5HX9 | pdb_00005hx9

Crystal structure of Beta-lactamase from Burkholderia vietnamiensis

• PDB DOI: https://doi.org/10.2210/pdb5HX9/pdb

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


• Deposited: 2016-01-29 Released: 2016-02-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Beta-lactamase from Burkholderia vietnamiensis

Conrady, D.G., Abendroth, J., 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.

Macromolecule Content 

• Total Structure Weight: 29.6 kDa 
• Atom Count: 2,298 
• Modeled Residue Count: 259 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	283	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_5125 EC: 3.5.2.6
UniProt
Find proteins for A4JP73 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JP73  Go to UniProtKB:  A4JP73

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35HX9

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.5	α = 90
b = 63.31	β = 90
c = 99.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description