1PVJ | pdb_00001pvj

Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb1PVJ/pdb

• Classification: TOXIN
• Organism(s): Streptococcus pyogenes
• Mutation(s): No 


• Deposited: 2003-06-27 Released: 2004-09-28 
• Deposition Author(s): Ziomek, E., Sivaraman, J., Doran, J., Menard, R., Cygler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.288 (Depositor), 0.318 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.257 (DCC) 

Literature

Inhibition of autoprocessing of the streptococcal pyrogenic exotoxin B (speB). Crystal structure of the proenzyme-inhibitor complex

Ziomek, E., Sivaraman, J., Doran, J., Menard, R., Cygler, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 161.38 kDa 
• Atom Count: 11,052 
• Modeled Residue Count: 1,356 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pyrogenic exotoxin B	A, B, C, D	368	Streptococcus pyogenes	Mutation(s): 0  EC: 3.4.22.10
UniProt
Find proteins for P0C0J0 (Streptococcus pyogenes) Explore P0C0J0  Go to UniProtKB:  P0C0J0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZFB	E [auth A], F [auth B], G [auth C], H [auth D]	(3R)-3-{[(BENZYLOXY)CARBONYL]AMINO}-2-OXO-4-PHENYLBUTANE-1-DIAZONIUM C18 H18 N3 O3 VLIGBVLLNSWVMI-MRXNPFEDSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.288 (Depositor), 0.318 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.257 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.769	α = 90
b = 119.495	β = 90
c = 144.083	γ = 90

Software Package:

Software Name	Purpose
Adxv	data processing
HKL-2000	data reduction
AMoRE	phasing
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Ziomek, E., Sivaraman, J., Doran, J., Menard, R., Cygler, M.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-05-09
  Changes: Other
• Version 1.4: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.5: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary