SAXSdb — 9xum

▼

1. Structure Basics

entry_id	9xum
deposition_date	2025-11-24
title	3PGA-bound ADP-Glucose Pyrophosphorylase
keywords	heterotetramer, ADPG, PLANT PROTEIN, amylosynthesis; PLANT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.57 Å
rg_electron	35.61 Å
i0	560197000.00
molecular_weight	193660.0 kDa
excluded_volume	242970 Å³
envelope_volume	310780 Å³
shell_volume	68584 Å³
envelope_diameter	113.3 Å
shell_rg	44.88 Å
envelope_rg	35.45 Å
shape_rg	35.59 Å
total_rg	36.27 Å
total_atoms	13636
n_residues	1748
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	110.6 Å
rg_real	36.28 Å
rg_real_error	0.57 Å
i0_real	5.6020e+08
i0_real_error	7.4520e+06
rg_reciprocal	36.46 Å
i0_reciprocal	560300000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.9 Å
skewness	0.063
kurtosis	-0.522
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	192800000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.928

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
formula_weight	51517.1 kDa
ec_number	2.7.7.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13636

MGSHHHHHHHHGSGSGSGSGSVSDSQNSQTCLDPDASSSVLGIILGGGAGTRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAYASNMGGYKNEGFVEVLAAQQSPENPNWFQGTADAVRQYLWLFEEHNVLEYLILAGDHLYRMDYEKFIQAHRETDADITVAALPMDEQRATAFGLMKIDEEGRIIEFAEKPKGEHLKAMKVDTTILGLDDQRAKEMPFIASMGIYVVSRDVMLDLLRNQFPGANDFGSEVIPGATSLGLRVQAYLYDGYWEDIGTIEAFYNANLGITKKPVPDFSFYDRSAPIYTQPRYLPPSKMLDADVTDSVIGEGCVIKNCKIHHSVVGLRSCISEGAIIEDSLLMGADYYETATEKSLLSAKGSVPIGIGKNSHIKRAIIDKNARIGDNVKIINSDNVQEAARETDGYFIKSGIVTVIKDALIPTGTVI

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 polymer

description	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
formula_weight	52535.2 kDa
ec_number	2.7.7.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MGSWSHPQFEKGSGSGSGSGSSLNSVAGESKVQELETEKRDPRTVASIILGGGAGTRLFPLTKRRAKPAVPIGGAYRLIDVPMSNCINSGINKVYILTQYNSASLNRHLARAYNSNGLGFGDGYVEVLAATQTPGESGKRWFQGTADAVRQFHWLFEDARSKDIEDVLILSGDHLYRMDYMDFIQDHRQSGADISISCIPIDDRRASDFGLMKIDDKGRVISFSEKPKGDDLKAMAVDTTILGLSKEEAEKKPYIASMGVYVFKKEILLNLLRWRFPTANDFGSEIIPFSAKEFYVNAYLFNDYWEDIGTIRSFFEANLALTEHPGAFSFYDAAKPIYTSRRNLPPSKIDNSKLIDSIISHGSFLTNCLIEHSIVGIRSRVGSNVQLKDTVMLGADYYETEAEVAALLAEGNVPIGIGENTKIQECIIDKNARVGKNVIIANSEGIQEADRSSDGFYIRSGITVILKNSVIKDGVVI

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 3 non-polymer

description	3-PHOSPHOGLYCERIC ACID
formula_weight	186.1 kDa
src_method	syn
entity_count	4

▶

6. Citations (1)

▶

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	2.810 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.81 Å
resolution_method	—
num_particles	375402

fit	/app/data/saxs_computation/xu/9xum/9xum.fit
pddf	/app/data/pr_computation/xu/9xum/9xum.pr.out
profile	/app/data/saxs_computation/xu/9xum/9xum.dat

3PGA-bound ADP-Glucose Pyrophosphorylase

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

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)