← Back to search

9x2o

X-ray structure of antiviral protein from Mirabilis jalapa

Method: X-RAY DIFFRACTION D_max: 95.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9x2o
deposition_date	2025-10-07
title	X-ray structure of antiviral protein from Mirabilis jalapa
keywords	Plant Toxin, RNA N-glycosidase, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.59 Å
rg_electron	30.25 Å
i0	192140000.00
molecular_weight	113080.0 kDa
excluded_volume	142710 Å³
envelope_volume	173090 Å³
shell_volume	45883 Å³
envelope_diameter	99.6 Å
shell_rg	38.72 Å
envelope_rg	30.40 Å
shape_rg	30.22 Å
total_rg	31.09 Å
total_atoms	7945
n_residues	1004
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

▼

3. P(r) Analysis (GNOM)

dmax	95.5 Å
rg_real	31.38 Å
rg_real_error	0.48 Å
i0_real	1.9210e+08
i0_real_error	2.6430e+06
rg_reciprocal	31.47 Å
i0_reciprocal	192200000.0000
total_estimate	0.9061
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.1 Å
skewness	0.115
kurtosis	-0.569
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	39640000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.923

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Antiviral protein MAP
formula_weight	28662.7 kDa
ec_number	3.2.2.22
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8723

APTLETIASLDLNNPTTYLSFITNIRTKVADKTEQCTIQKISKTFTQRYSYIDLIVSSTQKITLAIDMADLYVLGYSDIANNKGRAFFFKDVTEAVANNFFPGATGTNRIKLTFTGSYGDLEKNGGLRKDNPLGIFRLENSIVNIYGKAGDVKKQAKFFLLAIQMVSQAAQFKYISDKIPSEKYEEVTVDEYMTALENNWAKLSTAVYNSKPSTTTATKCQLATSPVTISPWIFKTVEEIKLVMGLLKSSHHHHHH

Source

organism	Mirabilis jalapa
common_name	;garden four-o'clock ;
ncbi_taxonomy_id	3538
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	13

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	778

▶

6. Citations (1)

▶

length_a	214.312 Å
length_b	60.645 Å
length_c	79.254 Å
angle_alpha	90.00 °
angle_beta	109.02 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.100 Å
resolution_low	43.970 Å
r_factor	0.1928
r_work	0.1901
r_free	0.2457

fit	/app/data/saxs_computation/x2/9x2o/9x2o.fit
pddf	/app/data/pr_computation/x2/9x2o/9x2o.pr.out
profile	/app/data/saxs_computation/x2/9x2o/9x2o.dat

X-ray structure of antiviral protein from Mirabilis jalapa

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