SAXSdb — 9ysf

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

Endonuclease/exonuclease/phosphatase family domain-containing protein 1

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 254–543	Not recorded	EDO 1,2-ETHANEDIOL × 8 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 25% w/v PEG3350	Resolution 1.59 Å R-free 0.204

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 9YSF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YI2 Human EEPD1 EEP domain dimer Deposited 2025-10-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–569（568 aa） Chain B 2–569（568 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9YXY Crystal structure of EEPD1 EEP domain dimer at pH 5.5 Deposited 2025-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 245–543（299 aa） Chain B 245–543（299 aa）	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；0.1 M Bis-Tris, pH 5.5, 25% PEG3350	Resolution 2.00 Å R-free 0.232

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EEPD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–293； UniProt 254–543

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	9ysf
Deposition date deposition_date	2025-10-17
Structure title title	Crystal structure of EEPD1 EEP domain dimer with Mg(II)
Keywords keywords	Endonuclease/Exonuclease/Phosphatase Fold, Dimerization, Replication stress response, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	18.95 Å
Radius of gyration Rg (electron density) rg_electron	17.74 Å
Forward intensity I(0) i0	15391600.00
Molecular weight molecular_weight	29572.0 kDa
Excluded volume excluded_volume	37052 Å³
Envelope volume envelope_volume	42501 Å³
Hydration-shell volume shell_volume	19575 Å³
Envelope diameter envelope_diameter	62.4 Å
Shell Rg shell_rg	24.58 Å
Envelope Rg envelope_rg	18.16 Å
Shape Rg shape_rg	17.73 Å
Total Rg total_rg	18.78 Å
Total atoms total_atoms	4151
Residues n_residues	262
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	62.7 Å
Rg (real space) rg_real	18.82 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.5390e+07
I(0) uncertainty (real space) i0_real_error	2.1620e+05
Rg (reciprocal space) rg_reciprocal	18.84 Å
I(0) (reciprocal space) i0_reciprocal	15390000.0000
Solution quality estimate total_estimate	0.7957
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.352
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3553000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Endonuclease/exonuclease/phosphatase family domain-containing protein 1
Molecular weight formula_weight	32311.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4343

GPMTRDGRPVLRLATWNLQGCSVEKANNPGVREVVCMTLLENSIKLLAVQELLDREALEKFCTELNQPTLPNIRKWKGPRGCWKAVVAEKPSNQLQKGAGYAGFLWDAAAGMELRDAGSQESSPSNGHGKLAGPSPYLGRFKVGSHDLTLVNLHLAALTLLGSENPSKNHSDGHRLASFAQTLQETLKGEKDVIILGDFGQGPDSNDYDILRKEKFHHLIPAHTFTNISTKNPQGSKSLDNIWISKSLKKVFTGHWAVVREGLTNPWIPDNWSWGGVASEHCPVLAEFYTEKD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

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8. Citations (1)

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Unit-cell length a length_a	87.318 Å
Unit-cell length b length_b	48.210 Å
Unit-cell length c length_c	73.695 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	38.720 Å
R factor r_factor	0.1677
R_work r_work	0.1660
R_free r_free	0.2043

fit	/app/data/saxs_computation/ys/9ysf/9ysf.fit
pddf	/app/data/pr_computation/ys/9ysf/9ysf.pr.out
profile	/app/data/saxs_computation/ys/9ysf/9ysf.dat

Crystal structure of EEPD1 EEP domain dimer with Mg(II)

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

Endonuclease/exonuclease/phosphatase family domain-containing protein 1

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