SAXSdb — 9p8u

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

DNTP triphosphohydrolase

Salmonella enterica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 8 DNA 8	;5'-triphosphothymidyl-3'5'-thymidine (p3diT) ; × 8 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 8 MAGNESIUM ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A5H6DAK1_SALET
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–473； UniProt 1–471 Author chain B； PDBConstruct 3–473； UniProt 1–471 Author chain D； PDBConstruct 3–473； UniProt 1–471 Author chain E； PDBConstruct 3–473； UniProt 1–471 Author chain G； PDBConstruct 3–473； UniProt 1–471 Author chain H； PDBConstruct 3–473； UniProt 1–471 Author chain J； PDBConstruct 3–473； UniProt 1–471 Author chain K； PDBConstruct 3–473； UniProt 1–471

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	9p8u
Deposition date deposition_date	2025-06-23
Structure title title	Structure of CloA in complex with dGTP and p3diT
Keywords keywords	deoxynucleoside triphosphohydrolase, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9p8u__assembly_1__model_1

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

Download this curve (.dat)

9p8u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p8u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.80 Å
Rg (electron density)	48.90 Å
Total Rg	49.22 Å
Atom count	30920
Residues	3768
Excluded volume	544030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p8u__assembly_1__model_1`	hexadecameric （16）	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	DNTP triphosphohydrolase
Molecular weight formula_weight	54257.2 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K
Atom count atom_count	30920

GSMHWNDLLNSNRRKPKNEKKESSQDTSKGRQQIERDYDRILFAAPTRRLADKTQVFPLDKNDSVRTRLTHSHEVANLSRGIGMRLAFELEDDVFKDVSEDICLKRDVPALLAAIGLVHDMGNPPFGAQGAKAMSEWFTKNLPEHSDNYKDKIYGDFRHFDGNSQTLRLVTKLQILNDTYGLNLTYATLASMIKYPRSSESDSSLWKKHGFFLSEKDVVQDIWNNTGLSEGVRHPFTYIMEACDDIAYSVLDAEDIIKKGFASFHDLIDFIQSNQFCKEDDVAKRVIENCKKIHADYAQQKLSPAELNDMSMQMFRVYAIAELVDAVVIAFKDNINEFLNDTCEIKDLISCSSGKNLCQALKKFDSSRGYQHRSVLKLELEGSNYIKGLMDMLWLGIKGRATGDTQYDTPFGRYVYGRISENYRRIFEQENNLPACYKEAQLLADAISGMTDSYLIALHDELRALHQYECRQR

Source Source

Source organism organism	Salmonella enterica
NCBI taxonomy ID ncbi_taxonomy_id	28901
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;5'-triphosphothymidyl-3'5'-thymidine (p3diT) ;
Molecular weight formula_weight	723.4 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,N,O,P,Q,R,S,T

XT

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	8

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	8

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.56 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1498407

Structure of CloA in complex with dGTP and p3diT

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

DNTP 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

9p8u__assembly_1__model_1

9p8u__assembly_1__model_1 | I(q)

9p8u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Structure of CloA in complex with dGTP and p3diT

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

DNTP 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

9p8u__assembly_1__model_1

9p8u__assembly_1__model_1 | I(q)

9p8u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)