2rdj

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

Method: X-RAY DIFFRACTION

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

DNA polymerase IV

Sulfolobus 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	;DNA (5'-D(DGPDGPDGPDAPDCPDCPDCPDTPDTPDCPDGPDAPDAPDT)-3') ; × 1 ;DNA (5'-D(PDTPDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCPDC)-3') ; × 1 CALCIUM ION × 2 THYMIDINE-5'-PHOSPHATE × 1 GLYCEROL × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(DGPDGPDGPDAPDCPDCPDCPDTPDTPDCPDGPDAPDAPDT)-3') ; × 1 ;DNA (5'-D(PDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCP*DC)-3') ; × 1 CALCIUM ION × 2 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO42_SULSO
Isoform	—
PDB entities	4
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	2rdj
Deposition date deposition_date	2007-09-24
Structure title title	Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms
Keywords keywords	;DNA polymerase, DNA-enzyme complex, Y-family, DNA damage, DNA repair, DNA replication, DNA-binding, DNA-directed DNA polymerase, Magnesium, Metal-binding, Mutator protein, Nucleotidyltransferase, 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.

2rdj__assembly_1__model_1

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

Download this curve (.dat)

2rdj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rdj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.57 Å
Rg (electron density)	22.85 Å
Total Rg	23.62 Å
Atom count	3383
Residues	371
Excluded volume	59228 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rdj__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rdj__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 (5'-D(DGPDGPDGPDAPDCPDCPDCPDTPDTPDCPDGPDAPDAPDT)-3') ;
Molecular weight formula_weight	4280.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,E
Atom count atom_count	7024

GGGACCCTTCGAAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PDTPDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCPDC)-3') ;
Molecular weight formula_weight	4889.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTATTCGAAGGGTCCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCP*DC)-3') ;
Molecular weight formula_weight	4585.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TATTCGAAGGGTCCC

Entity 4 Entity 4 polymer

Description description	DNA polymerase IV
Molecular weight formula_weight	40257.9 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

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEAIGLDKFFDT

Source Source

Source organism organism	Sulfolobus solfataricus
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	305

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2rdja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
Family Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

Domain ID domain_id	d2rdja2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

Domain ID domain_id	d2rdjb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.240 — Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily Superfamily superfamily	d.240.1 — Lesion bypass DNA polymerase (Y-family), little finger domain
Family Family family	d.240.1.1 — Lesion bypass DNA polymerase (Y-family), little finger domain

Domain ID domain_id	d2rdjb2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.7 — Lesion bypass DNA polymerase (Y-family), catalytic domain

CATH v4.4 (8 domains)

Domain ID domain_id	2rdjA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	2rdjA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2rdjA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	2rdjA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

Domain ID domain_id	2rdjB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	2rdjB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2rdjB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	2rdjB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	100 — DNA polymerase, Y-family, little finger domain

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Unit-cell length a length_a	97.993 Å
Unit-cell length b length_b	102.510 Å
Unit-cell length c length_c	106.109 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	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	24.110 Å
R factor r_factor	0.2210
R_work r_work	0.2100
R_free r_free	0.2560

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

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

2rdj__assembly_1__model_1

2rdj__assembly_1__model_1 | I(q)

2rdj__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

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

2rdj__assembly_1__model_1

2rdj__assembly_1__model_1 | I(q)

2rdj__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)