4TXW | pdb_00004txw

Crystal structure of CBM32-4 from the Clostridium perfringens NagH

• PDB DOI: https://doi.org/10.2210/pdb4TXW/pdb

• Classification: carbohydrate-binding module
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-07 Released: 2015-12-09 
• Deposition Author(s): Grondin, J.M., Ficko-Blean, E., Boraston, A.B., Smith, S.P.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Solution Structure and Dynamics of Full-length GH84A, a multimodular B-N-acetylglucosaminidase from Clostridium perfringens

Grondin, J.M., Chitayat, S., Ficko-Blean, E., Czjzek, M., Boraston, A.B., Smith, S.P.

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)

Macromolecule Content 

• Total Structure Weight: 19.14 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 159 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronoglucosaminidase	A	173	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: nagH, CPF_0184 EC: 3.2.1.35
UniProt
Find proteins for A0A0H2YRL1 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YRL1  Go to UniProtKB:  A0A0H2YRL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.102	α = 90
b = 64.709	β = 94.52
c = 37.723	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Grondin, J.M., Ficko-Blean, E., Boraston, A.B., Smith, S.P.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP 68913

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations