SAXSdb — 2hrm

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase ;

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE × 3 1,2-ETHANEDIOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DUT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–152； UniProt 1–151

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	2hrm
Deposition date deposition_date	2006-07-20
Structure title title	Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP
Keywords keywords	JELLY ROLL, ENZYME-SUBSTRATE ANALOGUE LIGAND COMPLEX, 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.

2hrm__assembly_1__model_1

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

Download this curve (.dat)

2hrm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hrm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.03 Å
Rg (electron density)	20.82 Å
Total Rg	21.60 Å
Atom count	3120
Residues	411
Excluded volume	55909 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hrm__assembly_1__model_1`	trimeric （3）	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	;Deoxyuridine 5'-triphosphate nucleotidohydrolase ;
Molecular weight formula_weight	16302.6 kDa
EC 编号 ec_number	3.6.1.23
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	1209

MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ

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 non-polymer

Description description	2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE
Molecular weight formula_weight	386.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2hrma2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.1 — dUTPase-like

Domain ID domain_id	d2hrma3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2hrmA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

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Unit-cell length a length_a	75.650 Å
Unit-cell length b length_b	75.650 Å
Unit-cell length c length_c	101.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1696
R_work r_work	0.1682
R_free r_free	0.1956

Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase ;

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

2hrm__assembly_1__model_1

2hrm__assembly_1__model_1 | I(q)

2hrm__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (3)

Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP

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

;Deoxyuridine 5'-triphosphate nucleotidohydrolase ;

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

2hrm__assembly_1__model_1

2hrm__assembly_1__model_1 | I(q)

2hrm__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (3)