8EP4 | pdb_00008ep4

Structure of Bacple_01703

PDB DOI: https://doi.org/10.2210/pdb8EP4/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius DSM 17135
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-05 Released: 2022-11-09
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: 1.94 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8EP4

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: 96.59 kDa
Atom Count: 7,471
Modeled Residue Count: 792
Deposited Residue Count: 801
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 16	A, B, C	267	Phocaeicola plebeius DSM 17135	Mutation(s): 0 Gene Names: BACPLE_01703
UniProt
Find proteins for B5CYA6 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CYA6 Go to UniProtKB: B5CYA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5CYA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth C]	D [auth A], H [auth B], O [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	E [auth A] F [auth A] I [auth B] K [auth B] L [auth B] E [auth A], F [auth A], I [auth B], K [auth B], L [auth B], P [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B]	G [auth A], M [auth B], N [auth B], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.193 (Depositor), 0.193 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.33	α = 90
b = 85.33	β = 90
c = 112.91	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Ulaganathan, T.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-05-10
Changes: Database references
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.