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9smo

Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound ART5537

Method: X-RAY DIFFRACTION D_max: 71.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9smo
deposition_date	2025-09-08
title	Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound ART5537
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	22.73 Å
rg_electron	21.83 Å
i0	74210800.00
molecular_weight	43108.0 kDa
excluded_volume	40595 Å³
envelope_volume	69231 Å³
shell_volume	26050 Å³
envelope_diameter	72.2 Å
shell_rg	29.09 Å
envelope_rg	21.95 Å
shape_rg	21.79 Å
total_rg	22.52 Å
total_atoms	3215
n_residues	367
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	71.0 Å
rg_real	22.60 Å
rg_real_error	0.35 Å
i0_real	7.4210e+07
i0_real_error	8.8390e+05
rg_reciprocal	22.64 Å
i0_reciprocal	74210000.0000
total_estimate	0.9015
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.1 Å
skewness	0.166
kurtosis	-0.458
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	12550000.0000
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: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 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	A
atom_count	3265

MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	C

CGCTAGTCGTCAT

Entity 3 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 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1-(4-chloranyl-2,7-naphthyridin-1-yl)-5-oxidanyl-3-[(1~{S})-1-phenylethyl]-2~{H}-pyrido[2,1-f][1,2,4]triazine-4,6-dione
formula_weight	447.9 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	49

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6. Citations (1)

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length_a	69.705 Å
length_b	69.705 Å
length_c	181.759 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	2.199 Å
resolution_low	65.080 Å
r_factor	0.2404
r_work	0.2387
r_free	0.2706

fit	/app/data/saxs_computation/sm/9smo/9smo.fit
pddf	/app/data/pr_computation/sm/9smo/9smo.pr.out
profile	/app/data/saxs_computation/sm/9smo/9smo.dat

Crystal Structure of human exonuclease 1 (Exo1) with DNA and compound ART5537

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)