SAXSdb — 5omb

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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 4	DNA damage checkpoint protein LCD1 × 2 （Q6CUV9） CHLORIDE ION × 3 1,2-ETHANEDIOL × 1 water × 4	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 A； PDBConstruct 3–134； UniProt 1–132 Author chain B； PDBConstruct 3–134； UniProt 1–132

DNA damage checkpoint protein LCD1

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

UniProt Q6CUV9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Replication factor A protein 1 × 2 （P22336） CHLORIDE ION × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCD1_KLULA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–111； UniProt 1–109 Author chain D； PDBConstruct 3–111； UniProt 1–109

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	5omb
Deposition date deposition_date	2017-07-28
Structure title title	Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain
Keywords keywords	Oligonucleotide-binding fold, coiled-coil domain, complex, nucleus, 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.

5omb__assembly_1__model_1

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

Download this curve (.dat)

5omb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5omb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.89 Å
Rg (electron density)	44.67 Å
Total Rg	44.05 Å
Atom count	3662
Residues	440
Excluded volume	65233 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5omb__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Replication factor A protein 1
Molecular weight formula_weight	15616.8 kDa
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	3915

GPMSSVQLSRGDFHSIFTNKQRYDNPTGGVYQVYNTRKSDGANSNRKNLIMISDGIYHMKALLRNQAASKFQSMELQRGDIIRVIIAEPAIVRERKKYVLLVDDFELVQSRADMVNQTSTFLDNYFSEHPNETL

Source Source

Source organism organism	Saccharomyces cerevisiae
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	DNA damage checkpoint protein LCD1
Molecular weight formula_weight	12946.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPMADLWDDNDDDDDILELVNRPPMSQMAVPIKPPESQAEQLMKAKGEVGVLRQKLSMLEKTLREHDDNQKKLESSLKSSHEEEVTKLKIELERLEDERKFMLLEQKHLFT

Source Source

Source organism organism	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Common name common_name	Yeast
NCBI taxonomy ID ncbi_taxonomy_id	284590
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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Unit-cell length a length_a	34.050 Å
Unit-cell length b length_b	94.940 Å
Unit-cell length c length_c	170.470 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	48.760 Å
R factor r_factor	0.1871
R_work r_work	0.1854
R_free r_free	0.2204

Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain

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

5omb__assembly_1__model_1

5omb__assembly_1__model_1 | I(q)

5omb__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)

Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain

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

5omb__assembly_1__model_1

5omb__assembly_1__model_1 | I(q)

5omb__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)