8YJC

Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A

• PDB DOI: https://doi.org/10.2210/pdb8YJC/pdb

• Classification: TOXIN
• Organism(s): Vibrio vulnificus MO6-24/O
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-03-01 Released: 2024-07-10 
• Deposition Author(s): Chen, L., Khan, H., Tan, L., Li, X., Zhang, G., Im, Y.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.189 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Structural basis of the activation of MARTX cysteine protease from Vibrio vunificus

Chen, L., Khan, H., Tan, L., Li, X., Zhang, G., Im, Y.J.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.15 kDa 
• Atom Count: 2,001 
• Modelled Residue Count: 210 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional autoprocessing repeat-in-toxin (MARTX)	A	225	Vibrio vulnificus MO6-24/O	Mutation(s): 0  Gene Names: rtxa

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	C [auth A]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.189 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.06	α = 90
b = 69.816	β = 107.69
c = 40.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Chen, L., Khan, H., Tan, L., Li, X., Zhang, G., Im, Y.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2023-00241410

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release