1F0L | pdb_00001f0l

1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN

• PDB DOI: https://doi.org/10.2210/pdb1F0L/pdb

• Classification: TOXIN
• Organism(s): Corynebacterium diphtheriae
• Mutation(s): No 


• Deposited: 2000-05-16 Released: 2000-11-16 
• Deposition Author(s): Steere, B., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.238 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Characterization of High-Order Oligomerization and Energetics in Diphtheria Toxin

Steere, B.

(2001) Thesis 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 118.45 kDa 
• Atom Count: 10,204 
• Modeled Residue Count: 1,042 
• Deposited Residue Count: 1,070 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPHTHERIA TOXIN	A, B	535	Corynebacterium diphtheriae	Mutation(s): 0  EC: 2.4.2.36
UniProt
Find proteins for P00588 (Corynephage beta) Explore P00588  Go to UniProtKB:  P00588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APU	G [auth A], M [auth B]	ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE C19 H25 N7 O15 P2 FZCSEXOMUJFOHQ-KPKSGTNCSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.238 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.77	α = 90
b = 134.88	β = 90
c = 46.87	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXL	refinement
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-16 
Deposition Author(s): Steere, B., Eisenberg, D.

Revision History  

• Version 1.0: 2000-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary