6RKY | pdb_00006rky

STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE

PDB DOI: https://doi.org/10.2210/pdb6RKY/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-04-30 Released: 2019-12-25
Deposition Author(s): Cea-Rama, I., Sanz-Aparicio, J.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.276 (Depositor), 0.329 (DCC)
R-Value Work:
0.239 (Depositor)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 4.2 of the entry. See complete history.

Literature

Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis

Alonso, S., Santiago, G., Cea-Rama, I., Fernandez-Lopez, L., Coscolin, C., Modregger, J., Ressmann, A.K., Martinez-Martinez, M., Marrero, H., Bargiela, R., Pita, M., Gonzalez-Alfonso, J.L., Briand, M.L., Rojo, D., Barbas, C., Plou, F.J., Golyshin, P.N., Shahgaldian, P., Sanz-Aparicio, J., Guallar, V., Ferrer, M.

(2020) Nat Catal 3

DOI: https://doi.org/10.1038/s41929-019-0394-4

Macromolecule Content

Total Structure Weight: 144.74 kDa
Atom Count: 9,764
Modeled Residue Count: 1,260
Deposited Residue Count: 1,316
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EH1AB1	A, B, C, D	329	metagenome	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZK8 (Subject of Investigation/LOI) Query on ZK8 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], N [auth C], R [auth D]	hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphinic acid C₁₆ H₂₁ N₂ O₄ P QYCWYIQRYAMGGW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain N [auth C] Focus chain R [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C]	K [auth C], L [auth C], M [auth C], Q [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A] G [auth B] I [auth C] J [auth C] O [auth D] E [auth A], G [auth B], I [auth C], J [auth C], O [auth D], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.276 (Depositor), 0.329 (DCC)
R-Value Work: 0.239 (Depositor)
R-Value Observed: 0.241 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.766	α = 90
b = 201.92	β = 112.19
c = 90.637	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Cea-Rama, I.

Sanz-Aparicio, J.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	Project BIO2016-76601-C3-3-R

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 2.0: 2020-10-14
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2020-12-16
Changes: Database references
Version 3.0: 2021-06-30
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 3.1: 2022-10-26
Changes: Database references
Version 4.0: 2023-07-05
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
Version 4.1: 2024-02-07
Changes: Data collection, Refinement description
Version 4.2: 2024-10-23
Changes: Structure summary