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3gii

Dpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation

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

DNA polymerase IV

Sulfolobus solfataricus P2

UniProt Q97W02

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*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' × 1 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 3 SODIUM ION × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2rdi

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jx4 1jxl 1n48 1n56 1n56 1ryr 1rys 1rys 1s0m 1s0m 1s0n 1s0o

182 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPO42_SULSO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–341； UniProt 2–341

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_id3gii
Deposition date deposition_date2009-03-05
Structure title titleDpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation
Keywords keywords;DNA POLYMERASE, 8-OXOGUANINE, Y-FAMILY, LESION BYPASS, DNA damage, DNA repair, DNA replication, DNA-binding, DNA-directed DNA polymerase, Magnesium, Metal-binding, Mutator protein, Nucleotidyltransferase, Transferase, TRANSFERASE-DNA COMPLEX ;; TRANSFERASE/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.

3gii__assembly_1__model_1

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

Download this curve (.dat)

3gii__assembly_1__model_1 | I(q)

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

3gii__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）23.74 Å
Rg (electron density)23.03 Å
Total Rg23.81 Å
Atom count3403
Residues371
Excluded volume59433 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3gii__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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3giiA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id3giiA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3giiA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id3giiA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
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7. Citations (1)