5NGG

Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion

• PDB DOI: https://doi.org/10.2210/pdb5NGG/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium diazoefficiens USDA 110
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-17 Released: 2017-09-27 
• Deposition Author(s): Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.146 
• R-Value Work: 0.121 
• R-Value Observed: 0.122 

Starting Model: experimental

Literature

Boric acid and acetate anion binding to subclass B3 metallo-Beta-lactamase BJP-1 provides clues for mechanism of action and inhibitor design

Di Pisa, F., Pozzi, C., Benvenuti, M., Docquier, J.-D., De Luca, F., Mangani, S.

(2017) Inorganica Chim Acta 

• DOI: https://doi.org/10.1016/j.ica.2017.07.030

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.48 kDa 
• Atom Count: 4,983 
• Modelled Residue Count: 548 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blr6230 protein	A, B	294	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0  Gene Names: blr6230
UniProt
Find proteins for Q89GW5 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89GW5  Go to UniProtKB:  Q89GW5

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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	F [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.146 
• R-Value Work: 0.121 
• R-Value Observed: 0.122 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.31	α = 78.88
b = 44.64	β = 89.41
c = 75.91	γ = 61.99

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Pozzi, C., Di Pisa, F., Benvenuti, M., Mangani, S.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description