SAXSdb — 2jhn

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

3-METHYLADENINE DNA-GLYCOSYLASE

ARCHAEOGLOBUS FULGIDUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MERCURIBENZOIC ACID × 1 MERCURY (II) ION × 1 SODIUM ION × 2 GLYCEROL × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MERCURIBENZOIC ACID × 1 MERCURY (II) ION × 1 SODIUM ION × 2 GLYCEROL × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28163_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 1–295 Author chain B； PDBConstruct 1–295； UniProt 1–295

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	2jhn
Deposition date deposition_date	2007-02-22
Structure title title	3-methyladenine dna-glycosylase from Archaeoglobus fulgidus
Keywords keywords	ALKA, DNA REPAIR, N1-METHYLADENINE, N3-METHYLCYTOSINE, HYPERTHERMOPHILES, ARCHAEOGLOBUS FULGIDUS, 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.

2jhn__assembly_2__model_1

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

Download this curve (.dat)

2jhn__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jhn__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.89 Å
Rg (electron density)	19.40 Å
Total Rg	20.56 Å
Atom count	2446
Residues	291
Excluded volume	44036 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jhn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jhn__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 (7)

Entity 1 Entity 1 polymer

Description description	3-METHYLADENINE DNA-GLYCOSYLASE
Molecular weight formula_weight	34281.5 kDa
EC 编号 ec_number	3.2.2.21
Mutation mutation	YES
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	5493

MWRIELKHAVNWELKMKFFVLPELPTPDVVESGVWRRAIVLDGRAVAVMAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQNPEELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFFSKKTELV

Source Source

Source organism organism	ARCHAEOGLOBUS FULGIDUS
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MERCURIBENZOIC ACID
Molecular weight formula_weight	321.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	495

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2jhnA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	2jhnA02
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	2jhnA03
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	2jhnB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	2jhnB02
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	2jhnB03
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)

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Unit-cell length a length_a	69.494 Å
Unit-cell length b length_b	49.968 Å
Unit-cell length c length_c	105.798 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1870
R_work r_work	0.1850
R_free r_free	0.2230

3-methyladenine dna-glycosylase from Archaeoglobus fulgidus

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

2jhn__assembly_2__model_1

2jhn__assembly_2__model_1 | I(q)

2jhn__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

3-methyladenine dna-glycosylase from Archaeoglobus fulgidus

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

2jhn__assembly_2__model_1

2jhn__assembly_2__model_1 | I(q)

2jhn__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)