7D5Y

Cystein protease domain from MARTX toxin

• PDB DOI: https://doi.org/10.2210/pdb7D5Y/pdb

• Classification: TOXIN
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-28 Released: 2021-05-12 
• Deposition Author(s): Kim, M.-H., Hwang, J., Choi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Cystein protease domain from MARTX toxin

Kim, M.-H., Hwang, J., Choi, S.

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: 23.23 kDa 
• Atom Count: 1,732 
• Modelled Residue Count: 210 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MARTX	A	210	Vibrio vulnificus	Mutation(s): 0
UniProt
Find proteins for A0A023NA98 (Vibrio vulnificus) Explore A0A023NA98  Go to UniProtKB:  A0A023NA98

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.307	α = 90
b = 125.307	β = 90
c = 125.307	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Kim, M.-H., Hwang, J., Choi, S.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description