4whr

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

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 × 8 （P00437） Protocatechuate 3,4-dioxygenase beta chain × 4 （P00437） 4-fluorobenzene-1,2-diol × 56 BETA-MERCAPTOETHANOL × 16 FE (III) ION × 12 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 4-fluorooxepine-2,7-dione × 4 CHLORIDE ION × 4 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 C； PDBConstruct 1–200； UniProt 2–201 Author chain E； 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） 4-fluorobenzene-1,2-diol × 56 BETA-MERCAPTOETHANOL × 16 FE (III) ION × 12 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 4-fluorooxepine-2,7-dione × 4 CHLORIDE ION × 4 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, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 2–239 Author chain D； PDBConstruct 1–238； UniProt 2–239 Author chain F； 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	4whr
Deposition date deposition_date	2014-09-23
Structure title title	Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5
Keywords keywords	dioxygen activation, non-heme iron, intradiol dioxygenase, aromatic ring cleavage, catalytic intermediates, 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.

4whr__assembly_1__model_1

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

Download this curve (.dat)

4whr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4whr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.98 Å
Rg (electron density)	52.89 Å
Total Rg	53.11 Å
Atom count	42076
Residues	5228
Excluded volume	741190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4whr__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 (10)

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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,C
Atom count atom_count	11542

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	26712.3 kDa
EC 编号 ec_number	1.13.11.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC

Source Source

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

Entity 3 Entity 3 polymer

Description description	Protocatechuate 3,4-dioxygenase beta chain
Molecular weight formula_weight	26728.3 kDa
EC 编号 ec_number	1.13.11.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

Source Source

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

Entity 4 Entity 4 non-polymer

Description description	4-fluorobenzene-1,2-diol
Molecular weight formula_weight	128.1 kDa
Source method src_method	syn
Copy count entity_count	14

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	4

Entity 6 Entity 6 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	4-fluorooxepine-2,7-dione
Molecular weight formula_weight	142.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	947

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4whra_
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	d4whrb_
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	d4whrc_
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	d4whrd_
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	d4whre_
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	d4whrf_
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 (6 domains)

Domain ID domain_id	4whrA00
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	4whrB00
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	4whrC00
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	4whrD00
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	4whrE00
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	4whrF00
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	128.437 Å
Unit-cell length b length_b	140.644 Å
Unit-cell length c length_c	168.291 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	31.470 Å
R factor r_factor	0.1506
R_work r_work	0.1484
R_free r_free	0.1918

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

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

4whr__assembly_1__model_1

4whr__assembly_1__model_1 | I(q)

4whr__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

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

4whr__assembly_1__model_1

4whr__assembly_1__model_1 | I(q)

4whr__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)