SAXSdb — 9xum

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 72–520 Chain C； UniProt 72–520	Not recorded	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic × 2 （P55229） 3PG 3-PHOSPHOGLYCERIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.81 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XUK ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 72–520（449 aa） Chain C 72–520（449 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9XUL Pi-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 72–520（449 aa） Chain C 72–520（449 aa）	Not recorded	PO4 PHOSPHATE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9XUR ADPG-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 72–520（449 aa） Chain C 72–520（449 aa）	Not recorded	3PG 3-PHOSPHOGLYCERIC ACID × 4 ADQ ADENOSINE-5'-DIPHOSPHATE-GLUCOSE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9XUS ATP-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 72–520（449 aa） Chain C 72–520（449 aa）	Not recorded	3PG 3-PHOSPHOGLYCERIC ACID × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLGS_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–470； UniProt 72–520 Author chain C； PDBConstruct 22–470； UniProt 72–520

Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic

Arabidopsis thaliana

UniProt P55229

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 67–522 Chain D； UniProt 67–522	Not recorded	Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic × 2 （P55228） 3PG 3-PHOSPHOGLYCERIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.81 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XUK ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 67–522（456 aa） Chain D 67–522（456 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9XUL Pi-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 67–522（456 aa） Chain D 67–522（456 aa）	Not recorded	PO4 PHOSPHATE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9XUR ADPG-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 67–522（456 aa） Chain D 67–522（456 aa）	Not recorded	3PG 3-PHOSPHOGLYCERIC ACID × 4 ADQ ADENOSINE-5'-DIPHOSPHATE-GLUCOSE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9XUS ATP-bound ADP-Glucose Pyrophosphorylase Deposited 2025-11-24	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 67–522（456 aa） Chain D 67–522（456 aa）	Not recorded	3PG 3-PHOSPHOGLYCERIC ACID × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLGL1_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 22–477； UniProt 67–522 Author chain D； PDBConstruct 22–477； UniProt 67–522

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xum
Deposition date deposition_date	2025-11-24
Structure title title	3PGA-bound ADP-Glucose Pyrophosphorylase
Keywords keywords	heterotetramer, ADPG, PLANT PROTEIN, amylosynthesis; PLANT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.57 Å
Radius of gyration Rg (electron density) rg_electron	35.61 Å
Forward intensity I(0) i0	560197000.00
Molecular weight molecular_weight	193660.0 kDa
Excluded volume excluded_volume	242970 Å³
Envelope volume envelope_volume	310780 Å³
Hydration-shell volume shell_volume	68584 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	44.88 Å
Envelope Rg envelope_rg	35.45 Å
Shape Rg shape_rg	35.59 Å
Total Rg total_rg	36.27 Å
Total atoms total_atoms	13636
Residues n_residues	1748
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	110.6 Å
Rg (real space) rg_real	36.28 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	5.6020e+08
I(0) uncertainty (real space) i0_real_error	7.4520e+06
Rg (reciprocal space) rg_reciprocal	36.46 Å
I(0) (reciprocal space) i0_reciprocal	560300000.0000
Solution quality estimate total_estimate	0.8977
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.9 Å
Skewness Skewness skewness	0.063
Kurtosis Kurtosis kurtosis	-0.522
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	192800000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic
Molecular weight formula_weight	51517.1 kDa
EC 编号 ec_number	2.7.7.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	13636

MGSHHHHHHHHGSGSGSGSGSVSDSQNSQTCLDPDASSSVLGIILGGGAGTRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAYASNMGGYKNEGFVEVLAAQQSPENPNWFQGTADAVRQYLWLFEEHNVLEYLILAGDHLYRMDYEKFIQAHRETDADITVAALPMDEQRATAFGLMKIDEEGRIIEFAEKPKGEHLKAMKVDTTILGLDDQRAKEMPFIASMGIYVVSRDVMLDLLRNQFPGANDFGSEVIPGATSLGLRVQAYLYDGYWEDIGTIEAFYNANLGITKKPVPDFSFYDRSAPIYTQPRYLPPSKMLDADVTDSVIGEGCVIKNCKIHHSVVGLRSCISEGAIIEDSLLMGADYYETATEKSLLSAKGSVPIGIGKNSHIKRAIIDKNARIGDNVKIINSDNVQEAARETDGYFIKSGIVTVIKDALIPTGTVI

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic
Molecular weight formula_weight	52535.2 kDa
EC 编号 ec_number	2.7.7.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MGSWSHPQFEKGSGSGSGSGSSLNSVAGESKVQELETEKRDPRTVASIILGGGAGTRLFPLTKRRAKPAVPIGGAYRLIDVPMSNCINSGINKVYILTQYNSASLNRHLARAYNSNGLGFGDGYVEVLAATQTPGESGKRWFQGTADAVRQFHWLFEDARSKDIEDVLILSGDHLYRMDYMDFIQDHRQSGADISISCIPIDDRRASDFGLMKIDDKGRVISFSEKPKGDDLKAMAVDTTILGLSKEEAEKKPYIASMGVYVFKKEILLNLLRWRFPTANDFGSEIIPFSAKEFYVNAYLFNDYWEDIGTIRSFFEANLALTEHPGAFSFYDAAKPIYTSRRNLPPSKIDNSKLIDSIISHGSFLTNCLIEHSIVGIRSRVGSNVQLKDTVMLGADYYETEAEVAALLAEGNVPIGIGENTKIQECIIDKNARVGKNVIIANSEGIQEADRSSDGFYIRSGITVILKNSVIKDGVVI

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	3-PHOSPHOGLYCERIC ACID
Molecular weight formula_weight	186.1 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.81 Å
Resolution测定方法 resolution_method	—
颗粒数 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)