6EZT | pdb_00006ezt

Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A inactive mutant from Vibrio harveyi

• PDB DOI: https://doi.org/10.2210/pdb6EZT/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.60 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (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: 149.11 kDa 
• Atom Count: 10,764 
• Modeled Residue Count: 1,278 
• Deposited Residue Count: 1,298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylglucosaminidase Nag2	A, B	649	Vibrio harveyi	Mutation(s): 1  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
PG4	C [auth A], F [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	D [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.42	α = 90
b = 129.24	β = 112.2
c = 98.36	γ = 90

Software Package:

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

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: 2024-01-17
  Changes: Data collection, Database references, Refinement description