SAXSdb — 3c3i

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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 × 1 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 1–141； UniProt 1–141 Author chain B； PDBConstruct 1–141； UniProt 1–141 Author chain C； PDBConstruct 1–141； UniProt 1–141 Author chain D； PDBConstruct 1–141； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3c3i
Deposition date deposition_date	2008-01-28
Structure title title	Evolution of chlorella virus dUTPase
Keywords keywords	dUTPase Chlorella virus, 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.

3c3i__assembly_1__model_1

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

Download this curve (.dat)

3c3i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c3i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.01 Å
Rg (electron density)	19.95 Å
Total Rg	20.97 Å
Atom count	2923
Residues	381
Excluded volume	52407 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c3i__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c3i__assembly_2__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 triphosphatase
Molecular weight formula_weight	14824.9 kDa
EC 编号 ec_number	3.6.1.23
Mutation mutation	E81S, T84R
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4053

MSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDSDYRGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFGSTGI

Source Source

Source organism organism	Paramecium bursaria Chlorella virus IL3A
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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3c3ia_
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	d3c3ib_
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	d3c3ic_
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	d3c3id_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3c3iA00
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	3c3iB00
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	3c3iC00
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	3c3iD00
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	132.069 Å
Unit-cell length b length_b	132.069 Å
Unit-cell length c length_c	53.451 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	24

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	33.610 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2580

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

3c3i__assembly_1__model_1

3c3i__assembly_1__model_1 | I(q)

3c3i__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

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

3c3i__assembly_1__model_1

3c3i__assembly_1__model_1 | I(q)

3c3i__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)