9NER | pdb_00009ner

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

PDB DOI: https://doi.org/10.2210/pdb9NER/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 56.27 kDa
Atom Count: 3,534
Modeled Residue Count: 435
Deposited Residue Count: 495
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-3-chloroacrylic acid dehalogenase	A, B, C	165	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKR Query on AKR Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	ACRYLIC ACID C₃ H₄ O₂ NIXOWILDQLNWCW-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
A1BXY Query on A1BXY Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C]	D [auth A], F [auth C]	prop-2-ynoic acid C₃ H₂ O₂ UORVCLMRJXCDCP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.193 (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

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Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
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.