7SNK | pdb_00007snk

Structure of Bacple_01702, a GH29 family glycoside hydrolase

PDB DOI: https://doi.org/10.2210/pdb7SNK/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius DSM 17135
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

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: 2.00 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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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: 68.27 kDa
Atom Count: 4,970
Modeled Residue Count: 564
Deposited Residue Count: 597
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A	597	Phocaeicola plebeius DSM 17135	Mutation(s): 0 Gene Names: BACPLE_01702 EC: 3.2.1.51
UniProt
Find proteins for B5CYA5 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CYA5 Go to UniProtKB: B5CYA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5CYA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.214 (Depositor), 0.214 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.45	α = 90
b = 77.43	β = 90
c = 133.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-05

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

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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.