9YTU | pdb_00009ytu

cis-CaaD E114D mutant with a covalent intermediates of the hydration of acetylenecarboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb9YTU/pdb
• Entry: 9YTU supersedes: 9NER

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


• Deposited: 2025-10-21 Released: 2025-11-05 
• 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: 2.51 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

cis-CaaD E114D mutant with a covalent intermediates of the hydration 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: 55.91 kDa 
• Atom Count: 3,535 
• Modeled Residue Count: 435 
• Deposited Residue Count: 492 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	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	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	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
A1BXY (Subject of Investigation/LOI)	D [auth A], E [auth C]	prop-2-ynoic acid C3 H2 O2 UORVCLMRJXCDCP-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
N80	A	L-PEPTIDE LINKING	C7 H11 N O2		PRO
ZI0	B	L-PEPTIDE LINKING	C8 H11 N O5		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.256	α = 90
b = 98.828	β = 90
c = 142.409	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: 2025-11-05 
Deposition Author(s): Silva, K., Geiger, J.H., Draths, K.
• This entry supersedes: 9NER

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release