SAXSdb — 8b4j

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

Replication factor A protein 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA damage checkpoint protein LCD1 × 1 （Q04377） 1,2-ETHANEDIOL × 1 ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFA1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain O； PDBConstruct 3–134； UniProt 1–132

DNA damage checkpoint protein LCD1

Saccharomyces cerevisiae

UniProt Q04377

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Replication factor A protein 1 × 1 （P22336） 1,2-ETHANEDIOL × 1 ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCD1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–21； UniProt 4–24

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	8b4j
Deposition date deposition_date	2022-09-20
Structure title title	Rfa1-N-terminal domain in complex with phosphorylated Ddc2
Keywords keywords	Complex, OB-fold, Replication Protein A, DNA damage response, Replication, PROTEIN BINDING; PROTEIN BINDING
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.

8b4j__assembly_1__model_1

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

Download this curve (.dat)

8b4j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8b4j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.77 Å
Rg (electron density)	14.15 Å
Total Rg	15.50 Å
Atom count	2178
Residues	139
Excluded volume	19710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8b4j__assembly_1__model_1`	dimeric （2）	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	Replication factor A protein 1
Molecular weight formula_weight	15382.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O
Atom count atom_count	2250

GPMSSVQLSRGDFHSIFTNKQRYDNPTGGVYQVYNTRKSDGANSNRKNLIMISDGIYHMKALLRNQAASKFQSMELQRGDIIRVIIAEPAIVRERKKYVLLVDDFELVQSRADMVNQTSTFLDNYFSEHPNETL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	DNA damage checkpoint protein LCD1
Molecular weight formula_weight	2407.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ETVGEFSSDDDDDILLELGTR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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Unit-cell length a length_a	39.996 Å
Unit-cell length b length_b	39.996 Å
Unit-cell length c length_c	282.062 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	47.010 Å
R factor r_factor	0.1933
R_work r_work	0.1912
R_free r_free	0.2294

Rfa1-N-terminal domain in complex with phosphorylated Ddc2

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

Replication factor A protein 1

State in the Current Structure

Other States of the Same Protein in the Database

DNA damage checkpoint protein LCD1

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

8b4j__assembly_1__model_1

8b4j__assembly_1__model_1 | I(q)

8b4j__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 (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

7. Citations (1)

Rfa1-N-terminal domain in complex with phosphorylated Ddc2

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

Replication factor A protein 1

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 damage checkpoint protein LCD1

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

8b4j__assembly_1__model_1

8b4j__assembly_1__model_1 | I(q)

8b4j__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 (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

7. Citations (1)