SAXSdb — 1ud9

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

DNA polymerase sliding clamp A

Sulfolobus tokodaii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 8 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 5 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 6 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 17 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA1_SULTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–245； UniProt 2–245 Author chain B； PDBConstruct 2–245； UniProt 2–245 Author chain C； PDBConstruct 2–245； UniProt 2–245 Author chain D； PDBConstruct 2–245； UniProt 2–245

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	1ud9
Deposition date deposition_date	2003-04-28
Structure title title	Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii
Keywords keywords	DNA-binding, DNA replication, 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.

1ud9__assembly_1__model_1

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

Download this curve (.dat)

1ud9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ud9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.63 Å
Rg (electron density)	19.19 Å
Total Rg	20.37 Å
Atom count	1902
Residues	242
Excluded volume	34553 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ud9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ud9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ud9__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ud9__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1ud9__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase sliding clamp A
Molecular weight formula_weight	27254.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7996

AHIVYDDVRDLKAIIQALLKLVDEALFDIKPEGIQLVAIDKAHISLIKIELPKEMFKEYDVPEEFKFGFNTQYMSKLLKAAKRKEEIIIDADSPEVVKLTLSGALNRVFNVNNIEVLPPEVPEVNLEFDIKATINASGLKNAIGEIAEVADTLLISGNEEKVVVKGEGENKVEVEFSKDTGSLADIEFNKESSSAYDVEYLNDIISLTKLSDYVKVAFADQKPMQLEFNMEGGGKVTYLLAPKLS

Source Source

Source organism organism	Sulfolobus tokodaii
NCBI taxonomy ID ncbi_taxonomy_id	111955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	459

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ud9a1
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9a2
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9b1
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9b2
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9c1
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9c2
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9d1
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.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1ud9d2
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.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (4 domains)

Domain ID domain_id	1ud9A00
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	1ud9B00
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	1ud9C00
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	1ud9D00
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	79.400 Å
Unit-cell length b length_b	75.440 Å
Unit-cell length c length_c	88.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2380

Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii

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

DNA polymerase sliding clamp A

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

1ud9__assembly_1__model_1

1ud9__assembly_1__model_1 | I(q)

1ud9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii

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

DNA polymerase sliding clamp A

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

1ud9__assembly_1__model_1

1ud9__assembly_1__model_1 | I(q)

1ud9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)