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9t4m

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) N112S mutant in complex with IP6

Method: X-RAY DIFFRACTION D_max: 52.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t4m
deposition_date	2025-10-30
last_revision	2026-06-10
title	Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) N112S mutant in complex with IP6
keywords	Inositol metabolism, phosphatase, NUDIX hydrolases, DIPP1, IP6, 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	15.92 Å
rg_electron	14.81 Å
i0	7094020.00
molecular_weight	17964.0 kDa
excluded_volume	21925 Å³
envelope_volume	25574 Å³
shell_volume	14325 Å³
envelope_diameter	49.9 Å
shell_rg	21.05 Å
envelope_rg	15.24 Å
shape_rg	14.80 Å
total_rg	15.96 Å
total_atoms	1248
n_residues	148
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	52.9 Å
rg_real	15.82 Å
rg_real_error	0.32 Å
i0_real	7.0940e+06
i0_real_error	8.4740e+04
rg_reciprocal	15.83 Å
i0_reciprocal	7094000.0000
total_estimate	0.8769
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	20.1 Å
skewness	0.161
kurtosis	-0.386
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	2138000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Diphosphoinositol polyphosphate phosphohydrolase 1
formula_weight	17088.3 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 N112S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1569

MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVSIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	193

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6. Citations (1)

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length_a	100.131 Å
length_b	100.131 Å
length_c	34.060 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 61
int_tables_number	169
crystal_system	—

resolution	1.780 Å
resolution_low	50.070 Å
r_factor	—
r_work	0.1867
r_free	0.2421

fit	/app/data/saxs_computation/t4/9t4m/9t4m.fit
pddf	/app/data/pr_computation/t4/9t4m/9t4m.pr.out
profile	/app/data/saxs_computation/t4/9t4m/9t4m.dat