SAXSdb — 5msn

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

DCC1 protein

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 90–380	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M potassium sodium tartrate and 18% PEG 3,350	Resolution 2.00 Å R-free 0.230
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 90–380	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M potassium sodium tartrate and 18% PEG 3,350	Resolution 2.00 Å R-free 0.230
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 90–380	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M potassium sodium tartrate and 18% PEG 3,350	Resolution 2.00 Å R-free 0.230
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 90–380	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2M potassium sodium tartrate and 18% PEG 3,350	Resolution 2.00 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5MSN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5MSM Structure of the Dcc1-Ctf8-Ctf18C Trimer Deposited 2017-01-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Bis-Tris Propane pH 6.3, 0.2M NaBr and 17% PEG 3,350	Resolution 2.29 Å R-free 0.260
5MSM Structure of the Dcc1-Ctf8-Ctf18C Trimer Deposited 2017-01-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Bis-Tris Propane pH 6.3, 0.2M NaBr and 17% PEG 3,350	Resolution 2.29 Å R-free 0.260
5OKC Crystal structure of the Ctf18-1-8 module from Ctf18-RFC Deposited 2017-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–380（380 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；16% PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M potassium nitrate	Resolution 2.30 Å R-free 0.260
5OKC Crystal structure of the Ctf18-1-8 module from Ctf18-RFC Deposited 2017-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–380（380 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；16% PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M potassium nitrate	Resolution 2.30 Å R-free 0.260
5OKI Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon Deposited 2017-07-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 10000, 0.1 M MES pH 6.5, 0.2 M ammonium chloride	Resolution 4.50 Å R-free 0.312
5OKI Crystal structure of the Ctf18-1-8 module from Ctf18-RFC in complex with a 63 kDa fragment of DNA Polymerase epsilon Deposited 2017-07-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 10000, 0.1 M MES pH 6.5, 0.2 M ammonium chloride	Resolution 4.50 Å R-free 0.312
6S1C P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex Deposited 2019-06-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 14% PEG 20000, 0.1 M HEPES pH 7.0	Resolution 6.10 Å R-free 0.333
6S1C P3221 crystal form of the Ctf18-1-8/Pol2(1-528) complex Deposited 2019-06-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–380（380 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M NaCl, 14% PEG 20000, 0.1 M HEPES pH 7.0	Resolution 6.10 Å R-free 0.333
6S2E Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase epsilon Deposited 2019-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–380（380 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6S2F Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase epsilon (Class 2) Deposited 2019-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–380（380 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
8TW9 Cryo-EM structure of S. cerevisiae PolE-Ctf18-8-1-DNA Deposited 2023-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–380（380 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8TWA Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex Deposited 2023-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain B 1–380（380 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCC1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–293； UniProt 90–380 Author chain B； PDBConstruct 3–293； UniProt 90–380 Author chain C； PDBConstruct 3–293； UniProt 90–380 Author chain D； PDBConstruct 3–293； UniProt 90–380

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	5msn
Deposition date deposition_date	2017-01-05
Structure title title	Structure of the Dcc1 Protein
Keywords keywords	winged-helix, DNA repair, cell cycle; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.77 Å
Radius of gyration Rg (electron density) rg_electron	34.99 Å
Forward intensity I(0) i0	199392000.00
Molecular weight molecular_weight	118560.0 kDa
Excluded volume excluded_volume	150530 Å³
Envelope volume envelope_volume	200200 Å³
Hydration-shell volume shell_volume	47340 Å³
Envelope diameter envelope_diameter	112.1 Å
Shell Rg shell_rg	41.96 Å
Envelope Rg envelope_rg	34.42 Å
Shape Rg shape_rg	34.98 Å
Total Rg total_rg	35.53 Å
Total atoms total_atoms	8358
Residues n_residues	1025
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	113.7 Å
Rg (real space) rg_real	35.71 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	1.9940e+08
I(0) uncertainty (real space) i0_real_error	3.6570e+06
Rg (reciprocal space) rg_reciprocal	35.75 Å
I(0) (reciprocal space) i0_reciprocal	199400000.0000
Solution quality estimate total_estimate	0.9049
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.615
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33510000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	68.682 Å
Unit-cell length b length_b	100.697 Å
Unit-cell length c length_c	83.495 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.67 °
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	2.002 Å
Low-resolution limit resolution_low	29.357 Å
R factor r_factor	0.1912
R_work r_work	0.1892
R_free r_free	0.2301

Description description	DCC1 protein
Molecular weight formula_weight	33790.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8931

Structure of the Dcc1 Protein

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

DCC1 protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae S288c
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	573

fit	/app/data/saxs_computation/ms/5msn/5msn.fit
pddf	/app/data/pr_computation/ms/5msn/5msn.pr.out
profile	/app/data/saxs_computation/ms/5msn/5msn.dat