6JTU | pdb_00006jtu

Crystal structure of MHETase from Ideonella sakaiensis

PDB DOI: https://doi.org/10.2210/pdb6JTU/pdb

Classification: HYDROLASE
Organism(s): Piscinibacter sakaiensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-12 Released: 2020-04-15
Deposition Author(s): Sagong, H.-Y., Seo, H., Kim, K.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.198 (Depositor), 0.207 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Decomposition of PET film by MHETase using Exo-PETase function

Sagong, H.-Y., Seo, H., Kim, T., Son, H., Joo, S., Lee, S., Kim, S., Woo, J.-S., Hwang, S., Kim, K.-J.

(2020) ACS Catal 10: 4805-4812

DOI: https://doi.org/10.1021/acscatal.9b05604

Macromolecule Content

Total Structure Weight: 193.92 kDa
Atom Count: 13,224
Modeled Residue Count: 1,683
Deposited Residue Count: 1,839
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mono(2-hydroxyethyl) terephthalate hydrolase	A, B, C	613	Piscinibacter sakaiensis	Mutation(s): 0 EC: 3.1.1.102
UniProt
Find proteins for A0A0K8P8E7 (Piscinibacter sakaiensis) Explore A0A0K8P8E7 Go to UniProtKB: A0A0K8P8E7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K8P8E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A] K [auth B] L [auth B] M [auth B] N [auth B] E [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain Q [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain F [auth A]	F [auth A], Q [auth B], V [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B] Focus chain V [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain R [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain R [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.198 (Depositor), 0.207 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.931	α = 90
b = 173.163	β = 119.86
c = 107.225	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Sagong, H.-Y.

Seo, H.

Kim, K.-J.

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2020-10-28
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary