6EB3 | pdb_00006eb3

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 (Depositor), 0.236 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 119.01 kDa
Atom Count: 8,791
Modeled Residue Count: 1,063
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

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| 3D Structure

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	3D Interactions
J3G Query on J3G Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	2-hydroxypropane-1,3-diyl dibutanoate C₁₁ H₂₀ O₅ KBWFWZJNPVZRRG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
J3J Query on J3J Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,3-dihydroxypropan-2-yl butanoate C₇ H₁₄ O₄ PVPWPCLNZDBNFK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ABU Query on ABU Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	L [auth C], Q [auth D]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain L [auth C] Focus chain Q [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	M [auth C], N [auth C], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain T [auth D]	E [auth A], F [auth A], G [auth A], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain T [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	I [auth B], O [auth C], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain I [auth B] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.233 (Depositor), 0.236 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-07

Deposition Author(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 (Full details and data files)

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