3ej3

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-subunit of trans-3-chloroacrylic acid dehalogenase

Pseudomonas pavonaceae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Beta-subunit of trans-3-chloroacrylic acid dehalogenase × 3 （Q9EV84） ACETATE ION × 3 PHOSPHATE ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Beta-subunit of trans-3-chloroacrylic acid dehalogenase × 3 （Q9EV84） ACETATE ION × 3 PHOSPHATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9EV85_PSEPV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76 Author chain I； PDBConstruct 1–76； UniProt 1–76 Author chain K； PDBConstruct 1–76； UniProt 1–76

Beta-subunit of trans-3-chloroacrylic acid dehalogenase

Pseudomonas pavonaceae

UniProt Q9EV84

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Alpha-subunit of trans-3-chloroacrylic acid dehalogenase × 3 （Q9EV85） ACETATE ION × 3 PHOSPHATE ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Alpha-subunit of trans-3-chloroacrylic acid dehalogenase × 3 （Q9EV85） ACETATE ION × 3 PHOSPHATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9EV84_PSEPV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–70； UniProt 2–71 Author chain D； PDBConstruct 1–70； UniProt 2–71 Author chain F； PDBConstruct 1–70； UniProt 2–71 Author chain H； PDBConstruct 1–70； UniProt 2–71 Author chain J； PDBConstruct 1–70； UniProt 2–71 Author chain L； PDBConstruct 1–70； UniProt 2–71

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ej3
Deposition date deposition_date	2008-09-17
Structure title title	Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity
Keywords keywords	trans-3-chloroacrylic acid dehalogenase, CaaD, dehalogenase, Isomerase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ej3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ej3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ej3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.17 Å
Rg (electron density)	18.98 Å
Total Rg	19.84 Å
Atom count	2840
Residues	364
Excluded volume	50313 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ej3__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ej3__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
Molecular weight formula_weight	8486.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	6413

MPMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVPGNANDKALIAKLK

Source Source

Source organism organism	Pseudomonas pavonaceae
NCBI taxonomy ID ncbi_taxonomy_id	47881
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-subunit of trans-3-chloroacrylic acid dehalogenase
Molecular weight formula_weight	7516.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGEAASTERTPAVS

Source Source

Source organism organism	Pseudomonas pavonaceae
NCBI taxonomy ID ncbi_taxonomy_id	47881
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	560

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3ej3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3i_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3j_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3k_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d3ej3l_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

CATH v4.4 (12 domains)

Domain ID domain_id	3ej3A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3G00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3H00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3I00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3J00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3K00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	3ej3L00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Unit-cell length a length_a	50.696 Å
Unit-cell length b length_b	97.314 Å
Unit-cell length c length_c	69.022 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	68.680 Å
R factor r_factor	0.1812
R_work r_work	0.1792
R_free r_free	0.2182

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-subunit of trans-3-chloroacrylic acid dehalogenase

State in the Current Structure

Other States of the Same Protein in the Database

Beta-subunit of trans-3-chloroacrylic acid dehalogenase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ej3__assembly_1__model_1

3ej3__assembly_1__model_1 | I(q)

3ej3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-subunit of trans-3-chloroacrylic acid dehalogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-subunit of trans-3-chloroacrylic acid dehalogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ej3__assembly_1__model_1

3ej3__assembly_1__model_1 | I(q)

3ej3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)