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9q3h

GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC

Method: X-RAY DIFFRACTION D_max: 61.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q3h
deposition_date	2025-08-18
last_revision	2025-09-10
title	GspB Siglec domain bound to sialyl T antigen linked to serine-FMOC
keywords	SLBR, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	19.55 Å
rg_electron	18.70 Å
i0	15621900.00
molecular_weight	29506.0 kDa
excluded_volume	36711 Å³
envelope_volume	42296 Å³
shell_volume	19027 Å³
envelope_diameter	64.8 Å
shell_rg	24.67 Å
envelope_rg	18.71 Å
shape_rg	18.70 Å
total_rg	19.50 Å
total_atoms	3942
n_residues	247
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	61.6 Å
rg_real	19.43 Å
rg_real_error	0.31 Å
i0_real	1.5620e+07
i0_real_error	1.9270e+05
rg_reciprocal	19.45 Å
i0_reciprocal	15620000.0000
total_estimate	0.8985
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.140
kurtosis	-0.466
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	4139000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Platelet binding protein GspB
formula_weight	13952.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4117

GPGSDTERPVVNVPSEITVYRGESFEYFATVTDNSNAFDLAKTVVRWLYSNQPGRGTEWLQYSVTQVGNQLKVRIFGNVPIDTTIGDYTRYVVATDAAGNVNATQTEMGNAAVDKTSVNGQFKLIIR

Source

organism	Streptococcus
ncbi_taxonomy_id	1301
host_organism	Escherichia coli

Entity 2 branched

description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
formula_weight	674.6 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	Fluorenylmethyloxycarbonyl chloride
formula_weight	258.7 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SERINE
formula_weight	105.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	133

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6. Citations (1)

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length_a	37.987 Å
length_b	38.111 Å
length_c	47.054 Å
angle_alpha	70.20 °
angle_beta	68.01 °
angle_gamma	62.08 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.890 Å
resolution_low	23.100 Å
r_factor	0.1851
r_work	0.1837
r_free	0.2109

fit	/app/data/saxs_computation/q3/9q3h/9q3h.fit
pddf	/app/data/pr_computation/q3/9q3h/9q3h.pr.out
profile	/app/data/saxs_computation/q3/9q3h/9q3h.dat