8V31

Structure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2

PDB DOI: https://doi.org/10.2210/pdb8V31/pdb

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

Deposited: 2023-11-25 Released: 2024-06-19
Deposition Author(s): Lazarski, A.C., Worrall, L.J., Strynadka, N.C.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.244
R-Value Work: 0.197

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

An alternative broad-specificity pathway for glycan breakdown in bacteria

Nasseri, S.A., Lazarski, A.C., Lemmer, I.L., Zhang, C.Y., Brencher, E., Chen, H., Sim, L., Panwar, D., Betschart, L., Worrall, L.J., Brumer, H., Strynadka, N.C.J., Withers, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 61.97 kDa
Atom Count: 3,980
Modelled Residue Count: 494
Deposited Residue Count: 554
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase	A, B [auth C]	277	Alistipes	Mutation(s): 0 Gene Names: A3BBH6_04590
UniProt
Find proteins for A0A1Y3R144 (Alistipes onderdonkii) Explore A0A1Y3R144 Go to UniProtKB: A0A1Y3R144
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y3R144
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C] mmCIF format, chain C [auth A] mmCIF format, chain D [auth C]	C [auth A], D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.244
R-Value Work: 0.197
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.088	α = 90
b = 95.088	β = 90
c = 159.542	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Strynadka, N.C.J.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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.