SAXSdb — 9s7v

▼

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

Glycogen phosphorylase

Escherichia coli

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–815 Chain B； UniProt 1–815	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9S7V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9S86 Structure of glycogen phosphorylase - tetrameric form - from Escherichia coli Deposited 2025-08-05	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9S8B Structure of glycogen phosphorylase - dimeric form - in complex with HPr from Escherichia coli Deposited 2025-08-05	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å
9S8K Structure of glycogen phosphorylase - tetrameric form - in complex with HPr from Escherichia coli Deposited 2025-08-05	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.06 Å
9UKQ Crystal structure of glycogen phosphorylase from Escherichia coli Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Protein conc: 10.4mg/mL; 0.1M MES pH 6.0, 9% (v/v) PEG 3350	Resolution 3.50 Å R-free 0.273
9UKQ Crystal structure of glycogen phosphorylase from Escherichia coli Deposited 2025-04-18	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–815（815 aa） Chain F 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Protein conc: 10.4mg/mL; 0.1M MES pH 6.0, 9% (v/v) PEG 3350	Resolution 3.50 Å R-free 0.273
9UKR Crystal structure of glycogen phosphorylase from E. coli in complex with AMP Deposited 2025-04-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	AMP ADENOSINE MONOPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Protein conc: 10.4mg/mL; Reservoir: 0.1M MES pH 6.0, 9% (v/v) PEG 3350	Resolution 3.55 Å R-free 0.272
9UKR Crystal structure of glycogen phosphorylase from E. coli in complex with AMP Deposited 2025-04-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–815（815 aa） Chain F 1–815（815 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	AMP ADENOSINE MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Protein conc: 10.4mg/mL; Reservoir: 0.1M MES pH 6.0, 9% (v/v) PEG 3350	Resolution 3.55 Å R-free 0.272
9V16 Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP Deposited 2025-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF)	AMP ADENOSINE MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% v/v 1,4-dioxane, 0.1M Tris pH 8.0, 15% w/v polyethylene glycol 3350 (The crystal was soaked in a solution supplemented with 40 mM AMP before data collection)	Resolution 3.45 Å R-free 0.235
9V17 Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant Deposited 2025-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–815（815 aa） Chain B 1–815（815 aa） Chain C 1–815（815 aa） Chain D 1–815（815 aa）	Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：N185A/R267E Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% v/v 1,4-dioxane, 0.1M Tris pH 8.0, 15% w/v polyethylene glycol 3350	Resolution 3.70 Å R-free 0.229

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHSG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–832； UniProt 1–815 Author chain B； PDBConstruct 18–832； UniProt 1–815

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9s7v
Deposition date deposition_date	2025-08-05
Structure title title	Structure of glycogen phosphorylase - dimeric form - from Escherichia coli
Keywords keywords	Glycogen phosphorylase, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.65 Å
Radius of gyration Rg (electron density) rg_electron	37.20 Å
Forward intensity I(0) i0	415269000.00
Molecular weight molecular_weight	166990.0 kDa
Excluded volume excluded_volume	209170 Å³
Envelope volume envelope_volume	263390 Å³
Hydration-shell volume shell_volume	58385 Å³
Envelope diameter envelope_diameter	128.4 Å
Shell Rg shell_rg	43.76 Å
Envelope Rg envelope_rg	37.02 Å
Shape Rg shape_rg	37.21 Å
Total Rg total_rg	37.59 Å
Total atoms total_atoms	22738
Residues n_residues	1591
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

▼

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

Maximum dimension Dmax dmax	126.2 Å
Rg (real space) rg_real	37.65 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	4.1530e+08
I(0) uncertainty (real space) i0_real_error	7.3000e+06
Rg (reciprocal space) rg_reciprocal	37.65 Å
I(0) (reciprocal space) i0_reciprocal	415300000.0000
Solution quality estimate total_estimate	0.8837
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.1 Å
Skewness Skewness skewness	0.355
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	161400000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.930

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

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

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	260408

Description description	Glycogen phosphorylase
Molecular weight formula_weight	95536.6 kDa
EC 编号 ec_number	2.4.1.1
Source method src_method	man
Copy count entity_count	2

Structure of glycogen phosphorylase - dimeric form - from Escherichia coli

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

Glycogen phosphorylase

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	22738

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/s7/9s7v/9s7v.fit
pddf	/app/data/pr_computation/s7/9s7v/9s7v.pr.out
profile	/app/data/saxs_computation/s7/9s7v/9s7v.dat