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9t4q

Structure of the SUN4 domain of SIM1 from Saccharomyces cerevisiae

Method: X-RAY DIFFRACTION D_max: 62.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t4q
deposition_date	2025-10-30
title	Structure of the SUN4 domain of SIM1 from Saccharomyces cerevisiae
keywords	cell wall, carbohydrate-binding, thaumatin, CARBOHYDRATE; CARBOHYDRATE
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	19.36 Å
rg_electron	18.20 Å
i0	17672100.00
molecular_weight	30221.0 kDa
excluded_volume	37027 Å³
envelope_volume	42587 Å³
shell_volume	19362 Å³
envelope_diameter	62.4 Å
shell_rg	24.67 Å
envelope_rg	18.47 Å
shape_rg	18.19 Å
total_rg	19.12 Å
total_atoms	4059
n_residues	287
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	62.7 Å
rg_real	19.24 Å
rg_real_error	0.37 Å
i0_real	1.7670e+07
i0_real_error	2.0660e+05
rg_reciprocal	19.26 Å
i0_reciprocal	17670000.0000
total_estimate	0.8856
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.7 Å
skewness	0.198
kurtosis	-0.356
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	3648000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.959

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Probable secreted beta-glucosidase SIM1
formula_weight	31120.9 kDa
ec_number	3.2.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4708

MGSSHHHHHHSSGLVPRGSHMGSIYGDLADFSGPSEKFQDGTIPCDKFPSGQGVISIDWIGEGGWSGVENTDTSTGGSCKEGSYCSYSCQPGMSKTQWPSDQPSDGRSVGGLLCKNGYLYRSNTDADYLCEWGVEAAYVVSKLSKGVAICRTDYPGTENMVIPTYVEGGSSLPLTVVDQDTYFTWEGKKTSAQYYVNNAGVSVEDGCIWGTSGSGIGNWAPLNFGAGSTGGVTYLSLIPNPNNSDALNYNVKIVAADDSSNVIGECVYENGEFSGGADGCTVSVTSGKAHFVLYN

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	406

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6. Citations (1)

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length_a	41.037 Å
length_b	78.639 Å
length_c	80.195 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.230 Å
resolution_low	24.920 Å
r_factor	0.1454
r_work	0.1443
r_free	0.1659

fit	/app/data/saxs_computation/t4/9t4q/9t4q.fit
pddf	/app/data/pr_computation/t4/9t4q/9t4q.pr.out
profile	/app/data/saxs_computation/t4/9t4q/9t4q.dat

Structure of the SUN4 domain of SIM1 from Saccharomyces cerevisiae

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