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1ykk

Protocatechuate 3,4-Dioxygenase Y408C Mutant

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

UniProt P00436

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） FE (III) ION × 12 water × 24 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ykk 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1

37 assemblies; showing the first 12

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 C； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain G； PDBConstruct 1–200； UniProt 1–200 Author chain I； PDBConstruct 1–200； UniProt 1–200 Author chain K； PDBConstruct 1–200； UniProt 1–200

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） FE (III) ION × 12 water × 24 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ykk 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1

37 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PCXB_PSEPU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–238； UniProt 1–238 Author chain D； PDBConstruct 1–238； UniProt 1–238 Author chain F； PDBConstruct 1–238； UniProt 1–238 Author chain H； PDBConstruct 1–238； UniProt 1–238 Author chain J； PDBConstruct 1–238； UniProt 1–238 Author chain L； 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_id1ykk
Deposition date deposition_date2005-01-18
Structure title titleProtocatechuate 3,4-Dioxygenase Y408C Mutant
Keywords keywords3, 4-PCD, catechol, protocatechuate, dioxygenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-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.

1ykk__assembly_1__model_1

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

Download this curve (.dat)

1ykk__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1ykk__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）54.00 Å
Rg (electron density)52.88 Å
Total Rg53.10 Å
Atom count41340
Residues5244
Excluded volume727520 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ykk__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 (4)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1ykka_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkb1
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkc_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkd_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykke_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkf_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkg_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkh_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykki_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkj_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkk_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykkl_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (12 domains)

Domain ID domain_id1ykkA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykkL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
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7. Citations (1)