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4ihs

Crystal Structure of BenM_DBD/catB site 1 DNA Complex

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

HTH-type transcriptional regulator BenM

Acinetobacter sp.

UniProt O68014

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 catB site 1 DNA × 1 catB site 1 DNA - complement × 1 MALONATE ION × 1 water × 4 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 catB site 1 DNA × 1 catB site 1 DNA - complement × 1 MALONATE ION × 1 SODIUM ION × 1 water × 3 Consistent with all polymers
3 Protein–DNA Homooligomer Protein 4 DNA 4 catB site 1 DNA × 2 catB site 1 DNA - complement × 2 MALONATE ION × 2 SODIUM ION × 1 water × 7 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2f6g 2f6p 2f78 2f7a 2f8d 2f97 2h99 2h9b 3k1m 3k1m 3k1n 3k1n

14 assemblies; showing the first 12

Homotetramer
3k1m 3k1m 3k1n 3k1n 3k1p

5 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
4ihs 4ihs 4ihs 4iht 4iht

5 assemblies

View Construct and Data Evidence
UniProt name BENM_ACIAD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–87； UniProt 1–87 Author chain B； PDBConstruct 1–87； UniProt 1–87 Author chain C； PDBConstruct 1–87； UniProt 1–87 Author chain D； PDBConstruct 1–87； UniProt 1–87

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_id4ihs
Deposition date deposition_date2012-12-19
Structure title titleCrystal Structure of BenM_DBD/catB site 1 DNA Complex
Keywords keywordswHTH, HTH, Transcriptional regulator, catB promoter, Transcription-DNA complex; Transcription/DNA
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.

4ihs__assembly_3__model_1

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

Download this curve (.dat)

4ihs__assembly_3__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4ihs__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）29.14 Å
Rg (electron density)27.01 Å
Total Rg27.79 Å
Atom count9106
Residues461
Excluded volume82474 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ihs__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4ihs__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4ihs__assembly_3__model_1 octameric （8） 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 (6)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4ihsA00
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_id4ihsB00
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_id4ihsC00
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_id4ihsD00
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 (4)