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)

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), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RHY4
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RHY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth H] MOL2 format, chain I [auth C] MOL2 format, chain J [auth H] mmCIF format, chain I [auth C] mmCIF format, chain J [auth H]	I [auth C], J [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth C] Focus chain J [auth H] Interactions & Density Focus chain I [auth C] Focus chain J [auth H]

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), 0.197 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.