SAXSdb — 2io4

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

DNA polymerase sliding clamp B

Sulfolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase sliding clamp C × 1 （Q97Z84） (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase sliding clamp C × 1 （Q97Z84） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA polymerase sliding clamp C × 4 （Q97Z84） (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CALCIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA2_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–249； UniProt 1–249 Author chain C； PDBConstruct 1–249； UniProt 1–249

DNA polymerase sliding clamp C

Sulfolobus solfataricus

UniProt Q97Z84

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase sliding clamp B × 1 （P57766） (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CALCIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase sliding clamp B × 1 （P57766） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA polymerase sliding clamp B × 4 （P57766） (4S)-2-METHYL-2,4-PENTANEDIOL × 10 CALCIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA3_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–246； UniProt 1–245 Author chain D； PDBConstruct 2–246； UniProt 1–245

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	2io4
Deposition date deposition_date	2006-10-09
Structure title title	Crystal structure of PCNA12 dimer from Sulfolobus solfataricus.
Keywords keywords	PCNA12 heterodimer, protein-protein interaction, PCNA123 heterotrimer, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

2io4__assembly_1__model_1

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

Download this curve (.dat)

2io4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2io4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.76 Å
Rg (electron density)	30.10 Å
Total Rg	30.75 Å
Atom count	3913
Residues	495
Excluded volume	70801 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2io4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2io4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2io4__assembly_3__model_1`	octameric （8）	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 (5)

Entity 1 Entity 1 polymer

Description description	DNA polymerase sliding clamp B
Molecular weight formula_weight	27521.7 kDa
Mutation mutation	F2V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	7938

MVKIVYPNAKDFFSFINSITNVTDSIILNFTEDGIFSRHLTEDKVLMAIMRIPKDVLSEYSIDSPTSVKLDVSSVKKILSKASSKKATIELTETDSGLKIIIRDEKSGAKSTIYIKAEKGQVEQLTEPKVNLAVNFTTDESVLNVIAADVTLVGEEMRISTEEDKIKIEAGEEGKRYVAFLMKDKPLKELSIDTSASSSYSAEMFKDAVKGLRGFSAPTMVSFGENLPMKIDVEAVSGGHMIFWIAPRL

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA polymerase sliding clamp C
Molecular weight formula_weight	27592.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MMKAKVIDAVSFSYILRTVGDFLSEANFIVTKEGIRVSGIDPSRVVFLDIFLPSSYFEGFEVSQEKEIIGFKLEDVNDILKRVLKDDTLILSSNESKLTLTFDGEFTRSFELPLIQVESTQPPSVNLEFPFKAQLLTITFADIIDELSDLGEVLNIHSKENKLYFEVIGDLSTAKVELSTDNGTLLEASGADVSSSYGMEYVANTTKMRRASDSMELYFGSQIPLKLRFKLPQEGYGDFYIAPRAD

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2io4b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.0 — automated matches

Domain ID domain_id	d2io4b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.0 — automated matches

Domain ID domain_id	d2io4d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.0 — automated matches

Domain ID domain_id	d2io4d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2io4A01
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2io4B00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2io4C01
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2io4D00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	104.991 Å
Unit-cell length b length_b	112.727 Å
Unit-cell length c length_c	101.851 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2340
R_work r_work	0.2332
R_free r_free	0.2604

Crystal structure of PCNA12 dimer from Sulfolobus solfataricus.

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

DNA polymerase sliding clamp B

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase sliding clamp C

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

2io4__assembly_1__model_1

2io4__assembly_1__model_1 | I(q)

2io4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of PCNA12 dimer from Sulfolobus solfataricus.

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

DNA polymerase sliding clamp B

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 sliding clamp C

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

2io4__assembly_1__model_1

2io4__assembly_1__model_1 | I(q)

2io4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)