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1ykm

Protocatechuate 3,4-Dioxygenase Y408E 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_id1ykm
Deposition date deposition_date2005-01-18
Structure title titleProtocatechuate 3,4-Dioxygenase Y408E mutant
Keywords keywordscatechol, protocatechuate, 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.

1ykm__assembly_1__model_1

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

Download this curve (.dat)

1ykm__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.

1ykm__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）54.37 Å
Rg (electron density)53.24 Å
Total Rg53.46 Å
Atom count41376
Residues5244
Excluded volume727960 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ykm__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_idd1ykma_
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_idd1ykmb1
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_idd1ykmc_
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_idd1ykmd_
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_idd1ykme_
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_idd1ykmf_
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_idd1ykmg_
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_idd1ykmh_
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_idd1ykmi_
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_idd1ykmj_
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_idd1ykmk_
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_idd1ykml_
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_id1ykmA00
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_id1ykmB00
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_id1ykmC00
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_id1ykmD00
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_id1ykmE00
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_id1ykmF00
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_id1ykmG00
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_id1ykmH00
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_id1ykmI00
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_id1ykmJ00
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_id1ykmK00
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_id1ykmL00
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)