12RI | pdb_000012ri

Cryo-EM structure of a novel beta-galactosidase (HhGH116) from human gut

PDB DOI: https://doi.org/10.2210/pdb12RI/pdb
EM Map EMD-76708: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-04-15 Released: 2026-09-09
Deposition Author(s): Ciol, H., Noske, G.D., Stoffel, F., Morao, L.G., Martins, M.P., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

Validation slider image for 12RI

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

Literature

Cryo-EM structure of a novel beta-galactosidase (HhGH116) from human gut

Ciol, H., Noske, G.D., Stoffel, F., Morao, L.G., Martins, M.P., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 179.78 kDa
Atom Count: 11,434
Modeled Residue Count: 1,426
Deposited Residue Count: 1,584
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl Hydrolase family 116	A, B	792	metagenome	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/04891-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/09793-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/09386-8
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/03059-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	303898/2024-0

Revision History (Full details and data files)

Version 1.0: 2026-09-09
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.