2EBF

Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin

• PDB DOI: https://doi.org/10.2210/pdb2EBF/pdb

• Classification: TOXIN
• Organism(s): Pasteurella multocida
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-02-08 Released: 2007-03-06 
• Deposition Author(s): Kitadokoro, K., Horiguchi, Y., Kamitani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.06 kDa 
• Atom Count: 6,450 
• Modelled Residue Count: 711 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dermonecrotic toxin	A [auth X]	746	Pasteurella multocida	Mutation(s): 0  Gene Names: toxA
UniProt
Find proteins for P17452 (Pasteurella multocida) Explore P17452  Go to UniProtKB:  P17452

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B [auth A], C [auth B]	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PO	D [auth X]	PHOSPHONATE H O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	B [auth A], C [auth B]	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.971	α = 90
b = 150.406	β = 105.46
c = 77.139	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Kitadokoro, K., Horiguchi, Y., Kamitani, S.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary