The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site

Method: X-RAY DIFFRACTION D_max: 71.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e9l
deposition_date	2000-10-21
title	The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site
keywords	MACROPHAGE SECRETORY PROTEIN, INFLAMMATION, LECTIN, INDUCIBLE, SECRETORY; MACROPHAGE SECRETORY 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	21.36 Å
rg_electron	20.20 Å
i0	28689800.00
molecular_weight	41807.0 kDa
excluded_volume	52452 Å³
envelope_volume	58768 Å³
shell_volume	23777 Å³
envelope_diameter	72.1 Å
shell_rg	27.36 Å
envelope_rg	20.39 Å
shape_rg	20.18 Å
total_rg	21.14 Å
total_atoms	3583
n_residues	372
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	71.2 Å
rg_real	21.24 Å
rg_real_error	0.39 Å
i0_real	2.8690e+07
i0_real_error	3.5250e+05
rg_reciprocal	21.26 Å
i0_reciprocal	28690000.0000
total_estimate	0.8770
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.205
kurtosis	-0.347
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	7136000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	51.340 Å
length_b	60.660 Å
length_c	60.760 Å
angle_alpha	90.00 °
angle_beta	94.61 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.500 Å
resolution_low	20.000 Å
r_factor	0.1980
r_work	0.1980
r_free	0.2720

description	YM1 SECRETORY PROTEIN
formula_weight	42365.5 kDa
src_method	nat
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	4225

The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

description	2-amino-2-deoxy-beta-D-glucopyranose
formula_weight	179.2 kDa
src_method	man
entity_count	1

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	214

fit	/app/data/saxs_computation/e9/1e9l/1e9l.fit
pddf	/app/data/pr_computation/e9/1e9l/1e9l.pr.out
profile	/app/data/saxs_computation/e9/1e9l/1e9l.dat