9U8E | pdb_00009u8e

Crystal structure of Leminorella grimontii GatC in the presence of D-xylose

• PDB DOI: https://doi.org/10.2210/pdb9U8E/pdb

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


• Deposited: 2025-03-26 Released: 2025-10-15 
• Deposition Author(s): Takahashi, Y.S., Kohga, H., Yamamoto, K., Takahashi, J.F., Tanaka, Y., Ichikawa, M., Miyazaki, R., Tsukazaki, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: in silico

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, H., Ichikawa, M., Miyazaki, R., Hakoshima, T., Tsukazaki, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 102.3 kDa 
• Atom Count: 6,812 
• Modeled Residue Count: 896 
• Deposited Residue Count: 942 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.76	α = 90
b = 100.61	β = 90
c = 122.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Takahashi, Y.S., Kohga, H., Yamamoto, K., Takahashi, J.F., Tanaka, Y., Ichikawa, M., Miyazaki, R., Tsukazaki, T.

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

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release