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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6VPE5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6VPE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth C] SDF format, chain D [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth C] MOL2 format, chain D [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth C] mmCIF format, chain D [auth B]	D [auth B], E [auth C], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Focus chain E [auth C] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth C] Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
N80 Query on 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

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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
Version 1.1: 2025-05-14
Changes: Structure summary

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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.