4MSS | pdb_00004mss

Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-acetamido-4,5,6-trihydroxyazepane

• PDB DOI: https://doi.org/10.2210/pdb4MSS/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-18 Released: 2013-10-30 
• Deposition Author(s): Vadlamani, G., Mark, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.138 (DCC) 

Starting Model: experimental

Literature

Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to beta-lactams.

Mondon, M., Hur, S., Vadlamani, G., Rodrigues, P., Tsybina, P., Oliver, A., Mark, B.L., Vocadlo, D.J., Bleriot, Y.

(2013) Chem Commun (Camb) 49: 10983-10985

• PubMed: 24136176 
• DOI: https://doi.org/10.1039/c3cc46646a
• Primary Citation Related Structures: 
  4MSS


• PubMed Abstract: 
  

  AmpC β-lactamase confers resistance to β-lactam antibiotics in many Gram negative bacteria. Inducible expression of AmpC requires an N-acetylglucosaminidase termed NagZ. Here we describe the synthesis and characterization of hydroxyazepane inhibitors of NagZ. We find that these inhibitors enhance the susceptibility of clinically relevant Pseudomonas aeruginosa to β-lactams.

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Organizational Affiliation: 
• Université de Poitiers, IC2MP, UMR CNRS 7285, Équipe "Synthése Organique" Groupe Glycochimie, 4 rue Michel Brunet, 86022 Poitiers Cedex, France. [e-mail].

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: 76.92 kDa 
• Atom Count: 5,972 
• Modeled Residue Count: 679 
• 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): 0  Gene Names: BCAL1010, BCAL2860, BceJ2315_10000, BceJ2315_27960, nagZ, nagZ1, nagZ2 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
2CZ	C [auth A], E [auth B]	N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide C8 H16 N2 O4 RGHXJBVAPJFIEQ-RULNZFCNSA-N
GOL	D [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.138 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.76	α = 90
b = 87.58	β = 92.1
c = 67.21	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Vadlamani, G., Mark, B.L.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description