6XSX | pdb_00006xsx

The structure of the catalytic module of the metalloprotease ZmpA from Clostridium perfringens

• PDB DOI: https://doi.org/10.2210/pdb6XSX/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-16 Released: 2021-02-03 
• Deposition Author(s): Pluvinage, B., Boraston, A.B.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Canadian Glycomics Network (GLYCONET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Molecular insights into architecturally complex glycopeptidases

Pluvinage, B., Ficko-Blean, E., Noach, I., Stuart, C., Thompson, N., McClure, H., Buenbrazo, N., Wakarchuck, W., Boraston, A.B.

(2021) Proc Natl Acad Sci U S A 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.28 kDa 
• Atom Count: 4,256 
• Modeled Residue Count: 499 
• Deposited Residue Count: 529 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZmpA Glycopeptidase	A	529	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: CPF_1073
UniProt
Find proteins for A0A0H2YW34 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YW34  Go to UniProtKB:  A0A0H2YW34

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A], C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.168	α = 90
b = 54.553	β = 93.2
c = 90.984	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Pluvinage, B., Boraston, A.B.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Canadian Glycomics Network (GLYCONET)	Canada	--

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description