2w2a

Crystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism

Method: X-RAY DIFFRACTION

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

P-COUMARIC ACID DECARBOXYLASE

LACTOBACILLUS PLANTARUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88RY7_LACPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–194； UniProt 1–178 Author chain B； PDBConstruct 17–194； UniProt 1–178

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	2w2a
Deposition date deposition_date	2008-10-27
Structure title title	Crystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism
Keywords keywords	LYASE, ACTIVE SITE, COUMARIC ACIDS, DECARBOXYLATION, CATALYTIC MECHANISM; LYASE
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.

2w2a__assembly_1__model_1

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

Download this curve (.dat)

2w2a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w2a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.59 Å
Rg (electron density)	21.33 Å
Total Rg	22.23 Å
Atom count	2918
Residues	350
Excluded volume	51441 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w2a__assembly_1__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2w2aa_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.6 — Phenolic acid decarboxylase (PAD)

Domain ID domain_id	d2w2ab_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.6 — Phenolic acid decarboxylase (PAD)

CATH v4.4 (2 domains)

Domain ID domain_id	2w2aA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	2w2aB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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Unit-cell length a length_a	43.181 Å
Unit-cell length b length_b	43.181 Å
Unit-cell length c length_c	232.498 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.380 Å
Low-resolution limit resolution_low	40.490 Å
R factor r_factor	0.1920
R_work r_work	0.1910
R_free r_free	0.2090

Description description	P-COUMARIC ACID DECARBOXYLASE
Molecular weight formula_weight	22843.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3484

Crystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism

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

P-COUMARIC ACID DECARBOXYLASE

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

2w2a__assembly_1__model_1

2w2a__assembly_1__model_1 | I(q)

2w2a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	LACTOBACILLUS PLANTARUM
NCBI taxonomy ID ncbi_taxonomy_id	1590
Host organism host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	566

Crystal Structure of p-coumaric Acid Decarboxylase from Lactobacillus plantarum: structural insights into the active site and decarboxylation catalytic mechanism

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

P-COUMARIC ACID DECARBOXYLASE

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

2w2a__assembly_1__model_1

2w2a__assembly_1__model_1 | I(q)

2w2a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)