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2opf

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate

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

Endonuclease VIII

Escherichia coli

UniProt P50465

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*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*G)-3' × 1 5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' × 1 GLYCEROL × 5 ZINC ION × 1 SULFATE ION × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1q39 1q3b 1q3c

3 assemblies

Homodimer

None

Homotetramer
1q39 1q3c

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1k3w 1k3x 2ea0 2opf 2oq4 2oq4 6fbu

7 assemblies

View Construct and Data Evidence
UniProt name END8_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–262； UniProt 2–263

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_id2opf
Deposition date deposition_date2007-01-29
Structure title titleCrystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate
Keywords keywordsEndonuclease VIII, oxidative damage, DNA repair, base excision, covalent intermediate, reaction mechanism, 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.

2opf__assembly_1__model_1

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

Download this curve (.dat)

2opf__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.

2opf__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）21.03 Å
Rg (electron density)20.19 Å
Total Rg21.03 Å
Atom count2536
Residues278
Excluded volume43694 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2opf__assembly_1__model_1 trimeric （3） 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 (7)

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2opfa1
Class classa — All alpha proteins
Fold Fold folda.156 — S13-like H2TH domain
Superfamily Superfamily superfamilya.156.1 — S13-like H2TH domain
Family Family familya.156.1.2 — Middle domain of MutM-like DNA repair proteins
Domain ID domain_idd2opfa2
Class classb — All beta proteins
Fold Fold foldb.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamilyb.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family familyb.113.1.1 — N-terminal domain of MutM-like DNA repair proteins
Domain ID domain_idd2opfa3
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

CATH v4.4 (2 domains)

Domain ID domain_id2opfA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily10 — MutM-like, N-terminal
Domain ID domain_id2opfA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily50 —
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7. Citations (1)