9TP6 | pdb_00009tp6

Structure of LolA3 from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb9TP6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Porphyromonas gingivalis ATCC 33277
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-12-17 Released: 2026-02-18 
• Deposition Author(s): Jaiman, D., Persson, K.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.287 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: in silico

Literature

The LolB-like protein from Porphyromonas gingivalis

Jaiman, D., Persson, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.32 kDa 
• Atom Count: 5,944 
• Modeled Residue Count: 719 
• Deposited Residue Count: 819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane lipoprotein-sorting protein	A, B, C	273	Porphyromonas gingivalis ATCC 33277	Mutation(s): 0  Gene Names: PGN_0947, PGN_1919
UniProt
Find proteins for B2RJC1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RJC1  Go to UniProtKB:  B2RJC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	H [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.287 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.113	α = 90
b = 124.113	β = 90
c = 44.389	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
xia2	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Jaiman, D., Persson, K.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2024-02964

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release