SAXSdb — 3ko2

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Site-specific DNA endonuclease I-MsoI

Monomastix sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(GPCPAPGPAPCPCPGPTPCPGPTPGPAPGPAPCPAPGPTPTPCPCPG)-3' × 1 5'-D(CPGPGPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGPGPTPCPTPGPC)-3' × 1 CALCIUM ION × 3 water × 2	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(GPCPAPGPAPCPCPGPTPCPGPTPGPAPGPAPCPAPGPTPTPCPCPG)-3' × 1 5'-D(CPGPGPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGPGPTPCPTPGPC)-3' × 1 CALCIUM ION × 3 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

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 Author chain B； PDBConstruct 1–170； UniProt 1–170 Author chain F； PDBConstruct 1–170； UniProt 1–170 Author chain G； 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_id	3ko2
Deposition date deposition_date	2009-11-13
Structure title title	I-MsoI re-designed for altered DNA cleavage specificity (-7C)
Keywords keywords	redesign, protein-DNA complex, Chloroplast, Endonuclease, HYDROLASE-DNA complex; HYDROLASE/DNA
Experimental Method method	X-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.

3ko2__assembly_2__model_1

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

Download this curve (.dat)

3ko2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ko2__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.30 Å
Rg (electron density)	25.01 Å
Total Rg	25.66 Å
Atom count	3613
Residues	370
Excluded volume	61802 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ko2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ko2__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 (5)

Entity 1 Entity 1 polymer

Description description	Site-specific DNA endonuclease I-MsoI
Molecular weight formula_weight	19601.5 kDa
Mutation mutation	L28R, S43E, N70T, I85Y
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,F,G
Atom count atom_count	7232

MTTKNTLQPTEAAYIAGFLDGDGSIYARLIPRPDYKDIKYQVELAISFIQRKDKFPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKIESSP

Source Source

Source organism organism	Monomastix sp.
NCBI taxonomy ID ncbi_taxonomy_id	141716
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(GPCPAPGPAPCPCPGPTPCPGPTPGPAPGPAPCPAPGPTPTPCPCPG)-3'
Molecular weight formula_weight	7395.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,H

GCAGACCGTCGTGAGACAGTTCCG

Entity 3 Entity 3 polymer

Description description	5'-D(CPGPGPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGPGPTPCPTPGPC)-3'
Molecular weight formula_weight	7346.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,I

CGGAACTGTCTCACGACGGTCTGC

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ko2A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	3ko2B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	3ko2F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	3ko2G00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

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Unit-cell length a length_a	49.031 Å
Unit-cell length b length_b	70.006 Å
Unit-cell length c length_c	72.258 Å
Unit-cell angle α angle_alpha	81.66 °
Unit-cell angle β angle_beta	70.00 °
Unit-cell angle γ angle_gamma	89.48 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	33.560 Å
R factor r_factor	0.2520
R_work r_work	0.2480
R_free r_free	0.2860

I-MsoI re-designed for altered DNA cleavage specificity (-7C)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Site-specific DNA endonuclease I-MsoI

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ko2__assembly_2__model_1

3ko2__assembly_2__model_1 | I(q)

3ko2__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

I-MsoI re-designed for altered DNA cleavage specificity (-7C)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Site-specific DNA endonuclease I-MsoI

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ko2__assembly_2__model_1

3ko2__assembly_2__model_1 | I(q)

3ko2__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)