SAXSdb — 1q39

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

Endonuclease VIII

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 3 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 CALCIUM ION × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	END8_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 1–262

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	1q39
Deposition date deposition_date	2003-07-29
Structure title title	Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.
Keywords keywords	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.

1q39__assembly_1__model_1

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

Download this curve (.dat)

1q39__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1q39__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.58 Å
Rg (electron density)	21.77 Å
Total Rg	22.64 Å
Atom count	2030
Residues	257
Excluded volume	36162 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1q39__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1q39__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 (4)

Entity 1 Entity 1 polymer

Description description	Endonuclease VIII
Molecular weight formula_weight	29815.0 kDa
EC 编号 ec_number	3.2.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2044

PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1q39a1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.2 — Middle domain of MutM-like DNA repair proteins

Domain ID domain_id	d1q39a2
Class class	b — All beta proteins
Fold Fold fold	b.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamily	b.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family family	b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins

Domain ID domain_id	d1q39a3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

CATH v4.4 (2 domains)

Domain ID domain_id	1q39A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily	10 — MutM-like, N-terminal

Domain ID domain_id	1q39A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	57.721 Å
Unit-cell length b length_b	79.578 Å
Unit-cell length c length_c	169.653 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.020 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2990

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.

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

Endonuclease VIII

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

1q39__assembly_1__model_1

1q39__assembly_1__model_1 | I(q)

1q39__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 (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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.

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

Endonuclease VIII

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

1q39__assembly_1__model_1

1q39__assembly_1__model_1 | I(q)

1q39__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 (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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)