8K9H | pdb_00008k9h

Complex structure of Acetoacetate:butyrate/acetate coenzyme A transferase and Butyrate-acetoacetate CoA-transferase subunit B from Fusobacterium nucleatum ATCC 25586

• PDB DOI: https://doi.org/10.2210/pdb8K9H/pdb

• Classification: TRANSFERASE
• Organism(s): Fusobacterium nucleatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-01 Released: 2024-08-07 
• Deposition Author(s): Bai, X., Zhao, Z.D., Xu, Y.B.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Complex structure of Acetoacetate:butyrate/acetate coenzyme A transferase and Butyrate-acetoacetate CoA-transferase subunit B from Fusobacterium nucleatum ATCC 25586

Bai, X., Zhao, Z.D., Xu, Y.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 189.9 kDa 
• Atom Count: 12,298 
• Modeled Residue Count: 1,705 
• Deposited Residue Count: 1,776 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrate-acetoacetate CoA-transferase subunit B	A, C, E, G	219	Fusobacterium nucleatum	Mutation(s): 0  Gene Names: FN1856 EC: 2.8.3.9
UniProt
Find proteins for Q8RHY4 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RHY4  Go to UniProtKB:  Q8RHY4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoacetate:butyrate/acetate coenzyme A transferase	B, D, F, H	225	Fusobacterium nucleatum	Mutation(s): 0  Gene Names: FN1857 EC: 2.8.3.9
UniProt
Find proteins for Q8RHY3 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RHY3  Go to UniProtKB:  Q8RHY3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	I [auth C], J [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.518	α = 90
b = 166.518	β = 90
c = 191.377	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Bai, X., Zhao, Z.D., Xu, Y.B.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release