5JD6 | pdb_00005jd6

Crystal structure of MGS-MChE2, an alpha/beta hydrolase enzyme from the metagenome of sediments from the lagoon of Mar Chica, Morocco

• PDB DOI: https://doi.org/10.2210/pdb5JD6/pdb

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


• Deposited: 2016-04-15 Released: 2016-05-04 
• Deposition Author(s): Stogios, P.J., Xu, X., Nocek, B., Yim, V., Cui, H., Martinez-Martinez, M., Golyshin, P.N., Yakima, M.M., Ferrer, M., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MGS-MChE2, an alpha/beta hydrolase enzyme from the metagenome of sediments from the lagoon of Mar Chica, Morocco

Martinez-Martinez, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.9 kDa 
• Atom Count: 1,766 
• Modeled Residue Count: 219 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MGS-MChE2	A	254	uncultured bacterium	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.968	α = 90
b = 78.968	β = 90
c = 78.384	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Stogios, P.J., Xu, X., Nocek, B., Yim, V., Cui, H., Martinez-Martinez, M., Golyshin, P.N., Yakima, M.M., Ferrer, M., Savchenko, A.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description