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4u0y

Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

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

HTH-type transcriptional repressor YvoA

Bacillus subtilis subsp. subtilis str. 168

UniProt O34817

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 4 DNA 2 ;DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3') ; × 2 CHLORIDE ION × 2 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2wv0 2wv0 2wv0 2wv0 2wv0 2wv0 4u0v 4u0w

8 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4u0y 4wwc

2 assemblies

View Construct and Data Evidence
UniProt name YVOA_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–78； UniProt 1–75 Author chain B； PDBConstruct 4–78； UniProt 1–75 Author chain C； PDBConstruct 4–78； UniProt 1–75 Author chain D； PDBConstruct 4–78； UniProt 1–75

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_id4u0y
Deposition date deposition_date2014-07-14
Structure title titleCrystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA
Keywords keywords;Transcription, Repressor, Bacterial transcription regulation, Transcription factor, GntR/HutC family, Winged helix-turn-helix motif, N-acetylglucosamine utilization, DNA-binding, Operator-binding ;; 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.

4u0y__assembly_1__model_1

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

Download this curve (.dat)

4u0y__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.

4u0y__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）23.11 Å
Rg (electron density)23.25 Å
Total Rg23.86 Å
Atom count3036
Residues329
Excluded volume52406 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4u0y__assembly_1__model_1 Hexameric （6） 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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4u0yA00
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_id4u0yB00
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_id4u0yC00
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_id4u0yD00
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)