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3sm4

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

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

Exonuclease

Enterobacteria phage lambda

UniProt P03697

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 3 DNA 2 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3' × 1 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3' × 1 PHOSPHATE ION × 2 CHLORIDE ION × 2 MAGNESIUM ION × 2 water × 5 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
1avq

1 assemblies

Heteromeric or nucleic-acid complex
3slp 3sm4 4wuz 6m9k

4 assemblies

View Construct and Data Evidence
UniProt name EXO_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–229； UniProt 1–226 Author chain B； PDBConstruct 4–229； UniProt 1–226 Author chain C； PDBConstruct 4–229； UniProt 1–226

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_id3sm4
Deposition date deposition_date2011-06-27
Structure title titleCrystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium
Keywords keywords;homologous recombination, DNA repair, recombineering, single-strand annealing, Type II Restriction Endonuclease Fold, 5'-3' dsDNA exonuclease, 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.

3sm4__assembly_1__model_1

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

Download this curve (.dat)

3sm4__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.

3sm4__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）29.26 Å
Rg (electron density)28.81 Å
Total Rg29.49 Å
Atom count6023
Residues708
Excluded volume105060 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3sm4__assembly_1__model_1 pentameric （5） 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) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3sm4a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease
Domain ID domain_idd3sm4b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease
Domain ID domain_idd3sm4b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3sm4c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.13 — lambda exonuclease
Domain ID domain_idd3sm4c2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id3sm4A00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3sm4B00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3sm4C00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily10 —
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7. Citations (1)