9ERG | pdb_00009erg

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose-1-Phosphate

PDB DOI: https://doi.org/10.2210/pdb9ERG/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: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.211 (DCC)
R-Value Work:
0.175 (Depositor), 0.184 (DCC)

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

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: 79.11 kDa
Atom Count: 5,791
Modeled Residue Count: 693
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uhgb_MS mannoside synthase from an unknown human gut bacterium	A, B	351	metagenome	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M1P (Subject of Investigation/LOI) Query on M1P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-O-phosphono-alpha-D-mannopyranose C₆ H₁₃ O₉ P HXXFSFRBOHSIMQ-RWOPYEJCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.211 (DCC)
R-Value Work: 0.175 (Depositor), 0.184 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.534	α = 90
b = 83.368	β = 106.352
c = 73.206	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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

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.