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)

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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9C9F

This is version 1.0 of the entry. See complete history.

Literature

Crystal structures of two fluoroacetate dehalogenases

Hu, M., Caputo, A.T., Scott, C.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9BLX5
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.