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1omi

Crystal structure of PrfA,the transcriptional regulator in Listeria monocytogenes

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

Listeriolysin regulatory protein

Listeria monocytogenes

UniProt P22262

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 GLYCEROL × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 GLYCEROL × 1 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 GLYCEROL × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1omi 1omi

2 assemblies

Homodimer
1omi 2beo 2bgc 2bgc 2bgc 2bgc 5f1r 6eut 6ev0 6exk 6hck

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5lej 5lek 8cb4 8cb5 8cb7 8cb8 8cbg 8cbi 8cbp

9 assemblies

View Construct and Data Evidence
UniProt name PRFA_LISMO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 18–248； UniProt 7–237 Author chain B； PDBConstruct 18–248； UniProt 7–237

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_id1omi
Deposition date deposition_date2003-02-25
Structure title titleCrystal structure of PrfA,the transcriptional regulator in Listeria monocytogenes
Keywords keywords;Transcriptional regulator PrfA, CAP fold, LISTERIA MONOCYTOGENES, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, TRANSCRIPTION ;; TRANSCRIPTION
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.

1omi__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1omi__assembly_3__model_1 | I(q)

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

1omi__assembly_3__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）23.85 Å
Rg (electron density)22.54 Å
Total Rg23.57 Å
Atom count3700
Residues451
Excluded volume67083 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1omi__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1omi__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1omi__assembly_3__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) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1omia1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain
Domain ID domain_idd1omia2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.4 — CAP C-terminal domain-like
Domain ID domain_idd1omia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1omib1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.3 — Listeriolysin regulatory protein PrfA, N-terminal domain
Domain ID domain_idd1omib2
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.4 — CAP C-terminal domain-like
Domain ID domain_idd1omib3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id1omiA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id1omiA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily460 — Single helix bin
Domain ID domain_id1omiA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1omiB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id1omiB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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7. Citations (3)