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9ysf

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

Method: X-RAY DIFFRACTION D_max: 62.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ysf
deposition_date	2025-10-17
title	Crystal structure of EEPD1 EEP domain dimer with Mg(II)
keywords	Endonuclease/Exonuclease/Phosphatase Fold, Dimerization, Replication stress response, DNA BINDING PROTEIN; DNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	18.95 Å
rg_electron	17.74 Å
i0	15391600.00
molecular_weight	29572.0 kDa
excluded_volume	37052 Å³
envelope_volume	42501 Å³
shell_volume	19575 Å³
envelope_diameter	62.4 Å
shell_rg	24.58 Å
envelope_rg	18.16 Å
shape_rg	17.73 Å
total_rg	18.78 Å
total_atoms	4151
n_residues	262
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	62.7 Å
rg_real	18.82 Å
rg_real_error	0.35 Å
i0_real	1.5390e+07
i0_real_error	2.1620e+05
rg_reciprocal	18.84 Å
i0_reciprocal	15390000.0000
total_estimate	0.7957
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.128
kurtosis	-0.352
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	3553000.0000
n_real_points	73
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Endonuclease/exonuclease/phosphatase family domain-containing protein 1
formula_weight	32311.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4343

GPMTRDGRPVLRLATWNLQGCSVEKANNPGVREVVCMTLLENSIKLLAVQELLDREALEKFCTELNQPTLPNIRKWKGPRGCWKAVVAEKPSNQLQKGAGYAGFLWDAAAGMELRDAGSQESSPSNGHGKLAGPSPYLGRFKVGSHDLTLVNLHLAALTLLGSENPSKNHSDGHRLASFAQTLQETLKGEKDVIILGDFGQGPDSNDYDILRKEKFHHLIPAHTFTNISTKNPQGSKSLDNIWISKSLKKVFTGHWAVVREGLTNPWIPDNWSWGGVASEHCPVLAEFYTEKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

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6. Citations (1)

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length_a	87.318 Å
length_b	48.210 Å
length_c	73.695 Å
angle_alpha	90.00 °
angle_beta	110.02 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.590 Å
resolution_low	38.720 Å
r_factor	0.1677
r_work	0.1660
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