SAXSdb — 2yzj

▼

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

167aa long hypothetical dUTPase

Sulfolobus tokodaii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q970G0_SULTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–169； UniProt 1–167 Author chain B； PDBConstruct 3–169； UniProt 1–167 Author chain C； PDBConstruct 3–169； UniProt 1–167

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	2yzj
Deposition date deposition_date	2007-05-06
Structure title title	Crystal structure of dCTP deaminase from Sulfolobus tokodaii
Keywords keywords	;All beta proteins, Hypothetical protein, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2yzj__assembly_1__model_1

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

Download this curve (.dat)

2yzj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yzj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.92 Å
Rg (electron density)	20.71 Å
Total Rg	21.60 Å
Atom count	3836
Residues	468
Excluded volume	69016 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yzj__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	167aa long hypothetical dUTPase
Molecular weight formula_weight	19190.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4135

GHMKGLTEKLMILSHQSIKNLLGKVILNYSEENVRENGYDLRICGDKYYELVQGAELPEKKATLREIEFKERAILSANHTYLFESCEEFNMPADLAVLITLKSTLARNGFLAPPTVIDAGYKGKVNVAITAVYNSSLKKGMATHHLIFLKLDKPTERLYNGKYQGGILI

Source Source

Source organism organism	Sulfolobus tokodaii
NCBI taxonomy ID ncbi_taxonomy_id	111955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DEOXYURIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	388.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	299

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2yzjA01
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	2yzjB01
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	2yzjC01
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	53.770 Å
Unit-cell length b length_b	53.757 Å
Unit-cell length c length_c	53.757 Å
Unit-cell angle α angle_alpha	107.47 °
Unit-cell angle β angle_beta	107.52 °
Unit-cell angle γ angle_gamma	107.50 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.660 Å
Low-resolution limit resolution_low	31.650 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2270

Crystal structure of dCTP deaminase from Sulfolobus tokodaii

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

167aa long hypothetical dUTPase

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

2yzj__assembly_1__model_1

2yzj__assembly_1__model_1 | I(q)

2yzj__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of dCTP deaminase from Sulfolobus tokodaii

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

167aa long hypothetical dUTPase

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

2yzj__assembly_1__model_1

2yzj__assembly_1__model_1 | I(q)

2yzj__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)