SAXSdb — 2qxf

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

Exodeoxyribonuclease I

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	MAGNESIUM ION × 2 SODIUM ION × 1 THYMIDINE-5'-PHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EX1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475

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	2qxf
Deposition date deposition_date	2007-08-11
Structure title title	Product bound structure of exonuclease I at 1.5 angstrom resolution
Keywords keywords	;ALPHA-BETA DOMAIN, DNAQ SUPERFAMILY, SH3-LIKE DOMAIN, PRODUCT BOUND STRUCTURE, DNA damage, DNA repair, Exonuclease, Hydrolase, Nuclease ;; 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.

2qxf__assembly_1__model_1

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

Download this curve (.dat)

2qxf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qxf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.96 Å
Rg (electron density)	23.95 Å
Total Rg	24.88 Å
Atom count	3542
Residues	432
Excluded volume	62691 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qxf__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Exodeoxyribonuclease I
Molecular weight formula_weight	55510.6 kDa
EC 编号 ec_number	3.1.11.1
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	4290

MMNDGKQQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSFRLEHLTKANGIEHSNAHDAMADVYATIAMAKLVKTRQPRLFDYLFTHRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVIMVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLAQANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEAEPFTPSDNVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNFPGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLKALWQYADEIVEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	544

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2qxfa_
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

CATH v4.4 (4 domains)

Domain ID domain_id	2qxfA01
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	2qxfA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	20 — Exonuclease ExoI, domain 2

Domain ID domain_id	2qxfA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	70 — Exonuclease ExoI, domain 3

Domain ID domain_id	2qxfA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1240 —

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Unit-cell length a length_a	52.630 Å
Unit-cell length b length_b	91.849 Å
Unit-cell length c length_c	102.752 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	26.320 Å
R factor r_factor	0.2004
R_work r_work	0.1993
R_free r_free	0.2236

Product bound structure of exonuclease I at 1.5 angstrom resolution

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

Exodeoxyribonuclease I

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

2qxf__assembly_1__model_1

2qxf__assembly_1__model_1 | I(q)

2qxf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Product bound structure of exonuclease I at 1.5 angstrom resolution

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

Exodeoxyribonuclease I

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

2qxf__assembly_1__model_1

2qxf__assembly_1__model_1 | I(q)

2qxf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)