9C9F | pdb_00009c9f

Crystal structures fluoroacetate dehalogenase D4B from Delftia acidovorans strain D4B

• PDB DOI: https://doi.org/10.2210/pdb9C9F/pdb

• Classification: TRANSFERASE
• Organism(s): Delftia acidovorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-13 Released: 2025-08-27 
• Deposition Author(s): Caputo, A.T., Hu, M., Scott, C.
• Funding Organization(s): Commonwealth Scientific and Industrial Research Organisation (CSIRO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of two fluoroacetate dehalogenases

Hu, M., Caputo, A.T., Scott, C.

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 143.23 kDa 
• Atom Count: 10,117 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluoroacetate dehalogenase	A, B, C, D	320	Delftia acidovorans	Mutation(s): 0  Gene Names: Daci_4283
UniProt
Find proteins for A9BLX5 (Delftia acidovorans (strain DSM 14801 / SPH-1)) Explore A9BLX5  Go to UniProtKB:  A9BLX5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.936	α = 101.598
b = 83.778	β = 96.027
c = 84.917	γ = 94.673

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Caputo, A.T., Hu, M., Scott, C.

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Funding Organization	Location	Grant Number
Commonwealth Scientific and Industrial Research Organisation (CSIRO)	Australia	--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release