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3fd2

Crystal structure of mMsoI/DNA complex with calcium

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

Site-specific DNA endonuclease I-MsoI

Monomastix sp. OKE-1, unidentified

UniProt C0JWR6

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*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' × 1 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3' × 1 CALCIUM ION × 2 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3fd2 3ko2 3ko2

3 assemblies

View Construct and Data Evidence
UniProt name C0JWR6_MONSK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–170； UniProt 1–170

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_id3fd2
Deposition date deposition_date2008-11-24
Structure title titleCrystal structure of mMsoI/DNA complex with calcium
Keywords keywordsProtein-DNA complex, Chloroplast, 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.

3fd2__assembly_1__model_1

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

Download this curve (.dat)

3fd2__assembly_1__model_1 | I(q)

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

3fd2__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）25.38 Å
Rg (electron density)25.13 Å
Total Rg25.75 Å
Atom count3700
Residues386
Excluded volume63288 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3fd2__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 (5)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3fd2a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.2 — Homing endonucleases
Family Family familyd.95.2.1 — Group I mobile intron endonuclease
Domain ID domain_idd3fd2a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.2 — Homing endonucleases
Family Family familyd.95.2.1 — Group I mobile intron endonuclease

CATH v4.4 (2 domains)

Domain ID domain_id3fd2A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
Domain ID domain_id3fd2A02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology28 — Endonuclease I-creI
Homologous superfamily homologous superfamily10 — Homing endonucleases
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7. Citations (1)