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1wv4

X-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal form

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

;Pyridoxamine 5'-phosphate oxidase ;

Escherichia coli

UniProt P28225

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 PHOSPHATE ION × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1dnl 1g76 1g77 1g78 1g79 1jnw 1wv4

7 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name PDXH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–218； UniProt 0–217 Author chain B； PDBConstruct 1–218； UniProt 0–217

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_id1wv4
Deposition date deposition_date2004-12-11
Structure title titleX-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal form
Keywords keywords;PLP, FMN, pyridoxal, pyridoxine 5'-phosphate, oxidase, 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.

1wv4__assembly_1__model_1

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

Download this curve (.dat)

1wv4__assembly_1__model_1 | I(q)

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

1wv4__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）20.92 Å
Rg (electron density)19.60 Å
Total Rg20.61 Å
Atom count2701
Residues316
Excluded volume47629 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1wv4__assembly_1__model_1 dimeric （2） 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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1wv4a_
Class classb — All beta proteins
Fold Fold foldb.45 — Split barrel-like
Superfamily Superfamily superfamilyb.45.1 — FMN-binding split barrel
Family Family familyb.45.1.1 — PNP-oxidase like
Domain ID domain_idd1wv4b_
Class classb — All beta proteins
Fold Fold foldb.45 — Split barrel-like
Superfamily Superfamily superfamilyb.45.1 — FMN-binding split barrel
Family Family familyb.45.1.1 — PNP-oxidase like

CATH v4.4 (2 domains)

Domain ID domain_id1wv4A00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily10 — Electron Transport, Fmn-binding Protein; Chain A
Domain ID domain_id1wv4B00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily10 — Electron Transport, Fmn-binding Protein; Chain A
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7. Citations (1)