Crystal structure of TBC domain of human TBC1D17

Method: X-RAY DIFFRACTION D_max: 106.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9si7
deposition_date	2025-08-28
last_revision	2026-05-06
title	Crystal structure of TBC domain of human TBC1D17
keywords	GTP-ase activating protein, Rab-GAP, PROTEIN BINDING; PROTEIN BINDING
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	33.49 Å
rg_electron	33.14 Å
i0	75011100.00
molecular_weight	70272.0 kDa
excluded_volume	88458 Å³
envelope_volume	112730 Å³
shell_volume	29645 Å³
envelope_diameter	106.4 Å
shell_rg	38.20 Å
envelope_rg	32.97 Å
shape_rg	33.12 Å
total_rg	33.64 Å
total_atoms	4948
n_residues	604
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	106.4 Å
rg_real	33.65 Å
rg_real_error	0.80 Å
i0_real	7.5010e+07
i0_real_error	1.1700e+06
rg_reciprocal	33.56 Å
i0_reciprocal	75000000.0000
total_estimate	0.8579
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.4 Å
skewness	0.367
kurtosis	-0.755
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	12310000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.764; Smooth: 0.800

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	97.977 Å
length_b	97.977 Å
length_c	82.276 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32
int_tables_number	145
crystal_system	—

resolution	3.340 Å
resolution_low	48.000 Å
r_factor	0.2239
r_work	0.2146
r_free	0.2868

description	TBC1 domain family member 17
formula_weight	36840.3 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	4973

Crystal structure of TBC domain of human TBC1D17

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	25

fit	/app/data/saxs_computation/si/9si7/9si7.fit
pddf	/app/data/pr_computation/si/9si7/9si7.pr.out
profile	/app/data/saxs_computation/si/9si7/9si7.dat