4NZ5 | pdb_00004nz5

Structure of Vibrio cholerae chitin de-N-acetylase in complex with 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE (NDG) and cadmium ion

• PDB DOI: https://doi.org/10.2210/pdb4NZ5/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 str. NHCC-010F
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-11 Released: 2014-11-26 
• 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: 1.87 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Vibrio cholerae protein

Andres, E., Albesa-Jove, D., Biarnes, X., Moerschbacher, B.M., Guerin, M.E., Planas, A.

To be published.

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: 94.96 kDa 
• Atom Count: 6,992 
• Modeled 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): 0  EC: 3.5.1.41

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	F [auth A], K [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
CD	D [auth A], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL	G [auth A], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.664	α = 90
b = 112.525	β = 94.35
c = 69.815	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Albesa-Jove, D., Andres, E., Biarnes, X., Planas, A., Guerin, M.E.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• 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
• Version 2.2: 2024-11-13
  Changes: Structure summary