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9t7u

Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)

Method: X-RAY DIFFRACTION D_max: 122.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t7u
deposition_date	2025-11-11
title	Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)
keywords	;Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), protein copper binding, copper toxicity, copper homeostasis, Staphylococcus aureus, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	37.84 Å
rg_electron	37.59 Å
i0	331761000.00
molecular_weight	144920.0 kDa
excluded_volume	180170 Å³
envelope_volume	237540 Å³
shell_volume	52832 Å³
envelope_diameter	127.9 Å
shell_rg	43.47 Å
envelope_rg	37.50 Å
shape_rg	37.59 Å
total_rg	37.91 Å
total_atoms	10164
n_residues	1334
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	122.7 Å
rg_real	37.89 Å
rg_real_error	0.86 Å
i0_real	3.3180e+08
i0_real_error	5.7880e+06
rg_reciprocal	37.86 Å
i0_reciprocal	331800000.0000
total_estimate	0.6762
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	40.9 Å
skewness	0.340
kurtosis	-0.505
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	56230000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 0.996; Smooth: 0.805

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Glyceraldehyde-3-phosphate dehydrogenase 1
formula_weight	36320.8 kDa
ec_number	1.2.1.12
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	AAA,BBB,CCC,DDD
atom_count	10795

MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAELSK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	COPPER (I) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	631

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6. Citations (1)

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length_a	98.901 Å
length_b	98.901 Å
length_c	252.217 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.700 Å
resolution_low	46.830 Å
r_factor	—
r_work	0.1524
r_free	0.2094

fit	/app/data/saxs_computation/t7/9t7u/9t7u.fit
pddf	/app/data/pr_computation/t7/9t7u/9t7u.pr.out
profile	/app/data/saxs_computation/t7/9t7u/9t7u.dat