4U10 | pdb_00004u10

Probing the structure and mechanism of de-N-acetylase from aggregatibacter actinomycetemcomitans

• PDB DOI: https://doi.org/10.2210/pdb4U10/pdb

• Classification: HYDROLASE
• Organism(s): Aggregatibacter actinomycetemcomitans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2015-01-14 
• Deposition Author(s): Varudharasu, D., Narayanan, R.
• Funding Organization(s): United States Public Health Service

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Probing the structure and mechanism of de-N-acetylase from aggregatibacter actinomycetemcomitans

Varudharsu, D., Narayanan, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.1 kDa 
• Atom Count: 4,513 
• Modeled Residue Count: 526 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase	A, B	280	Aggregatibacter actinomycetemcomitans	Mutation(s): 0  Gene Names: pgaB
UniProt
Find proteins for A5HJW8 (Aggregatibacter actinomycetemcomitans) Explore A5HJW8  Go to UniProtKB:  A5HJW8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.24	α = 90
b = 67.1	β = 90
c = 101.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Varudharasu, D., Narayanan, R.

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Funding Organization	Location	Grant Number
United States Public Health Service	United States	DE22544

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary