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9yxy

Crystal structure of EEPD1 EEP domain dimer at pH 5.5

Method: X-RAY DIFFRACTION D_max: 96.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yxy
deposition_date	2025-10-27
title	Crystal structure of EEPD1 EEP domain dimer at pH 5.5
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	29.57 Å
rg_electron	29.25 Å
i0	54391100.00
molecular_weight	58275.0 kDa
excluded_volume	73091 Å³
envelope_volume	90620 Å³
shell_volume	26678 Å³
envelope_diameter	98.1 Å
shell_rg	35.45 Å
envelope_rg	29.04 Å
shape_rg	29.23 Å
total_rg	29.93 Å
total_atoms	8186
n_residues	526
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	96.8 Å
rg_real	29.75 Å
rg_real_error	0.75 Å
i0_real	5.4390e+07
i0_real_error	7.9990e+05
rg_reciprocal	29.68 Å
i0_reciprocal	54390000.0000
total_estimate	0.8369
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.9 Å
skewness	0.428
kurtosis	-0.613
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	16020000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.824

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Endonuclease/exonuclease/phosphatase family domain-containing protein 1
formula_weight	33213.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8446

GPMRPSVEAFGGTRDGRPVLRLATWNLQGCSVEKANNPGVREVVCMTLLENSIKLLAVQELLDREALEKFCTELNQPTLPNIRKWKGPRGCWKAVVAEKPSNQLQKGAGYAGFLWDAAAGMELRDAGSQESSPSNGHGKLAGPSPYLGRFKVGSHDLTLVNLHLAALTLLGSENPSKNHSDGHRLASFAQTLQETLKGEKDVIILGDFGQGPDSNDYDILRKEKFHHLIPAHTFTNISTKNPQGSKSLDNIWISKSLKKVFTGHWAVVREGLTNPWIPDNWSWGGVASEHCPVLAEFYTEKD

Source

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

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	188

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6. Citations (1)

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length_a	38.943 Å
length_b	116.320 Å
length_c	121.483 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.000 Å
resolution_low	38.240 Å
r_factor	0.1963
r_work	0.1944
r_free	0.2323

fit	/app/data/saxs_computation/yx/9yxy/9yxy.fit
pddf	/app/data/pr_computation/yx/9yxy/9yxy.pr.out
profile	/app/data/saxs_computation/yx/9yxy/9yxy.dat