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9t4d

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R41A mutant in complex with 5-(PP)-IP5 (5-IP7)

Method: X-RAY DIFFRACTION D_max: 50.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t4d
deposition_date	2025-10-30
last_revision	2026-06-10
title	Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R41A mutant in complex with 5-(PP)-IP5 (5-IP7)
keywords	Inositol metabolism, phosphatase, NUDIX hydrolases, DIPP1, IP7, 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	15.83 Å
rg_electron	14.78 Å
i0	7651260.00
molecular_weight	18178.0 kDa
excluded_volume	21890 Å³
envelope_volume	25417 Å³
shell_volume	14273 Å³
envelope_diameter	50.2 Å
shell_rg	20.97 Å
envelope_rg	15.21 Å
shape_rg	14.78 Å
total_rg	15.84 Å
total_atoms	1257
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	50.5 Å
rg_real	15.73 Å
rg_real_error	0.27 Å
i0_real	7.6510e+06
i0_real_error	7.6400e+04
rg_reciprocal	15.74 Å
i0_reciprocal	7651000.0000
total_estimate	0.8920
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.8 Å
skewness	0.143
kurtosis	-0.405
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1756000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Diphosphoinositol polyphosphate phosphohydrolase 1
formula_weight	17029.2 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 R41A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1519

MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSAHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	(1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate
formula_weight	740.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	FLUORIDE ION
formula_weight	19.0 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	99.950 Å
length_b	99.950 Å
length_c	34.469 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	1.500 Å
resolution_low	86.559 Å
r_factor	—
r_work	0.1625
r_free	0.1848

fit	/app/data/saxs_computation/t4/9t4d/9t4d.fit
pddf	/app/data/pr_computation/t4/9t4d/9t4d.pr.out
profile	/app/data/saxs_computation/t4/9t4d/9t4d.dat