6NI0 | pdb_00006ni0

Crystal Structure of the Beta Lactamase Class D YbxI from Burkholderia thailandensis

• PDB DOI: https://doi.org/10.2210/pdb6NI0/pdb

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


• Deposited: 2018-12-25 Released: 2019-01-16 
• Deposition Author(s): Kim, Y., Wu, R., Endres, R., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Beta Lactamase Class D YbxI from Burkholderia thailandensis

Kim, Y., Wu, R., Endres, R., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.32 kDa 
• Atom Count: 2,002 
• Modeled Residue Count: 246 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	249	Burkholderia thailandensis	Mutation(s): 0  Gene Names: A8H35_26135, A8H36_11295 EC: 3.5.2.6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.204	α = 90
b = 43.204	β = 90
c = 256.902	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kim, Y., Wu, R., Endres, R., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary