5I0P

Crystal Structure of a Beta-lactamase domain protein from Burkholderia ambifaria

• PDB DOI: https://doi.org/10.2210/pdb5I0P/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-04 Released: 2016-02-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Crystal Structure of a Beta-lactamase domain protein from Burkholderia ambifaria

Dranow, D.M., 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 and generated by PISA (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 164.45 kDa 
• Atom Count: 10,562 
• Modelled Residue Count: 1,328 
• Deposited Residue Count: 1,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase domain protein	A, B, C, D	366	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_2837
UniProt
Find proteins for B1YNR3 (Burkholderia ambifaria (strain MC40-6)) Explore B1YNR3  Go to UniProtKB:  B1YNR3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M35I0P

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.17	α = 90
b = 141.23	β = 90
c = 236.99	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing
Coot	model building
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description