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9t4i

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S mutant in complex with IP6

Method: X-RAY DIFFRACTION D_max: 51.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t4i
deposition_date	2025-10-30
last_revision	2026-06-10
title	Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S 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	15.84 Å
rg_electron	14.72 Å
i0	6755510.00
molecular_weight	17566.0 kDa
excluded_volume	21445 Å³
envelope_volume	24940 Å³
shell_volume	14111 Å³
envelope_diameter	51.3 Å
shell_rg	20.86 Å
envelope_rg	15.12 Å
shape_rg	14.72 Å
total_rg	15.85 Å
total_atoms	1221
n_residues	145
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	51.0 Å
rg_real	15.73 Å
rg_real_error	0.23 Å
i0_real	6.7560e+06
i0_real_error	7.4740e+04
rg_reciprocal	15.75 Å
i0_reciprocal	6756000.0000
total_estimate	0.8877
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.7 Å
skewness	0.140
kurtosis	-0.395
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1686000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.989

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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	17045.2 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 R89S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1569

MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQESKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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	215

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6. Citations (1)

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length_a	34.288 Å
length_b	65.483 Å
length_c	78.949 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.408 Å
resolution_low	39.470 Å
r_factor	—
r_work	0.1695
r_free	0.2113

fit	/app/data/saxs_computation/t4/9t4i/9t4i.fit
pddf	/app/data/pr_computation/t4/9t4i/9t4i.pr.out
profile	/app/data/saxs_computation/t4/9t4i/9t4i.dat