SAXSdb — 2ofi

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

3-methyladenine DNA glycosylase I, constitutive

Salmonella typhi

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(CPGPGPAPCPTP(3DR)PAPCPGPGPG)-3' × 1 5'-D(CPCPGPTPTPAPGPTPCPCPGPC)-3' × 1 ZINC ION × 1 SODIUM ION × 1 3-METHYL-3H-PURIN-6-YLAMINE × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8Z2A5_SALTI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–184； UniProt 1–184

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	2ofi
Deposition date deposition_date	2007-01-03
Structure title title	Crystal Structure of 3-methyladenine DNA Glycosylase I (TAG) bound to DNA/3mA
Keywords keywords	3-Methyladenine, DNA repair, Glycosylase, Base Excision, Helix-hairpin-Helix, 3-METHYLADENINE DNA GLYCOSYLASE I-DNA COMPLEX; 3-METHYLADENINE DNA GLYCOSYLASE I/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.

2ofi__assembly_1__model_1

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

Download this curve (.dat)

2ofi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ofi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.56 Å
Rg (electron density)	18.36 Å
Total Rg	19.23 Å
Atom count	1934
Residues	202
Excluded volume	32895 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ofi__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 (7)

Entity 1 Entity 1 polymer

Description description	5'-D(CPGPGPAPCPTP(3DR)PAPCPGPGPG)-3'
Molecular weight formula_weight	3614.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2127

CCGTTAGTCCGC

Entity 2 Entity 2 polymer

Description description	5'-D(CPCPGPTPTPAPGPTPCPCPGPC)-3'
Molecular weight formula_weight	3579.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CGGACTNACGGG

Entity 3 Entity 3 polymer

Description description	3-methyladenine DNA glycosylase I, constitutive
Molecular weight formula_weight	21107.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MQRCDWVSQDPLYIAYHDNEWGVPETDSRKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPIRIAAMQEEDVERLLQNTGIIRHRGKIQAIISNARAWLAMEQNGESFADFVWSFVDGQPQITQAASLDKIPTSTPASDALAKALKKRGFKFVGTTICYSFMQACGLVNDHITGCFCHPG

Source Source

Source organism organism	Salmonella typhi
NCBI taxonomy ID ncbi_taxonomy_id	601
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	3-METHYL-3H-PURIN-6-YLAMINE
Molecular weight formula_weight	149.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ofia_
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.4 — 3-Methyladenine DNA glycosylase I (Tag)

CATH v4.4 (1 domains)

Domain ID domain_id	2ofiA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

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Unit-cell length a length_a	101.963 Å
Unit-cell length b length_b	101.963 Å
Unit-cell length c length_c	55.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1767
R_work r_work	0.1756
R_free r_free	0.1978

Crystal Structure of 3-methyladenine DNA Glycosylase I (TAG) bound to DNA/3mA

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

3-methyladenine DNA glycosylase I, constitutive

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

2ofi__assembly_1__model_1

2ofi__assembly_1__model_1 | I(q)

2ofi__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of 3-methyladenine DNA Glycosylase I (TAG) bound to DNA/3mA

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

3-methyladenine DNA glycosylase I, constitutive

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

2ofi__assembly_1__model_1

2ofi__assembly_1__model_1 | I(q)

2ofi__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)