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9seb

Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound 20

Method: X-RAY DIFFRACTION D_max: 70.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9seb
deposition_date	2025-08-15
title	Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound 20
keywords	Exonuclease, HYDROLASE; HYDROLASE
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	22.65 Å
rg_electron	21.73 Å
i0	73198900.00
molecular_weight	42846.0 kDa
excluded_volume	40380 Å³
envelope_volume	68304 Å³
shell_volume	25845 Å³
envelope_diameter	72.0 Å
shell_rg	28.85 Å
envelope_rg	21.81 Å
shape_rg	21.65 Å
total_rg	22.47 Å
total_atoms	3212
n_residues	366
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	70.8 Å
rg_real	22.52 Å
rg_real_error	0.31 Å
i0_real	7.3200e+07
i0_real_error	8.5700e+05
rg_reciprocal	22.55 Å
i0_reciprocal	73200000.0000
total_estimate	0.9026
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.158
kurtosis	-0.464
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	11950000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	;DNA (5'-D(CP(GS)PCPTPAPGPTPCPGPTPCPAP*(PST))-3') ;
formula_weight	3974.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A
atom_count	3301

CGCTAGTCGTCAT

Entity 2 polymer

description	;DNA (5'-D(PAP(SC)PGPAPCPTPAPGPCP(GS))-3') ;
formula_weight	3086.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

ACGACTAGCG

Entity 3 polymer

description	Exonuclease 1
formula_weight	40354.8 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	1-(5-chloranyl-3-methyl-pyridin-2-yl)-5-oxidanyl-3-[(1~{S})-1-phenylethyl]-2~{H}-pyrido[2,1-f][1,2,4]triazine-4,6-dione
formula_weight	410.9 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	nat
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	88

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6. Citations (1)

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length_a	69.836 Å
length_b	69.836 Å
length_c	181.661 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.900 Å
resolution_low	65.190 Å
r_factor	0.2392
r_work	0.2360
r_free	0.2745

fit	/app/data/saxs_computation/se/9seb/9seb.fit
pddf	/app/data/pr_computation/se/9seb/9seb.pr.out
profile	/app/data/saxs_computation/se/9seb/9seb.dat

Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound 20

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)