5D8M

Crystal structure of the metagenomic carboxyl esterase MGS0156

• PDB DOI: https://doi.org/10.2210/pdb5D8M/pdb

• Classification: HYDROLASE
• Organism(s): uncultured organism
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-17 Released: 2016-10-05 
• Deposition Author(s): Cui, H., Nocek, B., Tchigvintsev, A., Popovic, A., Savchenko, A., Joachimiak, A., Yakunin, A.
• Funding Organization(s): Genome Canada and Ontario Genomics Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

Crystal structure of esterase (MGS0156)

Nocek, B., Cui, H., Tchigvintsev, A., Popovic, A., Savchenko, A., Joachimiak, A., Yakunin, A.

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: 37.08 kDa 
• Atom Count: 2,793 
• Modelled Residue Count: 332 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metagenomic carboxyl esterase MGS0156	A	347	uncultured organism	Mutation(s): 0
UniProt
Find proteins for A0A0G3FEJ8 (uncultured organism) Explore A0A0G3FEJ8  Go to UniProtKB:  A0A0G3FEJ8

Small Molecules

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: 1.95 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.764	α = 90
b = 95.907	β = 90
c = 135.604	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Cui, H., Nocek, B., Tchigvintsev, A., Popovic, A., Savchenko, A., Joachimiak, A., Yakunin, A.

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Funding Organization	Location	Grant Number
Genome Canada and Ontario Genomics Institute	Canada	BEEM project

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary