← Back to search

9rfd

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

Method: X-RAY DIFFRACTION D_max: 89.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9rfd
deposition_date	2025-06-04
title	Human ADP-ribosylhydrolase 3 (ARH3) in complex with ADP
keywords	ADP-ribosylation, ADP-ribosylhydrolase, ARH3, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	28.69 Å
rg_electron	28.07 Å
i0	94851300.00
molecular_weight	73932.0 kDa
excluded_volume	91326 Å³
envelope_volume	109770 Å³
shell_volume	32448 Å³
envelope_diameter	94.9 Å
shell_rg	35.49 Å
envelope_rg	28.17 Å
shape_rg	28.07 Å
total_rg	28.76 Å
total_atoms	5185
n_residues	680
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

▼

3. P(r) Analysis (GNOM)

dmax	89.5 Å
rg_real	28.73 Å
rg_real_error	0.59 Å
i0_real	9.4850e+07
i0_real_error	1.3100e+06
rg_reciprocal	28.72 Å
i0_reciprocal	94850000.0000
total_estimate	0.8922
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.351
kurtosis	-0.562
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	34080000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.862

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

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	5764

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	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	537

▶

6. Citations (1)

▶

length_a	44.790 Å
length_b	65.760 Å
length_c	69.920 Å
angle_alpha	116.40 °
angle_beta	94.79 °
angle_gamma	103.73 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.850 Å
resolution_low	34.765 Å
r_factor	0.1620
r_work	0.1611
r_free	0.1938

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