9B86 | pdb_00009b86

FetB apo from Porphyromonas gingivalis without heme group

• PDB DOI: https://doi.org/10.2210/pdb9B86/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-29 Released: 2025-04-09 
• Deposition Author(s): Ataide, S.F., Kwan, A., Phonok, Y., Gao, J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

FetB apo from Porphyromonas gingivalis without heme group

Ataide, S.F., Kwan, A., Phonok, Y., Gao, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.97 kDa 
• Atom Count: 2,242 
• Modeled Residue Count: 261 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-binding protein FetB	A	293	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: fetB
UniProt
Find proteins for Q7MWF2 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MWF2  Go to UniProtKB:  Q7MWF2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.631	α = 90
b = 49.817	β = 90
c = 98.912	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Ataide, S.F., Kwan, A., Phonok, Y., Gao, J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release