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9yh8

M17T Human DJ-1

Method: X-RAY DIFFRACTION D_max: 50.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yh8
deposition_date	2025-09-30
title	M17T Human DJ-1
keywords	PARK7, glyoxalase, cyclic phosphoglycerate anhydride hydrolase, 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	16.57 Å
rg_electron	15.19 Å
i0	7299400.00
molecular_weight	19881.0 kDa
excluded_volume	25065 Å³
envelope_volume	27851 Å³
shell_volume	15137 Å³
envelope_diameter	49.9 Å
shell_rg	21.48 Å
envelope_rg	15.56 Å
shape_rg	15.18 Å
total_rg	16.36 Å
total_atoms	2844
n_residues	187
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	50.1 Å
rg_real	16.41 Å
rg_real_error	0.21 Å
i0_real	7.2990e+06
i0_real_error	7.7590e+04
rg_reciprocal	16.43 Å
i0_reciprocal	7299000.0000
total_estimate	0.7755
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.035
kurtosis	-0.473
angular_range	— – 0.4800 Å⁻¹
current_alpha	0.0000
highest_alpha	1649000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 0.471; Positv: 1.000; Valcen: 0.977; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Parkinson disease protein 7
formula_weight	20169.2 kDa
ec_number	3.1.2.-,3.5.1.-,3.5.1.124
mutation	M17T
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3627

GSHMASKRALVILAKGAEETETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD

Source

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

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

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	297

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6. Citations (2)

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length_a	75.046 Å
length_b	75.046 Å
length_c	75.431 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.000 Å
resolution_low	37.520 Å
r_factor	0.1103
r_work	0.1097
r_free	0.1304

fit	/app/data/saxs_computation/yh/9yh8/9yh8.fit
pddf	/app/data/pr_computation/yh/9yh8/9yh8.pr.out
profile	/app/data/saxs_computation/yh/9yh8/9yh8.dat

M17T Human DJ-1

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