SAXSdb — 8ilf

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

Repair DNA polymerase X

African swine fever virus (strain Badajoz 1971 Vero-adapted)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 4	;DNA (5'-D(CPTPGPGPAPTPCPCP*A)-3') ; × 4 MANGANESE (II) ION × 2 ;[[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] phosphono hydrogen phosphate ; × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOLX_ASFB7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–178； UniProt 1–174 Author chain B； PDBConstruct 5–178； UniProt 1–174

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	8ilf
Deposition date deposition_date	2023-03-03
Structure title title	The crystal structure of dGTPalphaSe-Sp:DNApre-II:Pol X substrate ternary complex
Keywords keywords	DNA polymerase, substrate complex, dNTPalphaSe, configuration, REPLICATION-DNA complex; REPLICATION/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.

8ilf__assembly_1__model_1

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

Download this curve (.dat)

8ilf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ilf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.44 Å
Rg (electron density)	25.33 Å
Total Rg	26.13 Å
Atom count	3621
Residues	390
Excluded volume	63592 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ilf__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 (5)

Entity 1 Entity 1 polymer

Description description	Repair DNA polymerase X
Molecular weight formula_weight	20579.7 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3691

GGGGMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL

Source Source

Source organism organism	African swine fever virus (strain Badajoz 1971 Vero-adapted)
Common name common_name	Ba71V, ASFV
NCBI taxonomy ID ncbi_taxonomy_id	10498
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPGPGPAPTPCPCP*A)-3') ;
Molecular weight formula_weight	2715.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,H,J

CTGGATCCA

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;[[(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-selanyl-phosphoryl] phosphono hydrogen phosphate ;
Molecular weight formula_weight	570.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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Unit-cell length a length_a	59.666 Å
Unit-cell length b length_b	78.190 Å
Unit-cell length c length_c	101.304 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2065
R_work r_work	0.2044
R_free r_free	0.2446

The crystal structure of dGTPalphaSe-Sp:DNApre-II:Pol X substrate ternary complex

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

Repair DNA polymerase X

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

8ilf__assembly_1__model_1

8ilf__assembly_1__model_1 | I(q)

8ilf__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 (5)

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

Entity 5 Entity 5 water

7. Citations (1)

The crystal structure of dGTPalphaSe-Sp:DNApre-II:Pol X substrate ternary complex

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

Repair DNA polymerase X

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

8ilf__assembly_1__model_1

8ilf__assembly_1__model_1 | I(q)

8ilf__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 (5)

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

Entity 5 Entity 5 water

7. Citations (1)