific Cas protein, and was suggested to function in the adaptation process, during which parts of foreign nucleic acids are integrated into the host microbial genome to enable immunity against future invasion. Here, we report a 2.2 Å crystal structure of Streptococcus pyogenes Csn2. The structure revealed previously unseen calcium-dependent conformational changes in its tertiary and quaternary structure. This supports the proposed double-stranded DNA-binding function of S. pyogenes Csn2.

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Organizational Affiliation: 

Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 52.72 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 427 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	224	Streptococcus pyogenes serotype M1	Mutation(s): 0  Gene Names: M5005_Spy0772, SPy_1049
UniProt
Find proteins for Q99ZV9 (Streptococcus pyogenes serotype M1) Explore Q99ZV9  Go to UniProtKB:  Q99ZV9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.482	α = 90
b = 163.362	β = 90
c = 149.971	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Bae, E., Jung, D.K., Koo, Y.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release