← Back to search
2f8d

BenM effector-Binding domain crystallized from high pH conditions

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

HTH-type transcriptional regulator benM

Acinetobacter baylyi

UniProt O68014

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 BENZOIC ACID × 3 GLYCEROL × 6 PHOSPHATE ION × 1 water × 2 Consistent with protein count

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 1–224； UniProt 81–304 Author chain B； PDBConstruct 1–224； UniProt 81–304

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2f8d
Deposition date deposition_date2005-12-02
Structure title titleBenM effector-Binding domain crystallized from high pH conditions
Keywords keywordsBenM, LTTR, LysR-type transcriptional regulator, tetramerization, Effector binding domain, Inducer binding domain, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION
▼

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.

2f8d__assembly_1__model_1

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

Download this curve (.dat)

2f8d__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.

2f8d__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）24.69 Å
Rg (electron density)23.32 Å
Total Rg24.24 Å
Atom count3571
Residues439
Excluded volume64193 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2f8d__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2f8dA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id2f8dA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id2f8dB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id2f8dB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
▶

7. Citations (2)