SAXSdb — 5xm9

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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 2	DNA (36-MER) × 1 DNA (23-mer) × 1	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	DNA (36-MER) × 1 DNA (23-mer) × 1	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 4–177； UniProt 1–174 Author chain B； PDBConstruct 4–177； UniProt 1–174 Author chain C； PDBConstruct 4–177； UniProt 1–174 Author chain D； PDBConstruct 4–177； 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	5xm9
Deposition date deposition_date	2017-05-13
Structure title title	Crystal structure of AsfvPolX in complex with DNA enzyme.
Keywords keywords	PolX, DNA enzyme, complex, TRANSFERASE-DNA complex; TRANSFERASE/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.

5xm9__assembly_1__model_1

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

Download this curve (.dat)

5xm9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xm9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.41 Å
Rg (electron density)	29.71 Å
Total Rg	30.39 Å
Atom count	4075
Residues	407
Excluded volume	70501 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xm9__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5xm9__assembly_2__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Repair DNA polymerase X
Molecular weight formula_weight	20551.7 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D51N
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8150

GGSMLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVNLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL

Source Source

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

Entity 2 Entity 2 polymer

Description description	DNA (36-MER)
Molecular weight formula_weight	10989.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

TGTAACGCACTGCCAGCGGCTCGAAATCTCTCTCGT

Entity 3 Entity 3 polymer

Description description	DNA (23-mer)
Molecular weight formula_weight	7194.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

ACGAGAGAGATGGGTGCGTTACA

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5xm9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5xm9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5xm9B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5xm9B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5xm9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5xm9C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	5xm9D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	5xm9D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

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Unit-cell length a length_a	98.940 Å
Unit-cell length b length_b	118.878 Å
Unit-cell length c length_c	235.955 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.053 Å
Low-resolution limit resolution_low	29.719 Å
R factor r_factor	0.2188
R_work r_work	0.2154
R_free r_free	0.2776

Crystal structure of AsfvPolX in complex with DNA enzyme.

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

5xm9__assembly_1__model_1

5xm9__assembly_1__model_1 | I(q)

5xm9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of AsfvPolX in complex with DNA enzyme.

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

5xm9__assembly_1__model_1

5xm9__assembly_1__model_1 | I(q)

5xm9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)