SAXSdb — 3rb4

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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(GPTPTPGPGPAPTPGPGPTPAPGP(DDG))-3') ; × 1 ;DNA (5'-D(CCPTPAPAPCP(ME6)PCPTPAPCPCPAPTPCPCPAPAPCP*C)-3') ; × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 3 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPTPTPGPGPAPTPGPGPTPAPGP(DDG))-3') ; × 1 ;DNA (5'-D(CCPTPAPAPCP(ME6)PCPTPAPCPCPAPTPCPCPAPAPCP*C)-3') ; × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 3 water × 2	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–341； UniProt 2–341 Author chain B； PDBConstruct 2–341； UniProt 2–341

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	3rb4
Deposition date deposition_date	2011-03-28
Structure title title	Dpo4 extension ternary complex with 3'-terminal primer G base opposite the 3-methylcytosine (m3c) lesion
Keywords keywords	;DNA DAMAGE, DNA REPAIR, DNA REPLICATION, DNA-BINDING, DNA-DIRECTED DNA POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR PROTEIN, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX, Lesion bypass, DNA polymerase, Y-family polymerase, dNTP binding, 3-methylcytosine ;; 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.

3rb4__assembly_1__model_1

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

Download this curve (.dat)

3rb4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rb4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.68 Å
Rg (electron density)	22.99 Å
Total Rg	23.75 Å
Atom count	3420
Residues	371
Excluded volume	59681 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rb4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rb4__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 (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase IV
Molecular weight formula_weight	38945.4 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	6700

GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

Source Source

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPTPTPGPGPAPTPGPGPTPAPGP*(DDG))-3') ;
Molecular weight formula_weight	4086.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

GTTGGATGGTAGG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CCPTPAPAPCP(ME6)PCPTPAPCPCPAPTPCPCPAPAPCPC)-3') ;
Molecular weight formula_weight	5942.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,J

CCTAACXCTACCATCCAACC

Entity 4 Entity 4 non-polymer

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

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	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3rb4A01
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	3rb4A02
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	3rb4A03
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	3rb4A04
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	3rb4B01
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	3rb4B02
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	3rb4B03
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	3rb4B04
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	53.267 Å
Unit-cell length b length_b	109.995 Å
Unit-cell length c length_c	101.535 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.805 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2077
R_work r_work	0.2050
R_free r_free	0.2564

Dpo4 extension ternary complex with 3'-terminal primer G base opposite the 3-methylcytosine (m3c) 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

3rb4__assembly_1__model_1

3rb4__assembly_1__model_1 | I(q)

3rb4__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Dpo4 extension ternary complex with 3'-terminal primer G base opposite the 3-methylcytosine (m3c) 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

3rb4__assembly_1__model_1

3rb4__assembly_1__model_1 | I(q)

3rb4__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)