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9tpe

The structure of the monoclinic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.

Method: X-RAY DIFFRACTION D_max: 84.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tpe
deposition_date	2025-12-17
last_revision	2026-01-21
title	The structure of the monoclinic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.
keywords	Ribosome inactivating protein N-glycosidase, TOXIN; TOXIN
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	25.93 Å
rg_electron	25.12 Å
i0	55847500.00
molecular_weight	57025.0 kDa
excluded_volume	70831 Å³
envelope_volume	84103 Å³
shell_volume	28491 Å³
envelope_diameter	86.6 Å
shell_rg	31.90 Å
envelope_rg	25.18 Å
shape_rg	25.11 Å
total_rg	25.85 Å
total_atoms	4013
n_residues	502
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	84.9 Å
rg_real	25.97 Å
rg_real_error	0.56 Å
i0_real	5.5850e+07
i0_real_error	7.6170e+05
rg_reciprocal	25.96 Å
i0_reciprocal	55850000.0000
total_estimate	0.8876
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.8 Å
skewness	0.407
kurtosis	-0.308
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	10990000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	N-glycosidase
formula_weight	26787.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4905

AKIHYKNSANPNITAYTQFITALRDRLSSGSHVHDFPQLRQPSNLPVANRFILVDLENGAGHTITVPIDVFNAYVVGYLVGDTFDYFTDAPPEALDIFPSATSRSLGFGGNYGNLGSRETQELGHAALNDAIDALFYSYSQRTSFLVIIQMVSEAARIRYIEHLVRRSMISNANFLPDPRALSLENSWDPLSTQIQLSGSRGVFIRPVWIQNISYQVVIINNVEEVLRGAALALLLFRCTA

Entity 2 polymer

description	Lectin
formula_weight	28893.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SCPSSETVTRSIIGRDQLCVDVRDGQNNDGNPIQLWQCTQQQNQRWTFKDDGTIRSLGKCLTTYGYSAGAYIMIYDCDSAVPDATVWALSNNGTIINPRSGLALTAENSSPGTTLTVETDINASRQAWTVGEYTQPAIVSYISGFREMCLQANDDDVLVWLESCEIGQQKQQWALYSDSTIRVFSDPSLCVTSSGHSSSDIIGILKCQGWGNQRWLFRADGTILNPNARLVMDVRGSDVSMREIILYEPTGNPNQQWLAYS

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	alpha-L-fucopyranose
formula_weight	164.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	807

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6. Citations (1)

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length_a	46.738 Å
length_b	94.215 Å
length_c	70.876 Å
angle_alpha	90.00 °
angle_beta	96.44 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.500 Å
resolution_low	29.711 Å
r_factor	—
r_work	0.1608
r_free	0.2065

fit	/app/data/saxs_computation/tp/9tpe/9tpe.fit
pddf	/app/data/pr_computation/tp/9tpe/9tpe.pr.out
profile	/app/data/saxs_computation/tp/9tpe/9tpe.dat

The structure of the monoclinic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.

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 (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)