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9ukq

Crystal structure of glycogen phosphorylase from Escherichia coli

Method: X-RAY DIFFRACTION Dmax: 224.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycogen phosphorylase

Escherichia coli K12

UniProt P0AC86

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) No other associated polymer 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
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) No other associated polymer 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

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 9UKQ 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 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 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 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 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
9UKR Crystal structure of glycogen phosphorylase from E. coli in complex with AMP 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) 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 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) 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 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) 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9ukq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ukq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ukq
Deposition date deposition_date2025-04-18
Structure title titleCrystal structure of glycogen phosphorylase from Escherichia coli
Keywords keywordsglycogen phosphorylase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier63.82 Å
Radius of gyration Rg (electron density) rg_electron64.26 Å
Forward intensity I(0) i04299650000.00
Molecular weight molecular_weight552030.0 kDa
Excluded volume excluded_volume689940 ų
Envelope volume envelope_volume964260 ų
Hydration-shell volume shell_volume128580 ų
Envelope diameter envelope_diameter237.4 Å
Shell Rg shell_rg62.38 Å
Envelope Rg envelope_rg63.04 Å
Shape Rg shape_rg64.25 Å
Total Rg total_rg64.26 Å
Total atoms total_atoms38963
Residues n_residues4813
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax224.3 Å
Rg (real space) rg_real64.34 Å
Rg uncertainty (real space) rg_real_error3.02 Å
I(0) (real space) i0_real4.3000e+09
I(0) uncertainty (real space) i0_real_error9.1380e+07
Rg (reciprocal space) rg_reciprocal63.35 Å
I(0) (reciprocal space) i0_reciprocal4292000000.0000
Solution quality estimate total_estimate0.8316
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary71.8 Å
Skewness Skewness skewness0.536
Kurtosis Kurtosis kurtosis-0.201
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha317400000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.568
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)