5HAL | pdb_00005hal

Crystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis

• PDB DOI: https://doi.org/10.2210/pdb5HAL/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia vietnamiensis G4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-30 Released: 2016-01-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Davies, D.R., Lorimer, D., Edwards, T.E.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 12.93 kDa 
• Atom Count: 902 
• Modeled Residue Count: 103 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	115	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_3604
UniProt
Find proteins for A4JJY8 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JJY8  Go to UniProtKB:  A4JJY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35HAL

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.84	α = 90
b = 110.84	β = 90
c = 110.84	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
ARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references
• Version 1.4: 2025-10-22
  Changes: Database references, Structure summary