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9t4f

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) E108N mutant

Method: X-RAY DIFFRACTION D_max: 51.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t4f
deposition_date	2025-10-30
last_revision	2026-06-10
title	Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) E108N mutant
keywords	Inositol metabolism, phosphatase, NUDIX hydrolases, DIPP1, 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	16.04 Å
rg_electron	14.64 Å
i0	5798700.00
molecular_weight	16693.0 kDa
excluded_volume	20629 Å³
envelope_volume	23950 Å³
shell_volume	13686 Å³
envelope_diameter	53.7 Å
shell_rg	20.69 Å
envelope_rg	15.02 Å
shape_rg	14.63 Å
total_rg	15.82 Å
total_atoms	1172
n_residues	143
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	51.8 Å
rg_real	15.91 Å
rg_real_error	0.31 Å
i0_real	5.7990e+06
i0_real_error	6.7060e+04
rg_reciprocal	15.93 Å
i0_reciprocal	5799000.0000
total_estimate	0.6691
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	21.0 Å
skewness	0.091
kurtosis	-0.399
angular_range	— – 0.4950 Å⁻¹
current_alpha	0.0000
highest_alpha	1255000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Diphosphoinositol polyphosphate phosphohydrolase 1
formula_weight	17100.4 kDa
ec_number	3.6.1.52,3.6.1.61,3.6.1.10,3.6.1.62,3.6.1.59
mutation	Deletion of the last 24 C-terminal residues (149-172) and E108N
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1387

MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWNDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (1)

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length_a	59.259 Å
length_b	59.259 Å
length_c	153.230 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	1.426 Å
resolution_low	51.320 Å
r_factor	—
r_work	0.1864
r_free	0.2185

fit	/app/data/saxs_computation/t4/9t4f/9t4f.fit
pddf	/app/data/pr_computation/t4/9t4f/9t4f.pr.out
profile	/app/data/saxs_computation/t4/9t4f/9t4f.dat

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) E108N mutant

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