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2p5l

Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site

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

Arginine repressor

Bacillus subtilis

UniProt P17893

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3') ; × 1 SULFATE ION × 1 water × 3 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3') ; × 1 SULFATE ION × 4 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2p5k

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1f9n 2p5m

2 assemblies

Heteromeric or nucleic-acid complex
2p5l 2p5l

2 assemblies

View Construct and Data Evidence
UniProt name ARGR_BACSU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–64； UniProt 1–64 Author chain D； PDBConstruct 1–64； UniProt 1–64 Author chain G； PDBConstruct 1–64； UniProt 1–64 Author chain H； PDBConstruct 1–64； UniProt 1–64

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_id2p5l
Deposition date deposition_date2007-03-15
Structure title titleCrystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site
Keywords keywordsDNA-binding domain, winged helix-turn-helix, ARG box, protein-DNA complex, transcription repressor; transcription repressor
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.

2p5l__assembly_1__model_1

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

Download this curve (.dat)

2p5l__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.

2p5l__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）19.06 Å
Rg (electron density)18.20 Å
Total Rg19.00 Å
Atom count1769
Residues163
Excluded volume29241 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2p5l__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2p5l__assembly_2__model_1 tetrameric （4） 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 (5)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2p5lc1
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.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain
Domain ID domain_idd2p5ld1
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.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain
Domain ID domain_idd2p5lg1
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.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain
Domain ID domain_idd2p5lh1
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.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id2p5lC00
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_id2p5lD00
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_id2p5lG00
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_id2p5lH00
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 (1)