SAXSdb — 1pu7

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

3-METHYLADENINE DNA GLYCOSYLASE

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O25323_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–218； UniProt 1–218 Author chain B； PDBConstruct 1–218； UniProt 1–218

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	1pu7
Deposition date deposition_date	2003-06-24
Structure title title	Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 3,9-dimethyladenine
Keywords keywords	Helix-hairpin-helix, 3-Methyladenine, BASE EXCISION REPAIR, GLYCOSYLASE, HYDROLASE; HYDROLASE
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.

1pu7__assembly_2__model_1

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

Download this curve (.dat)

1pu7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pu7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.49 Å
Rg (electron density)	17.47 Å
Total Rg	18.51 Å
Atom count	1747
Residues	215
Excluded volume	31501 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pu7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1pu7__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	3-METHYLADENINE DNA GLYCOSYLASE
Molecular weight formula_weight	25218.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3871

VLDSFEILKALKSLDLLKNAPAWWWPNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKIVEFSKQKLELKL

Source Source

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	362

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pu7a_
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.96.1.5 — 3-Methyladenine DNA glycosylase III (MagIII)

Domain ID domain_id	d1pu7b_
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.96.1.5 — 3-Methyladenine DNA glycosylase III (MagIII)

CATH v4.4 (4 domains)

Domain ID domain_id	1pu7A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	1pu7A02
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

Domain ID domain_id	1pu7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	1pu7B02
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	146.605 Å
Unit-cell length b length_b	44.399 Å
Unit-cell length c length_c	81.516 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1851
R_work r_work	0.1831
R_free r_free	0.2223

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 3,9-dimethyladenine

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

3-METHYLADENINE DNA GLYCOSYLASE

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

1pu7__assembly_2__model_1

1pu7__assembly_2__model_1 | I(q)

1pu7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 3,9-dimethyladenine

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

3-METHYLADENINE DNA GLYCOSYLASE

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

1pu7__assembly_2__model_1

1pu7__assembly_2__model_1 | I(q)

1pu7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)