6EB3

Structural and enzymatic characterization of an esterase from a metagenomic library

• PDB DOI: https://doi.org/10.2210/pdb6EB3/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Mutation(s): No 


• Deposited: 2018-08-03 Released: 2019-08-07 
• Deposition Author(s): Guzzo, C.R., Carvalho, C.F., Teixeira, R.D., Farah, C.S.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Functional and Structural characterisation of an Esterase from Amazonian Dark Soil

Guzzo, C.R., Maciel, N.K., Barbosa, A.S., Farah, C.S.

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)

Biological Assembly Evidence: gel filtration

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: 119.01 kDa 
• Atom Count: 8,791 
• Modelled Residue Count: 1,063 
• Deposited Residue Count: 1,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Est1	A, B, C, D	268	metagenome	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J3G	J [auth B]	2-hydroxypropane-1,3-diyl dibutanoate C11 H20 O5 KBWFWZJNPVZRRG-UHFFFAOYSA-N
J3J	H [auth A]	1,3-dihydroxypropan-2-yl butanoate C7 H14 O4 PVPWPCLNZDBNFK-UHFFFAOYSA-N
ABU	L [auth C], Q [auth D]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N
SO4	M [auth C], N [auth C], R [auth D], S [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	K [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], G [auth A], T [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth B], O [auth C], P [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.65	α = 90
b = 105.95	β = 90
c = 145.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Guzzo, C.R., Carvalho, C.F., Teixeira, R.D., Farah, C.S.

---

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/084147
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/18664-2
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	403965/2016-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	303677/2017-1

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection