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.

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), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Vibrio cholerae protein

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

To be published.

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

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| 3D Structure

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	3D Interactions
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

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), 0.179 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

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