SAXSdb — 2hxd

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

dCTP deaminase, dUMP-forming

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	MAGNESIUM ION × 3 ;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	MAGNESIUM ION × 6 ;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 6 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 24	MAGNESIUM ION × 24 ;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 24 water × 24	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

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	2hxd
Deposition date deposition_date	2006-08-03
Structure title title	Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium
Keywords keywords	beta barrel, 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.

2hxd__assembly_1__model_1

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

Download this curve (.dat)

2hxd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hxd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.75 Å
Rg (electron density)	22.68 Å
Total Rg	23.69 Å
Atom count	4905
Residues	597
Excluded volume	88195 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hxd__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hxd__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2hxd__assembly_3__model_1`	24-meric （24）	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	dCTP deaminase, dUMP-forming
Molecular weight formula_weight	23403.8 kDa
EC 编号 ec_number	3.5.4.30
Mutation mutation	E145A
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	1756

MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLAIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKTSKYAYQKSVMPSLIHLDNHKKD

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Entity 3 Entity 3 non-polymer

Description description	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ;
Molecular weight formula_weight	467.2 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	121

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2hxda_
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 (1 domains)

Domain ID domain_id	2hxdA00
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	171.513 Å
Unit-cell length b length_b	171.513 Å
Unit-cell length c length_c	171.513 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	48

Space group space_group	I 4 3 2
Space-group number int_tables_number	211
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	24.750 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.2210

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium

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

dCTP deaminase, dUMP-forming

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

2hxd__assembly_1__model_1

2hxd__assembly_1__model_1 | I(q)

2hxd__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium

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

dCTP deaminase, dUMP-forming

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

2hxd__assembly_1__model_1

2hxd__assembly_1__model_1 | I(q)

2hxd__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)