SAXSdb — 1ogh

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

BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

METHANOCALDOCOCCUS JANNASCHII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCD_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–204； UniProt 1–204 Author chain B； PDBConstruct 1–204； UniProt 1–204

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	1ogh
Deposition date deposition_date	2003-05-02
Structure title title	Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii
Keywords keywords	BIFUNCTIONAL ENZYME, NUCLEOTIDE METABOLISM, DCTP DEAMINASE, DUTPASE, HOMOTRIMER, 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.

1ogh__assembly_1__model_1

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

Download this curve (.dat)

1ogh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ogh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.92 Å
Rg (electron density)	22.72 Å
Total Rg	23.78 Å
Atom count	4242
Residues	525
Excluded volume	76649 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ogh__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ogh__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ogha_
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	d1oghb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	1oghA00
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	1oghB00
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	111.060 Å
Unit-cell length b length_b	111.060 Å
Unit-cell length c length_c	111.060 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	1.880 Å
Low-resolution limit resolution_low	19.650 Å
R factor r_factor	0.1480
R_work r_work	0.1470
R_free r_free	0.1840

Description description	BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
Molecular weight formula_weight	23461.9 kDa
EC 编号 ec_number	3.5.4.13, 3.6.1.23
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3356

Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii

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

BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

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

1ogh__assembly_1__model_1

1ogh__assembly_1__model_1 | I(q)

1ogh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Source organism organism	METHANOCALDOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	398

Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii

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

BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

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

1ogh__assembly_1__model_1

1ogh__assembly_1__model_1 | I(q)

1ogh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)