SAXSdb — 2ido

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

DNA polymerase III epsilon subunit

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Hot protein × 1 （Q71T70） MANGANESE (II) ION × 2 THYMIDINE-5'-PHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Hot protein × 1 （Q71T70） MANGANESE (II) ION × 3 THYMIDINE-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3E_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 1–186 Author chain C； PDBConstruct 1–186； UniProt 1–186

Hot protein

Enterobacteria phage

UniProt Q71T70

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase III epsilon subunit × 1 （P03007） MANGANESE (II) ION × 2 THYMIDINE-5'-PHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase III epsilon subunit × 1 （P03007） MANGANESE (II) ION × 3 THYMIDINE-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q71T70_BPP1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–83； UniProt 5–87 Author chain D； PDBConstruct 1–83； UniProt 5–87

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	2ido
Deposition date deposition_date	2006-09-15
Structure title title	Structure of the E. coli Pol III epsilon-Hot proofreading complex
Keywords keywords	Polymerase, exonuclease, Hot, epsilon, Pol III, TRANSFERASE; TRANSFERASE
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.

2ido__assembly_1__model_1

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

Download this curve (.dat)

2ido__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ido__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.49 Å
Rg (electron density)	18.45 Å
Total Rg	19.37 Å
Atom count	1988
Residues	248
Excluded volume	35245 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ido__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ido__assembly_2__model_1`	dimeric （2）	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	DNA polymerase III epsilon subunit
Molecular weight formula_weight	20741.7 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4450

MSTAITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTGGQTSMA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Hot protein
Molecular weight formula_weight	9710.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MYDWNIAAKSQEERDKVNVDLAASGVAYKERLNIPVIAEQVAREQPENLRTYFMERLRHYRQLSLQLPKGSDPAYQKDDAVKK

Source Source

Source organism organism	Enterobacteria phage
NCBI taxonomy ID ncbi_taxonomy_id	10678
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	429

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2idoa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2idob_
Class class	a — All alpha proteins
Fold Fold fold	a.237 — DNA polymerase III theta subunit-like
Superfamily Superfamily superfamily	a.237.1 — DNA polymerase III theta subunit-like
Family Family family	a.237.1.1 — DNA polymerase III theta subunit-like

Domain ID domain_id	d2idoc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2idod_
Class class	a — All alpha proteins
Fold Fold fold	a.237 — DNA polymerase III theta subunit-like
Superfamily Superfamily superfamily	a.237.1 — DNA polymerase III theta subunit-like
Family Family family	a.237.1.1 — DNA polymerase III theta subunit-like

CATH v4.4 (4 domains)

Domain ID domain_id	2idoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	2idoB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	250 — DNA polymerase III-theta

Domain ID domain_id	2idoC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	2idoD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	250 — DNA polymerase III-theta

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Unit-cell length a length_a	77.289 Å
Unit-cell length b length_b	77.289 Å
Unit-cell length c length_c	212.978 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	24.760 Å
R factor r_factor	0.2090
R_work r_work	0.2060
R_free r_free	0.2440

Structure of the E. coli Pol III epsilon-Hot proofreading complex

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

DNA polymerase III epsilon subunit

State in the Current Structure

Other States of the Same Protein in the Database

Hot protein

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

2ido__assembly_1__model_1

2ido__assembly_1__model_1 | I(q)

2ido__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the E. coli Pol III epsilon-Hot proofreading complex

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

DNA polymerase III epsilon subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hot protein

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

2ido__assembly_1__model_1

2ido__assembly_1__model_1 | I(q)

2ido__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)