9EQQ | pdb_00009eqq

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose

PDB DOI: https://doi.org/10.2210/pdb9EQQ/pdb

Classification: CARBOHYDRATE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-22 Released: 2025-10-08
Deposition Author(s): Cioci, G., Ladeveze, S., Potocki-Veronese, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.179 (Depositor), 0.187 (DCC)

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

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Ligand Structure Quality Assessment

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

Literature

Structure-function studies of novel bacterial mannoside synthase

Cioci, G., Ladeveze, S.

To be published.

Macromolecule Content

Total Structure Weight: 39.42 kDa
Atom Count: 2,909
Modeled Residue Count: 347
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uhgb_MS mannoside synthase from an unknown human gut bacterium	A	350	metagenome	Mutation(s): 0
UniProt
Find proteins for F0QZL2 (Phocaeicola salanitronis (strain DSM 18170 / JCM 13657 / CCUG 60908 / BL78)) Explore F0QZL2 Go to UniProtKB: F0QZL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F0QZL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.207 (Depositor), 0.208 (DCC)
R-Value Work: 0.179 (Depositor), 0.187 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.629	α = 90
b = 176.629	β = 90
c = 83.539	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Potocki-Veronese, G.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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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.