SAXSdb — 3ca9

▼

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

Deoxyuridine triphosphatase

Paramecium bursaria Chlorella virus IL3A

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 3 DEOXYURIDINE-5'-DIPHOSPHATE × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 3 DEOXYURIDINE-5'-DIPHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5I3E5_PBCVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–157； UniProt 1–141 Author chain B； PDBConstruct 17–157； UniProt 1–141

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ca9
Deposition date deposition_date	2008-02-19
Structure title title	Evolution of chlorella virus dUTPase
Keywords keywords	dUTPase Chlorella Virus, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3ca9__assembly_2__model_1

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

Download this curve (.dat)

3ca9__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ca9__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.82 Å
Rg (electron density)	19.89 Å
Total Rg	20.94 Å
Atom count	2911
Residues	378
Excluded volume	52326 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ca9__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ca9__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Deoxyuridine triphosphatase
Molecular weight formula_weight	17539.9 kDa
EC 编号 ec_number	3.6.1.23
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	1976

MASMTGGQQMGRGSEFMSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFGSTGILEHHHHHH

Source Source

Source organism organism	Paramecium bursaria Chlorella virus IL3A
Common name common_name	PBCV-IL3A
NCBI taxonomy ID ncbi_taxonomy_id	46019
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	DEOXYURIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	388.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ca9a1
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.85.4.0 — automated matches

Domain ID domain_id	d3ca9a2
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

Domain ID domain_id	d3ca9b1
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.85.4.0 — automated matches

Domain ID domain_id	d3ca9b2
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 (2 domains)

Domain ID domain_id	3ca9A00
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)

Domain ID domain_id	3ca9B00
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)

▶

Unit-cell length a length_a	105.647 Å
Unit-cell length b length_b	105.647 Å
Unit-cell length c length_c	105.647 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.500 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.3070

Evolution of chlorella virus dUTPase

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

Deoxyuridine triphosphatase

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

3ca9__assembly_2__model_1

3ca9__assembly_2__model_1 | I(q)

3ca9__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 (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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Evolution of chlorella virus dUTPase

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

Deoxyuridine triphosphatase

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

3ca9__assembly_2__model_1

3ca9__assembly_2__model_1 | I(q)

3ca9__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 (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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)