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5yhi

Crystal structure of YiiM from Escherichia coli

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

Protein YiiM

Escherichia coli (strain K12)

UniProt P32157

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 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1o65 1o65 1o65 1o67 1o67 1o67

6 assemblies

Homodimer
5yhi

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name YIIM_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–230； UniProt 1–224 Author chain B； PDBConstruct 7–230； UniProt 1–224

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_id5yhi
Deposition date deposition_date2017-09-28
Structure title titleCrystal structure of YiiM from Escherichia coli
Keywords keywordsenzyme, MOSC, 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.

5yhi__assembly_1__model_1

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

Download this curve (.dat)

5yhi__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.

5yhi__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）23.74 Å
Rg (electron density)23.14 Å
Total Rg23.76 Å
Atom count3203
Residues403
Excluded volume56569 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5yhi__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5yhia1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.2 — MOSC (MOCO sulphurase C-terminal) domain
Domain ID domain_idd5yhia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5yhib1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.2 — MOSC (MOCO sulphurase C-terminal) domain
Domain ID domain_idd5yhib2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id5yhiA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily20 — PK beta-barrel domain-like
Domain ID domain_id5yhiB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily20 — PK beta-barrel domain-like
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7. Citations (1)