SAXSdb — 9ukr

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

Glycogen phosphorylase

Escherichia coli K12

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–815 Chain B； UniProt 1–815 Chain C； UniProt 1–815 Chain D； UniProt 1–815	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–815 Chain F； UniProt 1–815	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

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 9UKR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9S7V Structure of glycogen phosphorylase - dimeric form - from Escherichia coli Deposited 2025-08-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	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 3.10 Å
9S86 Structure of glycogen phosphorylase - tetrameric form - from Escherichia coli Deposited 2025-08-05	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)	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 ligand/ion Different experimental method Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 ligand/ion 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 ligand/ion 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
9V16 Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP Deposited 2025-05-19	Different mutation/modification 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 mutation/modification Different ligand/ion 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 8 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 3–817； UniProt 1–815 Author chain B； PDBConstruct 3–817； UniProt 1–815 Author chain C； PDBConstruct 3–817； UniProt 1–815 Author chain D； PDBConstruct 3–817； UniProt 1–815 Author chain E； PDBConstruct 3–817； UniProt 1–815 Author chain F； PDBConstruct 3–817； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9ukr
Deposition date deposition_date	2025-04-18
Structure title title	Crystal structure of glycogen phosphorylase from E. coli in complex with AMP
Keywords keywords	glycogen phosphorylase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	65.24 Å
Radius of gyration Rg (electron density) rg_electron	65.80 Å
Forward intensity I(0) i0	4378770000.00
Molecular weight molecular_weight	555420.0 kDa
Excluded volume excluded_volume	693250 Å³
Envelope volume envelope_volume	975410 Å³
Hydration-shell volume shell_volume	126870 Å³
Envelope diameter envelope_diameter	232.0 Å
Shell Rg shell_rg	62.82 Å
Envelope Rg envelope_rg	64.98 Å
Shape Rg shape_rg	65.80 Å
Total Rg total_rg	65.76 Å
Total atoms total_atoms	39190
Residues n_residues	4818
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	205.4 Å
Rg (real space) rg_real	65.77 Å
Rg uncertainty (real space) rg_real_error	1.57 Å
I(0) (real space) i0_real	4.3780e+09
I(0) uncertainty (real space) i0_real_error	9.1980e+07
Rg (reciprocal space) rg_reciprocal	64.70 Å
I(0) (reciprocal space) i0_reciprocal	4370000000.0000
Solution quality estimate total_estimate	0.5973
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	68.5 Å
Skewness Skewness skewness	0.507
Kurtosis Kurtosis kurtosis	-0.355
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0005
Highest regularization parameter α highest_alpha	218300000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 0.999; Sysdev: 0.013; Positv: 1.000; Valcen: 0.997; Smooth: 0.037

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Glycogen phosphorylase
Molecular weight formula_weight	93697.7 kDa
EC 编号 ec_number	2.4.1.1
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	39190

MGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHNTRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

来源 Source

来源生物 organism	Escherichia coli K12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	134.915 Å
Unit-cell length b length_b	204.539 Å
Unit-cell length c length_c	263.337 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.550 Å
Low-resolution limit resolution_low	42.790 Å
R factor r_factor	0.2260
R_work r_work	0.2235
R_free r_free	0.2722

fit	/app/data/saxs_computation/uk/9ukr/9ukr.fit
pddf	/app/data/pr_computation/uk/9ukr/9ukr.pr.out
profile	/app/data/saxs_computation/uk/9ukr/9ukr.dat

Crystal structure of glycogen phosphorylase from E. coli in complex with AMP

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)