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9qw2

Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand

Method: X-RAY DIFFRACTION D_max: 76.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qw2
deposition_date	2025-04-14
title	Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand
keywords	;Trimeric recombinant collectin fragment, neck+CRD, alpha-helical coiled-coil, carbohydrate recognition domain, lectin, sugar binding protein, surfactant protein ;; SURFACTANT 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	26.22 Å
rg_electron	24.83 Å
i0	42470300.00
molecular_weight	48966.0 kDa
excluded_volume	60619 Å³
envelope_volume	73252 Å³
shell_volume	25377 Å³
envelope_diameter	78.3 Å
shell_rg	31.28 Å
envelope_rg	24.97 Å
shape_rg	24.77 Å
total_rg	25.74 Å
total_atoms	3425
n_residues	439
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	76.0 Å
rg_real	26.08 Å
rg_real_error	0.37 Å
i0_real	4.2470e+07
i0_real_error	5.5520e+05
rg_reciprocal	26.12 Å
i0_reciprocal	42470000.0000
total_estimate	0.9107
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	38.6 Å
skewness	0.014
kurtosis	-0.797
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	13640000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Pulmonary surfactant-associated protein D
formula_weight	18835.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	3765

GSPGLKGDKGIPGDKGAKGESGLPDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

Source

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

Entity 2 branched

description	L-glycero-alpha-D-manno-heptopyranose-(1-3)-4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose
formula_weight	482.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	9

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	335

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6. Citations (1)

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length_a	55.439 Å
length_b	108.179 Å
length_c	55.650 Å
angle_alpha	90.00 °
angle_beta	90.90 °
angle_gamma	90.00 °
z_pdb	6

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.920 Å
resolution_low	55.493 Å
r_factor	—
r_work	0.1805
r_free	0.2119

fit	/app/data/saxs_computation/qw/9qw2/9qw2.fit
pddf	/app/data/pr_computation/qw/9qw2/9qw2.pr.out
profile	/app/data/saxs_computation/qw/9qw2/9qw2.dat

Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand

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