6U8T | pdb_00006u8t

Crystal structure of YopT domain of Pasteurella Multocida PfhB2-toxin

• PDB DOI: https://doi.org/10.2210/pdb6U8T/pdb

• Classification: HYDROLASE
• Organism(s): Pasteurella multocida subsp. multocida str. Pm70
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-09-05 Released: 2020-09-09 
• Deposition Author(s): Kumar, S., Mattoo, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of YopT domain of Pasteurella Multocida PfhB2-Toxin

Kumar, S., Mattoo, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.59 kDa 
• Atom Count: 6,914 
• Modeled Residue Count: 854 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PfhB2	A, B [auth C], C [auth B], D	222	Pasteurella multocida subsp. multocida str. Pm70	Mutation(s): 1  Gene Names: pfhB2, PM0059
UniProt
Find proteins for Q9CPH9 (Pasteurella multocida (strain Pm70)) Explore Q9CPH9  Go to UniProtKB:  Q9CPH9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.652	α = 90
b = 62.957	β = 93.15
c = 164.342	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CRANK2	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Kumar, S., Mattoo, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM10092

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Derived calculations
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary