9nke

Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion

Method: X-RAY DIFFRACTION

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

DNA polymerase IV

Saccharolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	Extended Primer Strand × 1 Template DNA × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 CALCIUM ION × 2 PHOSPHATE ION × 1 water × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	Template DNA × 1 Primer Strand × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 CALCIUM ION × 1 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO4_SACS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–352； UniProt 1–352 Author chain B； PDBConstruct 1–352； UniProt 1–352

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	9nke
Deposition date deposition_date	2025-02-28
Structure title title	Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion
Keywords keywords	DNA polymerase Translesion synthesis 8oxoG damage, TRANSFERASE, 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.

9nke__assembly_1__model_1

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

Download this curve (.dat)

9nke__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nke__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.27 Å
Rg (electron density)	22.75 Å
Total Rg	23.46 Å
Atom count	6620
Residues	370
Excluded volume	59103 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nke__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9nke__assembly_2__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA polymerase IV
Molecular weight formula_weight	40171.8 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	R336A
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	13211

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVAFSKFIEAIGLDKFFDT

Source Source

Source organism organism	Saccharolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Extended Primer Strand
Molecular weight formula_weight	4329.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

GAGCGATACCGTGA

Entity 3 Entity 3 polymer

Description description	Template DNA
Molecular weight formula_weight	5179.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T,D

CGATCACGGTATCGCTC

Entity 4 Entity 4 polymer

Description description	Primer Strand
Molecular weight formula_weight	4016.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAGCGATACCGTG

Entity 5 Entity 5 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

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

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Unit-cell length a length_a	99.309 Å
Unit-cell length b length_b	103.575 Å
Unit-cell length c length_c	105.842 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	8

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	24.670 Å
R factor r_factor	0.2040
R_work r_work	0.1975
R_free r_free	0.2730

Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion

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

DNA polymerase IV

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

9nke__assembly_1__model_1

9nke__assembly_1__model_1 | I(q)

9nke__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion

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

DNA polymerase IV

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

9nke__assembly_1__model_1

9nke__assembly_1__model_1 | I(q)

9nke__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)