9NF3 | pdb_00009nf3

cis-CaaD E114D mutant with a covalent ethylene intermediate of the hydration and decarboxylation of cis-3-chloroacrylic acid

• PDB DOI: https://doi.org/10.2210/pdb9NF3/pdb

• Classification: HYDROLASE
• Organism(s): coryneform bacterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-20 Released: 2025-04-02 
• Deposition Author(s): Silva, K., Geiger, J.H., Draths, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

cis-CaaD E114D mutant with a covalent ethylene intermediate of the hydration and decarboxylation of acetylenecarboxylic acid

Silva, K., Geiger, J.H., Draths, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.97 kDa 
• Atom Count: 3,864 
• Modeled Residue Count: 436 
• Deposited Residue Count: 492 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	A [auth B], C [auth A]	164	coryneform bacterium	Mutation(s): 1  Gene Names: cis-caaD
UniProt
Find proteins for Q6VPE5 (coryneform bacterium) Explore Q6VPE5  Go to UniProtKB:  Q6VPE5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	B [auth C]	164	coryneform bacterium	Mutation(s): 1  Gene Names: cis-caaD
UniProt
Find proteins for Q6VPE5 (coryneform bacterium) Explore Q6VPE5  Go to UniProtKB:  Q6VPE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], E [auth C], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
N80	B [auth C]	L-PEPTIDE LINKING	C7 H11 N O2		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.534	α = 90
b = 99.939	β = 90
c = 142.794	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Silva, K., Geiger, J.H., Draths, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-05-14
  Changes: Structure summary