9U82 | pdb_00009u82

Cryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose

PDB DOI: https://doi.org/10.2210/pdb9U82/pdb
EM Map EMD-63950: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Leminorella grimontii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-25 Released: 2025-10-15
Deposition Author(s): Takahashi, Y.S., Kohga, H., Shigematsu, H., Miyazaki, R., Tsukazaki, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis of a phosphotransferase system xylose transporter

Takahashi, Y.S., Kohga, H., Chek, M.F., Yamamoto, K., Takahashi, J.F., Shigematsu, H., Tanaka, Y., Ichikawa, M., Miyazaki, R., Hakoshima, T., Tsukazaki, T.

To be published.

Macromolecule Content

Total Structure Weight: 100.16 kDa
Atom Count: 6,708
Modeled Residue Count: 896
Deposited Residue Count: 942
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS galactitol transporter subunit IIC	A, B	471	Leminorella grimontii	Mutation(s): 0 Gene Names: SOASR030_34840
UniProt
Find proteins for A0AAV5N9B3 (Leminorella grimontii) Explore A0AAV5N9B3 Go to UniProtKB: A0AAV5N9B3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAV5N9B3
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	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Takahashi, Y.S.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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.