9HFJ | pdb_00009hfj

Crystal structure of the NTE domain of SusCdex (BT3090) dextran transporter

PDB DOI: https://doi.org/10.2210/pdb9HFJ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-11-16 Released: 2025-11-26
Deposition Author(s): Feasey, M., Basle, A., van den Berg, B.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the NTE domain of SusCdex (BT3090) dextran transporter

Feasey, M., Basle, A., van den Berg, B.

To be published.

Macromolecule Content

Total Structure Weight: 9.66 kDa
Atom Count: 724
Modeled Residue Count: 80
Deposited Residue Count: 85
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusC homolog	A	85	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_3090
UniProt
Find proteins for Q8A365 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A365 Go to UniProtKB: Q8A365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A365
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], H [auth A], J [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.084	α = 90
b = 62.084	β = 90
c = 53.202	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data collection
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

van den Berg, B.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	214222/Z/18/Z

Revision History (Full details and data files)

Version 1.0: 2025-11-26
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.