9BHF | pdb_00009bhf

Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein

PDB DOI: https://doi.org/10.2210/pdb9BHF/pdb

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

Deposited: 2024-04-20 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: 1.90 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: 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: 69.29 kDa
Atom Count: 5,392
Modeled Residue Count: 614
Deposited Residue Count: 616
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	308	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
SLB (Subject of Investigation/LOI) Query on SLB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-acetyl-beta-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-PFQGKNLYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.166	α = 90
b = 49.54	β = 92.81
c = 121.389	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.