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9tpf

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

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tpf
deposition_date	2025-12-18
last_revision	2026-01-21
title	The structure of the orthorhombic 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	25.98 Å
rg_electron	25.15 Å
i0	57418100.00
molecular_weight	57536.0 kDa
excluded_volume	71319 Å³
envelope_volume	85448 Å³
shell_volume	28834 Å³
envelope_diameter	87.0 Å
shell_rg	32.07 Å
envelope_rg	25.19 Å
shape_rg	25.14 Å
total_rg	25.90 Å
total_atoms	4037
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	84.4 Å
rg_real	26.00 Å
rg_real_error	0.56 Å
i0_real	5.7420e+07
i0_real_error	7.6760e+05
rg_reciprocal	26.00 Å
i0_reciprocal	57420000.0000
total_estimate	0.8910
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.394
kurtosis	-0.322
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	12190000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

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	4739

AKIHYKNSANPNITAYTQFITALRDRLSSGSHVHDFPQLRQPSNLPVANRFILVDLENGAGHTITVPIDVFNAYVVGYLVGDTFDYFTDAPPEALDIFPSATSRSLGFGGNYGNLGSRETQELGHAALNDAIDALFYSYSQRTSFLVIIQMVSEAARIRYIEHLVRRSMISNANFLPDPRALSLENSWDPLSTQIQLSGSRGVFIRPVWIQNISYQVVIINNVEEVLRGAALALLLFRCTA

Entity 2 polymer

description	Lectin
formula_weight	28964.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ASCPSSETVTRSIIGRDQLCVDVRDGQNNDGNPIQLWQCTQQQNQRWTFKDDGTIRSLGKCLTTYGYSAGAYIMIYDCDSAVPDATVWALSNNGTIINPRSGLALTAENSSPGTTLTVETDINASRQAWTVGEYTQPAIVSYISGFREMCLQANDDDVLVWLESCEIGQQKQQWALYSDSTIRVFSDPSLCVTSSGHSSSDIIGILKCQGWGNQRWLFRADGTILNPNARLVMDVRGSDVSMREIILYEPTGNPNQQWLAYS

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

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

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	1-deoxy-alpha-D-mannopyranose
formula_weight	164.2 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	680

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6. Citations (1)

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length_a	80.589 Å
length_b	95.470 Å
length_c	96.339 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	—

resolution	1.800 Å
resolution_low	47.735 Å
r_factor	—
r_work	0.1823
r_free	0.2333

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

The structure of the orthorhombic 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 (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)