7COG

Cholesterol esterase from Burkholderia stabilis (monoclinic crystal form)

• PDB DOI: https://doi.org/10.2210/pdb7COG/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia stabilis
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2020-08-04 Released: 2020-12-16 
• Deposition Author(s): Yasutake, Y., Tamura, T.
• Funding Organization(s): New Energy and Industrial Technology Development Organization (NEDO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.237 

Literature

Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity.

Yasutake, Y., Konishi, K., Muramatsu, S., Yoshida, K., Aburatani, S., Sakasegawa, S.I., Tamura, T.

(2021) Int J Biol Macromol 167: 578-586

• DOI: https://doi.org/10.1016/j.ijbiomac.2020.11.184

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: homology

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: 133.1 kDa 
• Atom Count: 9,472 
• Modelled Residue Count: 1,280 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase	A, B, C, D	320	Burkholderia stabilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1Y1BQV9 (Burkholderia stabilis) Explore A0A1Y1BQV9  Go to UniProtKB:  A0A1Y1BQV9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.219 
• R-Value Observed: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.292	α = 90
b = 47.092	β = 90.05
c = 70.082	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Yasutake, Y., Tamura, T.

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Funding Organization	Location	Grant Number
New Energy and Industrial Technology Development Organization (NEDO)	Japan	--

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description