3pcd

PROTOCATECHUATE 3,4-DIOXYGENASE Y447H MUTANT

Method: X-RAY DIFFRACTION

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

PROTOCATECHUATE 3,4-DIOXYGENASE

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	PROTOCATECHUATE 3,4-DIOXYGENASE × 12 （P00437） CARBONATE ION × 12 FE (III) ION × 12 BETA-MERCAPTOETHANOL × 12 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCXA_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 1–200 Author chain B； PDBConstruct 1–200； UniProt 1–200 Author chain C； PDBConstruct 1–200； UniProt 1–200 Author chain D； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain F； PDBConstruct 1–200； UniProt 1–200

PROTOCATECHUATE 3,4-DIOXYGENASE

Pseudomonas putida

UniProt P00437

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	PROTOCATECHUATE 3,4-DIOXYGENASE × 12 （P00436） CARBONATE ION × 12 FE (III) ION × 12 BETA-MERCAPTOETHANOL × 12 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCXB_PSEPU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–238； UniProt 1–238 Author chain N； PDBConstruct 1–238； UniProt 1–238 Author chain O； PDBConstruct 1–238； UniProt 1–238 Author chain P； PDBConstruct 1–238； UniProt 1–238 Author chain Q； PDBConstruct 1–238； UniProt 1–238 Author chain R； PDBConstruct 1–238； UniProt 1–238

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	3pcd
Deposition date deposition_date	1997-11-24
Structure title title	PROTOCATECHUATE 3,4-DIOXYGENASE Y447H MUTANT
Keywords keywords	DIOXYGENASE, OXIDOREDUCTASE, IRON, NONHEME, METALLOPROTEIN, MUTANT; DIOXYGENASE
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.

3pcd__assembly_1__model_1

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

Download this curve (.dat)

3pcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.29 Å
Rg (electron density)	53.21 Å
Total Rg	53.42 Å
Atom count	41016
Residues	5196
Excluded volume	722170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pcd__assembly_1__model_1`	24-meric （24）	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 (6)

Entity 1 Entity 1 polymer

Description description	PROTOCATECHUATE 3,4-DIOXYGENASE
Molecular weight formula_weight	22278.8 kDa
EC 编号 ec_number	1.13.11.3
Mutation mutation	Y447H
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21930

PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Pseudomonas fluorescens

Entity 2 Entity 2 polymer

Description description	PROTOCATECHUATE 3,4-DIOXYGENASE
Molecular weight formula_weight	26671.3 kDa
EC 编号 ec_number	1.13.11.3
Mutation mutation	Y447H
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPHPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Pseudomonas fluorescens

Entity 3 Entity 3 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1422

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3pcda_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdb_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdc_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdd_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcde_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdf_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdm_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdn_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdo_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdp_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdq_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

Domain ID domain_id	d3pcdr_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.6 — Aromatic compound dioxygenase
Family Family family	b.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (12 domains)

Domain ID domain_id	3pcdA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdM00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdP00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdQ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

Domain ID domain_id	3pcdR00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily	10 — Aromatic compound dioxygenase

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Unit-cell length a length_a	197.400 Å
Unit-cell length b length_b	127.200 Å
Unit-cell length c length_c	134.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1800
R_free r_free	—

PROTOCATECHUATE 3,4-DIOXYGENASE Y447H MUTANT

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

PROTOCATECHUATE 3,4-DIOXYGENASE

State in the Current Structure

Other States of the Same Protein in the Database

PROTOCATECHUATE 3,4-DIOXYGENASE

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

3pcd__assembly_1__model_1

3pcd__assembly_1__model_1 | I(q)

3pcd__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (6)

PROTOCATECHUATE 3,4-DIOXYGENASE Y447H MUTANT

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

PROTOCATECHUATE 3,4-DIOXYGENASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTOCATECHUATE 3,4-DIOXYGENASE

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

3pcd__assembly_1__model_1

3pcd__assembly_1__model_1 | I(q)

3pcd__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (6)