← Back to search

9xzx

Staphylococcal Enterotoxin C in complex with NB C107 and NB C112

Method: ELECTRON MICROSCOPY D_max: 97.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9xzx
deposition_date	2025-08-27
title	Staphylococcal Enterotoxin C in complex with NB C107 and NB C112
keywords	Nanobody, VHH, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.00 Å
rg_electron	25.36 Å
i0	48694800.00
molecular_weight	53125.0 kDa
excluded_volume	65946 Å³
envelope_volume	80267 Å³
shell_volume	27484 Å³
envelope_diameter	102.7 Å
shell_rg	31.53 Å
envelope_rg	25.68 Å
shape_rg	25.33 Å
total_rg	26.13 Å
total_atoms	7356
n_residues	474
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

▼

3. P(r) Analysis (GNOM)

dmax	97.9 Å
rg_real	26.12 Å
rg_real_error	0.79 Å
i0_real	4.8690e+07
i0_real_error	6.9340e+05
rg_reciprocal	26.08 Å
i0_reciprocal	48690000.0000
total_estimate	0.8141
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.548
kurtosis	0.080
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	16880000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.602; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.779; Smooth: 0.994

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Enterotoxin type C-2
formula_weight	27278.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7356

PDPTPDELHKSSEFTGTMGNMKYLYDDHYVSATKVMSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDNVGKVTGGKTCMYGGITKHEGNHFDNGNLQNVLIRVYENKRNTISFEVQTDKKSVTAQELDIKARNFLINKKNLYEFNSSPYETGYIKFIENNGNTFWYDMMPAPGDKFDQSKYLMMYNDNKTVDSKSVKIEVHLTTKNG

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 polymer

description	NB C107
formula_weight	12440.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLVESGGGLVQPGGSLRLSCAPSGSTSGIYASGWYRQVPGKPQEWLADISRGGSTKYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTATYYCRVIDTLGAEYRGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 3 polymer

description	NB C112
formula_weight	13691.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

QVQLVESGGGLVQAGGSLRLSCTASERMYGIEMGWFRQAPGKERELVAAITWSGVVSHLQESVKGRFTISRDNPKKTVYLQMNSLKPEDTATYYCAGHRLQWASGYTRHDYGSWGQGTQVTVSS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

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	—

resolution	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	189726

fit	/app/data/saxs_computation/xz/9xzx/9xzx.fit
pddf	/app/data/pr_computation/xz/9xzx/9xzx.pr.out
profile	/app/data/saxs_computation/xz/9xzx/9xzx.dat

Staphylococcal Enterotoxin C in complex with NB C107 and NB C112

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)