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2qnc

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction

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

Recombination endonuclease VII

Enterobacteria phage T4

UniProt P13340

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 4 ;DNA (5'-D(*DCP*DG*DAP*DAP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DCP*DC)-3') ; × 1 ;DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DCP*DT)-3') ; × 1 ;DNA (5'-D(*DAP*DGP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DTP*DTP*DCP*DG)-3') ; × 1 MAGNESIUM ION × 2 ZINC ION × 2 1,2-ETHANEDIOL × 2 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1e7d 1e7l 1en7

3 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qnc 2qnf

2 assemblies

View Construct and Data Evidence
UniProt name END7_BPT4
Isoform —
PDB entities 5
Chains and sequence ranges Author chain A； PDBConstruct 1–157； UniProt 1–157 Author chain B； PDBConstruct 1–157； UniProt 1–157

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_id2qnc
Deposition date deposition_date2007-07-18
Structure title titleCrystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction
Keywords keywords;T4 Endonuclease VII, Endo VII, Holliday junction, four-way junction, resolvase, resolving-enzyme, Alternative initiation, Calcium, Hydrolase, Metal-binding, Zinc, 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.

2qnc__assembly_1__model_1

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

Download this curve (.dat)

2qnc__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2qnc__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）29.44 Å
Rg (electron density)28.86 Å
Total Rg29.40 Å
Atom count4449
Residues407
Excluded volume72989 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qnc__assembly_1__model_1 hexameric （6） 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 (9)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2qnca1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.4 — Recombination endonuclease VII, C-terminal and dimerization domains
Family Family familya.140.4.1 — Recombination endonuclease VII, C-terminal and dimerization domains
Domain ID domain_idd2qnca2
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.4.1.5 — Recombination endonuclease VII, N-terminal domain
Domain ID domain_idd2qncb1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.4 — Recombination endonuclease VII, C-terminal and dimerization domains
Family Family familya.140.4.1 — Recombination endonuclease VII, C-terminal and dimerization domains
Domain ID domain_idd2qncb2
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.4.1.5 — Recombination endonuclease VII, N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id2qncA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1800 — His-Me finger endonuclease fold
Homologous superfamily homologous superfamily10 — His-Me finger endonucleases
Domain ID domain_id2qncA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2qncB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1800 — His-Me finger endonuclease fold
Homologous superfamily homologous superfamily10 — His-Me finger endonucleases
Domain ID domain_id2qncB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily10 —
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7. Citations (1)