SAXSdb — 4xds

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

Deoxyguanosinetriphosphate triphosphohydrolase

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	NICKEL (II) ION × 6 SULFATE ION × 79 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DGTP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–505； UniProt 1–505 Author chain B； PDBConstruct 1–505； UniProt 1–505 Author chain C； PDBConstruct 1–505； UniProt 1–505 Author chain D； PDBConstruct 1–505； UniProt 1–505 Author chain E； PDBConstruct 1–505； UniProt 1–505 Author chain F； PDBConstruct 1–505； UniProt 1–505

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	4xds
Deposition date deposition_date	2014-12-19
Structure title title	Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel
Keywords keywords	TRIPHOSPHOHYDROLASE, HYDROLASE-DNA complex; HYDROLASE/DNA
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.

4xds__assembly_1__model_1

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

Download this curve (.dat)

4xds__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xds__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.05 Å
Rg (electron density)	43.39 Å
Total Rg	43.74 Å
Atom count	24520
Residues	2980
Excluded volume	433130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xds__assembly_1__model_1`	hexameric （6）	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	Deoxyguanosinetriphosphate triphosphohydrolase
Molecular weight formula_weight	59470.9 kDa
EC 编号 ec_number	3.1.5.1
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	24538

MAQIDFRKKINWHRRYRSPQGVKTEHEILRIFESDRGRIINSPAIRRLQQKTQVFPLERNAAVRTRLTHSMEVQQVGRYIAKEILSRLKELKLLEAYGLDELTGPFESIVEMSCLMHDIGNPPFGHFGEAAINDWFRQRLHPEDAESQPLTDDRCSVAALRLRDGEEPLNELRRKIRQDLCHFEGNAQGIRLVHTLMRMNLTWAQVGGILKYTRPAWWRGETPETHHYLMKKPGYYLSEEAYIARLRKELNLALYSRFPLTWIMEAADDISYCVADLEDAVEKRIFTVEQLYHHLHEAWGQHEKGSLFSLVVENAWEKSRSNSLSRSTEDQFFMYLRVNTLNKLVPYAAQRFIDNLPAIFAGTFNHALLEDASECSDLLKLYKNVAVKHVFSHPDVERLELQGYRVISGLLEIYRPLLSLSLSDFTELVEKERVKRFPIESRLFHKLSTRHRLAYVEAVSKLPSDSPEFPLWEYYYRCRLLQDYISGMTDLYAWDEYRRLMAVEQ

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	79

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4xdsA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4xdsB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4xdsC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4xdsD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4xdsE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	4xdsF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

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Unit-cell length a length_a	189.800 Å
Unit-cell length b length_b	189.800 Å
Unit-cell length c length_c	296.800 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.354 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1739
R_work r_work	0.1720
R_free r_free	0.2088

Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel

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

Deoxyguanosinetriphosphate triphosphohydrolase

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

4xds__assembly_1__model_1

4xds__assembly_1__model_1 | I(q)

4xds__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel

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

Deoxyguanosinetriphosphate triphosphohydrolase

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

4xds__assembly_1__model_1

4xds__assembly_1__model_1 | I(q)

4xds__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)