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9uaj

Ovorubin from the golden apple snail (Pomacea canaliculata)

Method: ELECTRON MICROSCOPY D_max: 113.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uaj
deposition_date	2025-04-01
title	Ovorubin from the golden apple snail (Pomacea canaliculata)
keywords	ovorubin, golden apple snail, Pomacea canaliculata, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
method	ELECTRON MICROSCOPY

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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	37.39 Å
rg_electron	36.52 Å
i0	1265820000.00
molecular_weight	196200.0 kDa
excluded_volume	190950 Å³
envelope_volume	339420 Å³
shell_volume	73005 Å³
envelope_diameter	114.1 Å
shell_rg	46.28 Å
envelope_rg	35.89 Å
shape_rg	36.50 Å
total_rg	36.97 Å
total_atoms	14889
n_residues	1817
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	113.3 Å
rg_real	37.09 Å
rg_real_error	0.53 Å
i0_real	1.2660e+09
i0_real_error	1.8440e+07
rg_reciprocal	37.28 Å
i0_reciprocal	1266000000.0000
total_estimate	0.8251
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.5 Å
skewness	0.082
kurtosis	-0.521
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	168300000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	PcOvo5
formula_weight	22841.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,F
atom_count	15208

MLVATLTLVALSAVFTNVYGSDQYTILDVYKASNVSVEDYKDLLKDLDVVHSFKVLGSSRVIFVVKMREDSYEKLSKINLPGDVYSIPAGDLSDKMQSVGVEWKRWDDLPDANLTLFERTLELKGEPLEGLASHMKAFGEKVSHVMELYPNKGFYLLGRTPPKAFVIVSLPFRCRQVRYGSDFALNYLNGPGDSSTKVEFVAKA

Entity 2 polymer

description	PcOvo3s
formula_weight	22252.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,J

MYALAIALLAFSTFVSNAFANKEYLLLDIRDATTSEIISALRDVEIELKVKAKGIARHLIVVKQNDANLQKLGEIDIPGRSCSTPVEDLDNLMEDIGISWPRNELTNVNVTLFERTLDLKDKTMEQFWSEAKAYGQLVKPVLSSFTYRAFKANGAYPPKVYFFVNLPRENLNDASSKGIDIFGGPGKARTTVQYVTKLS

Entity 3 polymer

description	Perivitellin ovorubin-1
formula_weight	22408.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,I

MFVATSLLLAIATLVVRASPHNYLIMDIEPPKSVSERDILNLLSPLQVKHSFRVTGSTRLLIVIRLDAQSYEKLDEITVPGKVEVIPAVNMADTMERCGVSWPRVELTDDNVTLFESESTLTDVTKEQLKAMLIGYGEHMSGLLQAHRFEYYQAAGATPHRHFVFVNSVPDEIEVFGREGVDIWGGPGEFVVKPQYVTRI

Entity 4 polymer

description	Perivitellin protein
formula_weight	22467.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MTAILALLLAMSILLPSGAVEDVQDLVFAEWDKGSSHEHACSALRNSSVIEKGLTVKEVGTSKFAAVLSEPILARLKFHGLVEAVPVVEVGTVMKRLNVSIPPAQDISDNNLTLIKMSPKLKGQTLQQIDAELRYLGEYMNTVLQKCSHRVYISKGTFPPKIYVFLNMPLDQIRQFYPSLDIFGGPSSTKNEISYVQILILRN

Entity 5 polymer

description	Perivitellin ovorubin-2
formula_weight	23827.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,G

MAEHRIPVLLLLVVVAASSLAQQIPLQKHYIIYEVRNIEKTPEEVKEEMKDTDILYSFKALGAPSYHIVVEVNPRNMRKLEEVELKGKIRMVPVVNMVDVAETLGVSWPRSGARLLDVNLTLIERTLNQEGLTSQESEAHLKGFMEELKDRLQQYNYQAFFTIGASPPKMYIYINIPYEEVDKFACIGINQFGGPAAVNTTVSFISSFPK

Entity 6 branched

description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	4

Entity 7 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	6

Entity 8 non-polymer

description	(Z)-docos-13-enoic acid
formula_weight	338.6 kDa
src_method	syn
entity_count	4

Entity 9 non-polymer

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

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	319

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.12 Å
resolution_method	—
num_particles	336633

fit	/app/data/saxs_computation/ua/9uaj/9uaj.fit
pddf	/app/data/pr_computation/ua/9uaj/9uaj.pr.out
profile	/app/data/saxs_computation/ua/9uaj/9uaj.dat

Ovorubin from the golden apple snail (Pomacea canaliculata)

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

EM 3D

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 branched

Entity 7 branched

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)