SAXSdb — 9tbj

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1. Structure Basics

entry_id	9tbj
deposition_date	2025-11-20
title	Leishmania mexicana secreted acid phosphatase
keywords	Leishmania, acid phosphatase, enzyme filaments, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	42.51 Å
rg_electron	42.45 Å
i0	339968000.00
molecular_weight	145790.0 kDa
excluded_volume	180100 Å³
envelope_volume	249470 Å³
shell_volume	51285 Å³
envelope_diameter	143.1 Å
shell_rg	45.13 Å
envelope_rg	42.02 Å
shape_rg	42.44 Å
total_rg	42.63 Å
total_atoms	10240
n_residues	1267
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	145.7 Å
rg_real	42.75 Å
rg_real_error	1.52 Å
i0_real	3.4000e+08
i0_real_error	6.0770e+06
rg_reciprocal	42.52 Å
i0_reciprocal	339900000.0000
total_estimate	0.8555
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	43.3 Å
skewness	0.434
kurtosis	-0.539
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	25950000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.858

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Secreted acid phosphatase 1 (SAP1)
formula_weight	62175.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	10259

MASRLVRVLAAAMLVAAAVSVDAHFVVRMVQVVHRHGARSALIDDNTTEICGTLYPCGELTGEGVEMVRAIGEFARSRYNNLSLVESPLFPSTRYNSSVVHTRSTHTQRTIQSATAFLRGLFQDDNFYPVVYSTNRTTETLLSTDAVPSVVARSWLDNPALHAALNPVIDEHLSWDAIQCAAKDAWVEGLCADYNARTSCVLDMYDVAAAFEAAGRLDNATNLKAVYPGLQEVNAAWFKYVFSWNHTSKLDLTQGSASQNLAQTVLANINAHRLSPSYNMFQYSAHDTTVTPLAVTFGDQGETTMRPPFAVTIFVELLQDTADASGWYVRLIRGNPVKAADGTYVFQESGIKAYCIDEAGNKYLAHTGICPLNNFRRMIDYSRPAVADGHCTMTQTQYSNMDCPPTIADNKSVPSRCWLYRYVCPSKACPDSYILSAVDHQCYPGSDVTNLTSSSSKSTSSSDVPSFKKPANWSPRVLSPERGRHIAGDIIRGVTNGVTIGAGVRKHDEYSRHRQQSRMDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPSGGCKLGLY

Source

organism	Leishmania mexicana
ncbi_taxonomy_id	5665
host_organism	Leishmania mexicana

Entity 2 branched

description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	nat
entity_count	2

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	nat
entity_count	7

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	nat
entity_count	6

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	nat
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.00 Å
resolution_method	—
num_particles	524666

fit	/app/data/saxs_computation/tb/9tbj/9tbj.fit
pddf	/app/data/pr_computation/tb/9tbj/9tbj.pr.out
profile	/app/data/saxs_computation/tb/9tbj/9tbj.dat

Leishmania mexicana secreted acid phosphatase

SAXS Profile

P(r) Distribution