5IHV | pdb_00005ihv

Crystal structure of a beta-lactamase from Burkholderia ambifaria

• PDB DOI: https://doi.org/10.2210/pdb5IHV/pdb

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


• Deposited: 2016-02-29 Released: 2016-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a beta-lactamase from Burkholderia ambifaria

Mayclin, S.J., Abendroth, J., Lorimer, D.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)

Macromolecule Content 

• Total Structure Weight: 28.32 kDa 
• Atom Count: 2,374 
• Modeled Residue Count: 261 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	269	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_4487 EC: 3.5.2.6
UniProt
Find proteins for B1YX81 (Burkholderia ambifaria (strain MC40-6)) Explore B1YX81  Go to UniProtKB:  B1YX81

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IHV

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.26	α = 90
b = 63.08	β = 90
c = 73.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description