9O2O | pdb_00009o2o

cis-CaaD E114Q mutant with a covalent hydroxypropionate intermediate of the hydration of acetylenecarboxylic acid

PDB DOI: https://doi.org/10.2210/pdb9O2O/pdb
Entry: 9O2O supersedes: 9NGN

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

Deposited: 2025-04-04 Released: 2025-04-16
Deposition Author(s): Silva, K., Geiger, J.H., Draths, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.214 (Depositor), 0.216 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

cis-CaaD E114Q mutant with a covalent hydroxypropionate intermediate of the hydration of acetylenecarboxylic acid

Silva, K., Geiger, J.H., Draths, K.

To be published.

Macromolecule Content

Total Structure Weight: 55.98 kDa
Atom Count: 3,677
Modeled Residue Count: 436
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	A, B, C	164	coryneform bacterium	Mutation(s): 1 Gene Names: cis-caaD
UniProt
Find proteins for Q6VPE5 (coryneform bacterium) Explore Q6VPE5 Go to UniProtKB: Q6VPE5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VPE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3OH (Subject of Investigation/LOI) Query on 3OH Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	D [auth A], E [auth B], F [auth C]	3-HYDROXY-PROPANOIC ACID C₃ H₆ O₃ ALRHLSYJTWAHJZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.238 (Depositor), 0.237 (DCC)
R-Value Work: 0.214 (Depositor), 0.216 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.374	α = 90
b = 100.42	β = 90
c = 147.177	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

This entry supersedes: 9NGN

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-16
Type: Initial release

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.