4NZ3

Structure of Vibrio cholerae chitin de-N-acetylase in complex with DI(N-ACETYL-D-GLUCOSAMINE) (CBS) in P 21 21 21

• PDB DOI: https://doi.org/10.2210/pdb4NZ3/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 str. NHCC-010F
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-11 Released: 2014-08-13 
• Deposition Author(s): Albesa-Jove, D., Andres, E., Biarnes, X., Planas, A., Guerin, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.213 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.19 kDa 
• Atom Count: 7,295 
• Modelled Residue Count: 808 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deacetylase DA1	A, B	419	Vibrio cholerae O1 str. NHCC-010F	Mutation(s): 1  EC: 3.5.1.41

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	F [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.213 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.684	α = 90
b = 98.142	β = 90
c = 152.988	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Albesa-Jove, D., Andres, E., Biarnes, X., Planas, A., Guerin, M.E.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary