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3knt

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine

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

N-glycosylase/DNA lyase

Methanocaldococcus jannaschii

UniProt Q58134

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 4 DNA 8 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 4 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 4 SODIUM ION × 4 water × 11 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 1 SODIUM ION × 1 water × 3 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 1 SODIUM ION × 1 water × 2 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 1 SODIUM ION × 1 water × 3 Consistent with all polymers
5 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' × 1 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' × 1 SODIUM ION × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3fhf

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3knt 3knt 3knt 3knt 3knt

5 assemblies

View Construct and Data Evidence
UniProt name OGG1_METJA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–207； UniProt 1–207 Author chain B； PDBConstruct 1–207； UniProt 1–207 Author chain C； PDBConstruct 1–207； UniProt 1–207 Author chain D； PDBConstruct 1–207； UniProt 1–207

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_id3knt
Deposition date deposition_date2009-11-12
Structure title titleCrystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine
Keywords keywords;protein-DNA complex, OGG, HELIX-HAIRPIN-HELIX, GLYCOSYLASE, 8-OXOGUANINE, 8-OXOG, DNA repair, DNA damage, Glycosidase, Multifunctional enzyme, Nuclease, HYDROLASE, LYASE-DNA complex ;; HYDROLASE, LYASE/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.

3knt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3knt__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3knt__assembly_2__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）20.51 Å
Rg (electron density)19.22 Å
Total Rg20.19 Å
Atom count2364
Residues236
Excluded volume40474 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3knt__assembly_1__model_1 dodecameric （12） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3knt__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3knt__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3knt__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3knt__assembly_5__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 (5)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3kntA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3kntA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3kntB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3kntB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3kntC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3kntC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3kntD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3kntD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
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7. Citations (1)