5JD4

Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

• PDB DOI: https://doi.org/10.2210/pdb5JD4/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., Alcaide, M., Yim, V., Cui, H., Martinez-Martinez, M., Ferrer, M., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.211 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

Martinez-Martinez, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 297.71 kDa 
• Atom Count: 22,038 
• Modelled Residue Count: 2,536 
• Deposited Residue Count: 2,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAE6	A, B, C, D, E, F, G, H	336	uncultured bacterium	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	KA [auth D], KB [auth H], N [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
BEN	CA [auth C], FB [auth G], LA [auth D], LB [auth H], O [auth A], RA [auth E], W [auth B], WA [auth F]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	DA [auth D], GB [auth H], HB [auth H], I [auth A], J [auth A], P [auth B], Q [auth B], X [auth C], XA [auth G], Y [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth C], BB [auth G], CB [auth G], DB [auth G], EA [auth D], EB [auth G], GA [auth D], HA [auth D], IA [auth D], IB [auth H], JB [auth H], K [auth A], M [auth A], NA [auth E], OA [auth E], PA [auth E], QA [auth E], R [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], YA [auth G], Z [auth C], ZA [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	AB [auth G], BA [auth C], FA [auth D], JA [auth D], L [auth A], MA [auth E], S [auth B], VA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.211 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.275	α = 68.02
b = 90.098	β = 79.6
c = 110.76	γ = 67.57

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	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., Alcaide, M., Yim, V., Cui, H., Martinez-Martinez, M., Ferrer, M., Savchenko, A.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Atomic model, Structure summary
• Version 2.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description