SAXSdb — 4f4y

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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	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPGPCPAPCPTPGPAPTPCPGPGPGPCPCPC)-3') ; × 1 ;DNA (5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP*C)-3') ; × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 3	Consistent with all polymers
2	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPGPCPAPCPTPGPAPTPCPGPGPGPCPCPC)-3') ; × 1 ;DNA (5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP*C)-3') ; × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 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	DPO4_SULAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 1–231 Author chain A； PDBConstruct 249–354； UniProt 249–354 Author chain B； PDBConstruct 1–231； UniProt 1–231 Author chain B； PDBConstruct 249–354； UniProt 249–354

DNA polymerase IV

Sulfolobus solfataricus

UniProt Q97W02

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPGPCPAPCPTPGPAPTPCPGPGPGPCPCPC)-3') ; × 1 ;DNA (5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP*C)-3') ; × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 3	Consistent with all polymers
2	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPGPCPAPCPTPGPAPTPCPGPGPGPCPCPC)-3') ; × 1 ;DNA (5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP*C)-3') ; × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 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	DPO4_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 232–248； UniProt 231–247 Author chain B； PDBConstruct 232–248； UniProt 231–247

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	4f4y
Deposition date deposition_date	2012-05-11
Structure title title	Y-family DNA polymerase chimera Dbh-Dpo4-Dbh
Keywords keywords	Y-family polymerase, 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.

4f4y__assembly_1__model_1

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

Download this curve (.dat)

4f4y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4f4y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.75 Å
Rg (electron density)	23.08 Å
Total Rg	23.81 Å
Atom count	3445
Residues	377
Excluded volume	60124 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4f4y__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4f4y__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	41094.9 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
Atom count atom_count	7148

MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRVRKSIGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIINKTNLSDFFDIGGHHHHHH

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(GPGPCPAPCPTPGPAPTPCPGPGPGPCPCPC)-3') ;
Molecular weight formula_weight	4900.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,P

GGCACTGATCGGGCCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP*C)-3') ;
Molecular weight formula_weight	5756.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,T

TTACGCCCTGATCAGTGCC

Entity 4 Entity 4 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	467.2 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	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	252

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4f4yA01
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	4f4yA02
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	4f4yA03
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	4f4yA04
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	4f4yB01
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	4f4yB02
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	4f4yB03
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	4f4yB04
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	53.076 Å
Unit-cell length b length_b	103.390 Å
Unit-cell length c length_c	112.988 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.76 °
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	2.338 Å
Low-resolution limit resolution_low	29.250 Å
R factor r_factor	0.2234
R_work r_work	0.2219
R_free r_free	0.2586

Y-family DNA polymerase chimera Dbh-Dpo4-Dbh

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

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

4f4y__assembly_1__model_1

4f4y__assembly_1__model_1 | I(q)

4f4y__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)

Y-family DNA polymerase chimera Dbh-Dpo4-Dbh

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

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

4f4y__assembly_1__model_1

4f4y__assembly_1__model_1 | I(q)

4f4y__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)