3GLD | pdb_00003gld

Crystal Structure of the Major Pilin from Streptococcus pyogenes E117A mutant

• PDB DOI: https://doi.org/10.2210/pdb3GLD/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-12 Released: 2009-06-02 
• Deposition Author(s): Kang, H.J., Baker, E.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus pyogenes

Kang, H.J., Baker, E.N.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.27 kDa 
• Atom Count: 7,243 
• Modeled Residue Count: 853 
• Deposited Residue Count: 885 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pilin	A, B, C	295	Streptococcus pyogenes serotype M1	Mutation(s): 2  Gene Names: M5005_Spy0109, spy0128, SPy_0128
UniProt
Find proteins for Q9A1S2 (Streptococcus pyogenes serotype M1) Explore Q9A1S2  Go to UniProtKB:  Q9A1S2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.307	α = 90
b = 52.149	β = 98.83
c = 127.316	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Kang, H.J., Baker, E.N.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary