9BH3 | pdb_00009bh3

Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein

PDB DOI: https://doi.org/10.2210/pdb9BH3/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Aggregatibacter actinomycetemcomitans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-19 Released: 2025-10-08
Deposition Author(s): King-Hudson, T.-R.J., Davies, J.S., Dobson, R.C.J.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.220 (Depositor), 0.218 (DCC)
R-Value Work:
0.189 (Depositor), 0.195 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Models: experimental
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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 of apo Aggregatibacter actinomycetemcomitans SiaP protein

King-Hudson, T.-R.J., Davies, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 136.48 kDa
Atom Count: 9,665
Modeled Residue Count: 1,224
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DctP family TRAP transporter solute-binding subunit	A, B, C, D	306	Aggregatibacter actinomycetemcomitans	Mutation(s): 0 Gene Names: FXB68_07930
UniProt
Find proteins for A0A5D0EK58 (Aggregatibacter actinomycetemcomitans) Explore A0A5D0EK58 Go to UniProtKB: A0A5D0EK58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5D0EK58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.220 (Depositor), 0.218 (DCC)
R-Value Work: 0.189 (Depositor), 0.195 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.667	α = 90
b = 141.394	β = 112.491
c = 109.405	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

King-Hudson, T.-R.J.

Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	UOC1506

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.