7SNO

Structure of Bacple_01701(H214N), a 6-O-galactose porphyran sulfatase

PDB DOI: https://doi.org/10.2210/pdb7SNO/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius DSM 17135
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2021-10-28 Released: 2022-10-05
Deposition Author(s): Ulaganathan, T., Cygler, M.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Mathieu, S., Touvrey, M., Poulet, L., Drouillard, S., Ulaganathan, T.S., Segurel, L., Cygler, M., Helbert, W.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.03.30.534863

Macromolecule Content

Total Structure Weight: 64.28 kDa
Atom Count: 4,468
Modelled Residue Count: 506
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arylsulfatase	A	536	Phocaeicola plebeius DSM 17135	Mutation(s): 1 Gene Names: BACPLE_01701 EC: 3.1.6
UniProt
Find proteins for B5CYA4 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CYA4 Go to UniProtKB: B5CYA4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5CYA4
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO 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 J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A]	E [auth A], F [auth A], G [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]