SAXSdb — 5oki

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

DNA polymerase epsilon catalytic subunit A

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P21951

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 8 × 1 （P38877） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 8 × 1 （P38877） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOE_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–524； UniProt 1–524 Author chain B； PDBConstruct 1–524； UniProt 1–524

Sister chromatid cohesion protein DCC1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P25559

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Chromosome transmission fidelity protein 8 × 1 （P38877） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Chromosome transmission fidelity protein 8 × 1 （P38877） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCC1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–380； UniProt 1–380 Author chain G； PDBConstruct 1–380； UniProt 1–380

Chromosome transmission fidelity protein 8

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38877

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 18 × 1 （P49956）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTF8_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–133； UniProt 1–133 Author chain H； PDBConstruct 1–133； UniProt 1–133

Chromosome transmission fidelity protein 18

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P49956

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 8 × 1 （P38877）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） Sister chromatid cohesion protein DCC1 × 1 （P25559） Chromosome transmission fidelity protein 8 × 1 （P38877）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTF18_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–26； UniProt 715–740 Author chain I； PDBConstruct 1–26； UniProt 715–740

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	5oki
Deposition date deposition_date	2017-07-25
Structure title title	Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon
Keywords keywords	Clamp loader DNA-binding protein DNA polymerase Winged-helix domain, REPLICATION; REPLICATION
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.

5oki__assembly_1__model_1

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

Download this curve (.dat)

5oki__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5oki__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.81 Å
Rg (electron density)	39.58 Å
Total Rg	39.85 Å
Atom count	7887
Residues	975
Excluded volume	141330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5oki__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5oki__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	DNA polymerase epsilon catalytic subunit A
Molecular weight formula_weight	59749.2 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D290A. E292A
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	15910

MMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGGNSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQA

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Sister chromatid cohesion protein DCC1
Molecular weight formula_weight	44133.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MSINLHSAPEYDPSYKLIQLTPELLDIIQDPVQNHQLRFKSLDKDKSEVVLCSHDKTWVLKQRKHSNTVLLMREFVPEQPITFDETLLFGLSKPYMDVVGFAKTESEFETRETHGELNLNSVPIYNGELDFSDKIMKRSSTKVIGTLEELLENSPCSALEGISKWHKIGGSVKDGVLCILSQDFLFKALHVLLMSAMAESLDLQHLNVEDTHHAVGKDIEDEFNPYTREIIETVLNKFAVQEQEAENNTWRLRIPFIAQWYGIQALRKYVSGISMPIDEFLIKWKSLFPPFFPCDIDIDMLRGYHFKPTDKTVQYIAKSTLPMDPKERFKVLFRLQSQWDLEDIKPLIEELNSRGMKIDSFIMKYARRKRLGKKTVVTSR

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Chromosome transmission fidelity protein 8
Molecular weight formula_weight	15189.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPSVDIDASQWQKLTQSREKQTTVITPLGMMMLEIQGELELPKDFASLARRDSPNEGRFSEQDGETLIRFGSLQIDGERATLFVGKKQRLLGKVTKLDVPMGIMHFNSKDNKVELVDVMKYKVIFKDRPLPIM

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Chromosome transmission fidelity protein 18
Molecular weight formula_weight	3171.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,I

TVKIWVKYNEGFSNAVRKNVTWNNLW

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

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Unit-cell length a length_a	121.678 Å
Unit-cell length b length_b	145.826 Å
Unit-cell length c length_c	378.752 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	4.500 Å
Low-resolution limit resolution_low	47.724 Å
R factor r_factor	0.2935
R_work r_work	0.2926
R_free r_free	0.3121

Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon

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

DNA polymerase epsilon catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Sister chromatid cohesion protein DCC1

State in the Current Structure

Other States of the Same Protein in the Database

Chromosome transmission fidelity protein 8

State in the Current Structure

Other States of the Same Protein in the Database

Chromosome transmission fidelity protein 18

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

5oki__assembly_1__model_1

5oki__assembly_1__model_1 | I(q)

5oki__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon

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

DNA polymerase epsilon catalytic subunit 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

Sister chromatid cohesion protein DCC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromosome transmission fidelity protein 8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromosome transmission fidelity protein 18

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

5oki__assembly_1__model_1

5oki__assembly_1__model_1 | I(q)

5oki__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)