9ZAV | pdb_00009zav

Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate

• PDB DOI: https://doi.org/10.2210/pdb9ZAV/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella melitensis 16M1W
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-11-19 Released: 2025-12-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with succinate

Liu, L., Lovell, S., Cooper, A., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 220.86 kDa 
• Atom Count: 15,092 
• Modeled Residue Count: 2,006 
• Deposited Residue Count: 2,045 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formyl-coenzyme a transferase	A, B, C, D, E	409	Brucella melitensis 16M1W	Mutation(s): 0  Gene Names: BMEII0224 EC: 2.8.3
UniProt
Find proteins for Q8YDF2 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YDF2  Go to UniProtKB:  Q8YDF2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth C]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39ZAV

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.59	α = 90
b = 189.59	β = 90
c = 199.316	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release