9U9U | pdb_00009u9u

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys181Lys/Trp185Tyr/His280Ala with (S)-2-fluoro-3-(4-(trifluoromethyl)phenyl)propanoic acid

PDB DOI: https://doi.org/10.2210/pdb9U9U/pdb

Classification: TRANSFERASE
Organism(s): Rhodopseudomonas palustris CGA009
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-03-29 Released: 2025-12-31
Deposition Author(s): Huang, H.S., Zhang, Z.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.254 (Depositor), 0.257 (DCC)
R-Value Work:
0.196 (Depositor), 0.201 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

A Route to Powerful Biocatalysts: Designing a Gate-based Synergetic Chain through Long-range Conformational Dynamics Analysis

Huang, H.S., Zhang, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 135.46 kDa
Atom Count: 9,622
Modeled Residue Count: 1,192
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluoroacetate dehalogenase	A, B, C, D	302	Rhodopseudomonas palustris CGA009	Mutation(s): 3 Gene Names: RPA1163 EC: 3.8.1.3
UniProt
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NAM1 Go to UniProtKB: Q6NAM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NAM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ES3 (Subject of Investigation/LOI) Query on A1ES3 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	3-[4-(trifluoromethyl)phenyl]propanoic acid C₁₀ H₉ F₃ O₂ OEIUMLSCWINLBB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254 (Depositor), 0.257 (DCC)
R-Value Work: 0.196 (Depositor), 0.201 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.698	α = 90
b = 86.952	β = 109.276
c = 86.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-31
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.