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1oup

Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA

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

Nuclease

Vibrio vulnificus

UniProt Q8DCA6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' × 2 CALCIUM ION × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 3 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3' × 1 5'-D(*GP*CP*GP*AP*TP*C)-3' × 1 5'-D(P*GP*C)-3' × 1 CALCIUM ION × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1ouo

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1oup 1oup

2 assemblies

View Construct and Data Evidence
UniProt name Q8DCA6_VIBVU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–213； UniProt 19–231 Author chain B； PDBConstruct 1–213； UniProt 19–231

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_id1oup
Deposition date deposition_date2003-03-25
Structure title titleCrystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA
Keywords keywordsNon-specific endonuclease, beta-beta-alpha metal motif, HYDROLASE-DNA COMPLEX; HYDROLASE/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.

1oup__assembly_1__model_1

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

Download this curve (.dat)

1oup__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.

1oup__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）18.76 Å
Rg (electron density)17.53 Å
Total Rg18.48 Å
Atom count2035
Residues226
Excluded volume34566 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1oup__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1oup__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 (6)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1oupa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.4 — His-Me finger endonucleases
Superfamily Superfamily superfamilyd.4.1 — His-Me finger endonucleases
Family Family familyd.4.1.6 — Endonuclease I
Domain ID domain_idd1oupb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.4 — His-Me finger endonucleases
Superfamily Superfamily superfamilyd.4.1 — His-Me finger endonucleases
Family Family familyd.4.1.6 — Endonuclease I
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7. Citations (1)