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1xdy

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bacterial Sulfite Oxidase

Escherichia coli

UniProt P76342

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
10 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 TUNGSTEN ION × 1 PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1xdq 1xdq 1xdq 1xdq 1xdq 1xdy 1xdy 1xdy 1xdy 1xdy 1xdy 1xdy

15 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name YEDY_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–290； UniProt 45–334 Author chain B； PDBConstruct 1–290； UniProt 45–334 Author chain C； PDBConstruct 1–290； UniProt 45–334 Author chain D； PDBConstruct 1–290； UniProt 45–334 Author chain E； PDBConstruct 1–290； UniProt 45–334 Author chain F； PDBConstruct 1–290； UniProt 45–334 Author chain G； PDBConstruct 1–290； UniProt 45–334 Author chain H； PDBConstruct 1–290； UniProt 45–334 Author chain I； PDBConstruct 1–290； UniProt 45–334 Author chain J； PDBConstruct 1–290； UniProt 45–334

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_id1xdy
Deposition date deposition_date2004-09-08
Structure title titleStructural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor
Keywords keywordsBioinformatics, sequence analysis, electron transfer, oxidoreductase, molybdoenzymes, molybdopterin; 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.

1xdy__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1xdy__assembly_4__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1xdy__assembly_4__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）18.41 Å
Rg (electron density)17.26 Å
Total Rg18.20 Å
Atom count2119
Residues263
Excluded volume37814 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1xdy__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1xdy__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1xdy__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1xdy__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1xdy__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1xdy__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 1xdy__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 1xdy__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 1xdy__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 1xdy__assembly_10__model_1 monomeric （1） 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) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd1xdya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdye_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain
Domain ID domain_idd1xdyj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.176 — Oxidoreductase molybdopterin-binding domain
Superfamily Superfamily superfamilyd.176.1 — Oxidoreductase molybdopterin-binding domain
Family Family familyd.176.1.1 — Oxidoreductase molybdopterin-binding domain

CATH v4.4 (10 domains)

Domain ID domain_id1xdyA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyC00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyD00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyE00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyG00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyH00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyI00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
Domain ID domain_id1xdyJ00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology420 — Sulfite Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Oxidoreductase, molybdopterin-binding domain
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7. Citations (1)