SAXSdb — 5o6g

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

Homing endonuclease I-DmoI

Desulfurococcus mucosus

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	DNA (25-MER) × 1 DNA (25-MER) × 1 MANGANESE (II) ION × 2 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	DNA (25-MER) × 1 DNA (25-MER) × 1 MANGANESE (II) ION × 2 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	DNA (25-MER) × 1 DNA (25-MER) × 1 MANGANESE (II) ION × 2 CHLORIDE ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DMO1_DESMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–189； UniProt 2–188 Author chain D； PDBConstruct 3–189； UniProt 2–188 Author chain G； PDBConstruct 3–189； UniProt 2–188

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	5o6g
Deposition date deposition_date	2017-06-06
Structure title title	Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI
Keywords keywords	Desulfurococcus mobilis, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

5o6g__assembly_1__model_1

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

Download this curve (.dat)

5o6g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o6g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.82 Å
Rg (electron density)	21.29 Å
Total Rg	22.11 Å
Atom count	2567
Residues	238
Excluded volume	42757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o6g__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5o6g__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5o6g__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Homing endonuclease I-DmoI
Molecular weight formula_weight	23445.2 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	7676

MAHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHFAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMQERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPPEAAALEHHHHHH

Source Source

Source organism organism	Desulfurococcus mucosus
NCBI taxonomy ID ncbi_taxonomy_id	2275
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7707.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E,H

GCCTTGCCGGGTAAGTTCCGGCGCG

Entity 3 Entity 3 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7654.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F,I

CGCGCCGGAACTTACCCGGCAAGGC

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	man
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5o6gA01
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	5o6gA02
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	5o6gD01
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	5o6gD02
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	5o6gG01
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	5o6gG02
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	107.280 Å
Unit-cell length b length_b	70.500 Å
Unit-cell length c length_c	107.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	56.184 Å
R factor r_factor	0.1803
R_work r_work	0.1772
R_free r_free	0.2322

Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI

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

Homing endonuclease I-DmoI

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

5o6g__assembly_1__model_1

5o6g__assembly_1__model_1 | I(q)

5o6g__assembly_1__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI

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

Homing endonuclease I-DmoI

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

5o6g__assembly_1__model_1

5o6g__assembly_1__model_1 | I(q)

5o6g__assembly_1__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)