4GNV | pdb_00004gnv

Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with bound N-Acetyl-D-Glucosamine

• PDB DOI: https://doi.org/10.2210/pdb4GNV/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-17 Released: 2012-08-29 
• Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.175 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with bound N-Acetyl-D-Glucosamine

Davies, D.R., Abendroth, J., Staker, B., Stewart, L.

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: 76.82 kDa 
• Atom Count: 5,835 
• Modeled Residue Count: 680 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase 1	A, B	350	Burkholderia cenocepacia J2315	Mutation(s): 1  Gene Names: nagZ1, nagZ2, BceJ2315_10000, BceJ2315_27960, BCAL1010, BCAL2860 EC: 3.2.1.52
UniProt
Find proteins for B4EA43 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EA43  Go to UniProtKB:  B4EA43

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	D [auth A], E [auth A], F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.175 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GNV

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.97	α = 90
b = 89.31	β = 91.73
c = 67.15	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Structure summary