3mi5

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Method: X-RAY DIFFRACTION

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

Protocatechuate 3,4-dioxygenase alpha chain

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 beta chain × 12 （P00437） SULFATE ION × 24 BETA-MERCAPTOETHANOL × 50 GLYCEROL × 84 CATECHOL × 24 FE (III) ION × 12 CHLORIDE ION × 10 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 2–201 Author chain B； PDBConstruct 1–200； UniProt 2–201 Author chain C； PDBConstruct 1–200； UniProt 2–201 Author chain D； PDBConstruct 1–200； UniProt 2–201 Author chain E； PDBConstruct 1–200； UniProt 2–201 Author chain F； PDBConstruct 1–200； UniProt 2–201

Protocatechuate 3,4-dioxygenase beta chain

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 alpha chain × 12 （P00436） SULFATE ION × 24 BETA-MERCAPTOETHANOL × 50 GLYCEROL × 84 CATECHOL × 24 FE (III) ION × 12 CHLORIDE ION × 10 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 2–239 Author chain N； PDBConstruct 1–238； UniProt 2–239 Author chain O； PDBConstruct 1–238； UniProt 2–239 Author chain P； PDBConstruct 1–238； UniProt 2–239 Author chain Q； PDBConstruct 1–238； UniProt 2–239 Author chain R； PDBConstruct 1–238； UniProt 2–239

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	3mi5
Deposition date deposition_date	2010-04-09
Structure title title	Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase
Keywords keywords	dioxygenase, non-heme, iron, intradiol, catechol, substrate analogue, protocatechuate, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3mi5__assembly_1__model_1

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

Download this curve (.dat)

3mi5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mi5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.19 Å
Rg (electron density)	53.04 Å
Total Rg	53.31 Å
Atom count	42534
Residues	5256
Excluded volume	750480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mi5__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 (9)

Entity 1 Entity 1 polymer

Description description	Protocatechuate 3,4-dioxygenase alpha chain
Molecular weight formula_weight	22278.8 kDa
EC 编号 ec_number	1.13.11.3
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	24211

PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protocatechuate 3,4-dioxygenase beta chain
Molecular weight formula_weight	26696.3 kDa
EC 编号 ec_number	1.13.11.3
Mutation mutation	Y148H/H163Y
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

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPHPWRNGPNDWRPAHIYFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	42

Entity 6 Entity 6 non-polymer

Description description	CATECHOL
Molecular weight formula_weight	110.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 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 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2300

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3mi5a_
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	d3mi5b_
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	d3mi5c_
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	d3mi5d_
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	d3mi5e_
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	d3mi5f_
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	d3mi5m_
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	d3mi5n_
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	d3mi5o_
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	d3mi5p_
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	d3mi5q_
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	d3mi5r_
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	3mi5A00
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	3mi5B00
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	3mi5C00
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	3mi5D00
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	3mi5E00
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	3mi5F00
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	3mi5M00
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	3mi5N00
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	3mi5O00
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	3mi5P00
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	3mi5Q00
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	3mi5R00
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	190.543 Å
Unit-cell length b length_b	167.995 Å
Unit-cell length c length_c	128.342 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	132.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	30.620 Å
R factor r_factor	0.1530
R_work r_work	0.1510
R_free r_free	0.1850

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

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

Protocatechuate 3,4-dioxygenase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Protocatechuate 3,4-dioxygenase beta chain

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

3mi5__assembly_1__model_1

3mi5__assembly_1__model_1 | I(q)

3mi5__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

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

Protocatechuate 3,4-dioxygenase alpha chain

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 beta chain

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

3mi5__assembly_1__model_1

3mi5__assembly_1__model_1 | I(q)

3mi5__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 (9)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)