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4k1g

Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair

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

Endonuclease 4

Escherichia coli

UniProt P0A6C1

State in the Current Structure

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

Other States of the Same Protein in the Database

Monomer
1qtw 2nqh 2nqj 8rly 8rly 8rly 8rly 8rly

8 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1qum 2nq9 2nqj 4k1g 4k1g

5 assemblies

View Construct and Data Evidence
UniProt name END4_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–285； UniProt 1–285 Author chain B； PDBConstruct 1–285； UniProt 1–285

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_id4k1g
Deposition date deposition_date2013-04-05
Structure title titleStructure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair
Keywords keywordsDNA endonuclease IV, 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.

4k1g__assembly_2__model_1

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

Download this curve (.dat)

4k1g__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.

4k1g__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）20.96 Å
Rg (electron density)19.72 Å
Total Rg20.59 Å
Atom count2749
Residues307
Excluded volume46726 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4k1g__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4k1g__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 (7)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4k1ga_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.15 — Xylose isomerase-like
Family Family familyc.1.15.1 — Endonuclease IV
Domain ID domain_idd4k1gb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.15 — Xylose isomerase-like
Family Family familyc.1.15.1 — Endonuclease IV

CATH v4.4 (2 domains)

Domain ID domain_id4k1gA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily150 — Divalent-metal-dependent TIM barrel enzymes
Domain ID domain_id4k1gB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily150 — Divalent-metal-dependent TIM barrel enzymes
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7. Citations (1)