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9rfe

Human ADP-ribosylhydrolase 3 (ARH3) in complex with an inhibitor

Method: X-RAY DIFFRACTION D_max: 94.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfe
deposition_date	2025-06-04
title	Human ADP-ribosylhydrolase 3 (ARH3) in complex with an inhibitor
keywords	ADP-ribosylation, ADP-ribosylhydrolase, ARH3, 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	28.42 Å
rg_electron	27.90 Å
i0	167188000.00
molecular_weight	67571.0 kDa
excluded_volume	64787 Å³
envelope_volume	107090 Å³
shell_volume	31976 Å³
envelope_diameter	92.6 Å
shell_rg	35.22 Å
envelope_rg	27.83 Å
shape_rg	27.91 Å
total_rg	28.40 Å
total_atoms	5099
n_residues	681
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	94.1 Å
rg_real	28.46 Å
rg_real_error	0.84 Å
i0_real	1.6720e+08
i0_real_error	2.7190e+06
rg_reciprocal	28.45 Å
i0_reciprocal	167200000.0000
total_estimate	0.8048
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.331
kurtosis	-0.610
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	37980000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	ADP-ribosylhydrolase ARH3
formula_weight	38201.8 kDa
ec_number	3.5.1.-,3.2.1.143,3.2.2.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5466

SMAGAARSLSRFRGCLAGALLGDCVGSFYEAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS

Source

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

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	2-[(2~{E})-2-[1-(4-aminophenyl)ethylidene]hydrazinyl]-6-methyl-1~{H}-pyrimidin-4-one
formula_weight	257.3 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	340

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6. Citations (1)

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length_a	45.220 Å
length_b	66.020 Å
length_c	70.860 Å
angle_alpha	115.28 °
angle_beta	96.39 °
angle_gamma	104.33 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.850 Å
resolution_low	35.995 Å
r_factor	—
r_work	0.1627
r_free	0.2029

fit	/app/data/saxs_computation/rf/9rfe/9rfe.fit
pddf	/app/data/pr_computation/rf/9rfe/9rfe.pr.out
profile	/app/data/saxs_computation/rf/9rfe/9rfe.dat