SAXSdb — 9xur

▼

1. Structure Basics

entry_id	9xur
deposition_date	2025-11-24
title	ADPG-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	36.18 Å
rg_electron	35.30 Å
i0	591969000.00
molecular_weight	197280.0 kDa
excluded_volume	246640 Å³
envelope_volume	305440 Å³
shell_volume	67745 Å³
envelope_diameter	111.5 Å
shell_rg	44.62 Å
envelope_rg	35.31 Å
shape_rg	35.27 Å
total_rg	35.94 Å
total_atoms	13872
n_residues	1758
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	107.7 Å
rg_real	35.90 Å
rg_real_error	0.66 Å
i0_real	5.9200e+08
i0_real_error	9.9870e+06
rg_reciprocal	36.07 Å
i0_reciprocal	592100000.0000
total_estimate	0.8971
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.0 Å
skewness	0.067
kurtosis	-0.540
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	235800000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.860

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

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	13872

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

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE
formula_weight	589.3 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 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	2.490 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.49 Å
resolution_method	—
num_particles	1285715

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

ADPG-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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)