SAXSdb — 6oiv

▼

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	MANGANESE (II) ION × 6 SULFATE ION × 9 water × 3	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 2–505； UniProt 2–505 Author chain B； PDBConstruct 2–505； UniProt 2–505 Author chain C； PDBConstruct 2–505； UniProt 2–505 Author chain D； PDBConstruct 2–505； UniProt 2–505 Author chain E； PDBConstruct 2–505； UniProt 2–505 Author chain F； PDBConstruct 2–505； UniProt 2–505

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6oiv
Deposition date deposition_date	2019-04-09
Structure title title	XFEL structure of Escherichia coli dGTPase
Keywords keywords	dNTP Triphosphohydrolase, Metalloenzyme, Metal Binding Protein, XFEL, E. coli dGTPase, hydrolase; metal binding protein, hydrolase
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.

6oiv__assembly_1__model_1

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

Download this curve (.dat)

6oiv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oiv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.01 Å
Rg (electron density)	43.54 Å
Total Rg	43.73 Å
Atom count	24770
Residues	2917
Excluded volume	440780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oiv__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Deoxyguanosinetriphosphate triphosphohydrolase
Molecular weight formula_weight	59986.7 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	24778

MAQIDFRKKINWHRRYRSPQGVKTEHEILRIFESDRGRIINSPAIRRLQQKTQVFPLERNAAVRTRLTHSMEVQQVGRYIAKEILSRLKELKLLEAYGLDELTGPFESIVEMSCLMHDIGNPPFGHFGEAAINDWFRQRLHPEDAESQPLTDDRCSVAALRLRDGEEPLNELRRKIRQDLCHFEGNAQGIRLVHTLMRMNLTWAQVGGILKYTRPAWWRGETPETHHYLMKKPGYYLSEEAYIARLRKELNLALYSRFPLTWIMEAADDISYCVADLEDAVEKRIFTVEQLYHHLHEAWGQHEKGSLFSLVVENAWEKSRSNSLSRSTEDQFFMYLRVNTLNKLVPYAAQRFIDNLPAIFAGTFNHALLEDASECSDLLKLYKNVAVKHVFSHPDVERLELQGYRVISGLLEIYRPLLSLSLSDFTELVEKERVKRFPIESRLFHKLSTRHRLAYVEAVSKLPSDSPEFPLWEYYYRCRLLQDYISGMTDLYAWDEYRRLMAVEQ

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6oivA01
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	6oivB01
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	6oivC01
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	6oivD01
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	6oivE01
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	6oivF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

▶

Unit-cell length a length_a	192.589 Å
Unit-cell length b length_b	192.589 Å
Unit-cell length c length_c	291.254 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	3.060 Å
Low-resolution limit resolution_low	61.200 Å
R factor r_factor	0.2260
R_work r_work	0.2250
R_free r_free	0.2480

XFEL structure of Escherichia coli dGTPase

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

6oiv__assembly_1__model_1

6oiv__assembly_1__model_1 | I(q)

6oiv__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)

XFEL structure of Escherichia coli dGTPase

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

6oiv__assembly_1__model_1

6oiv__assembly_1__model_1 | I(q)

6oiv__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)