6EZS | pdb_00006ezs

Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi in complex with N-acetylglucosamine

• PDB DOI: https://doi.org/10.2210/pdb6EZS/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-12-12 
• Deposition Author(s): Porfetye, A.T., Meekrathok, P., Burger, M., Vetter, I.R., Suginta, W.
• Funding Organization(s): Thailand Research Fund, DAAD

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi

Meekrathok, P., Porfetye, A.T., Burger, M., Vetter, I.R., Suginta, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 149.73 kDa 
• Atom Count: 11,254 
• Modeled Residue Count: 1,278 
• Deposited Residue Count: 1,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylglucosaminidase Nag2	A, B	652	Vibrio harveyi	Mutation(s): 0  EC: 3.2.1.52
UniProt
Find proteins for D9ISE0 (Vibrio harveyi) Explore D9ISE0  Go to UniProtKB:  D9ISE0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MLI	D [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.25	α = 90
b = 129.63	β = 114.36
c = 100	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Porfetye, A.T., Meekrathok, P., Burger, M., Vetter, I.R., Suginta, W.

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Funding Organization	Location	Grant Number
Thailand Research Fund	Thailand	PHD00842550
DAAD	Germany	BRG578001
Thailand Research Fund	Thailand	A/10/98020

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary