SAXSdb — 9v16

▼

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

Glycogen phosphorylase

Escherichia coli K-12

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	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

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 9V16	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 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 × 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 mutation/modification 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 construct Different mutation/modification 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 mutation/modification 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 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）	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 construct Different mutation/modification 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
9UKR Crystal structure of glycogen phosphorylase from E. coli in complex with AMP Deposited 2025-04-18	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）	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 construct Different mutation/modification 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
9V17 Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant Deposited 2025-05-19	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 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 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

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	9v16
Deposition date deposition_date	2025-05-19
Structure title title	Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant in complex with AMP
Keywords keywords	glycogen phosphorylase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	48.62 Å
Radius of gyration Rg (electron density) rg_electron	47.81 Å
Forward intensity I(0) i0	1924080000.00
Molecular weight molecular_weight	365240.0 kDa
Excluded volume excluded_volume	456200 Å³
Envelope volume envelope_volume	613950 Å³
Hydration-shell volume shell_volume	101860 Å³
Envelope diameter envelope_diameter	156.8 Å
Shell Rg shell_rg	56.95 Å
Envelope Rg envelope_rg	46.27 Å
Shape Rg shape_rg	47.80 Å
Total Rg total_rg	48.15 Å
Total atoms total_atoms	25769
Residues n_residues	3171
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	151.7 Å
Rg (real space) rg_real	48.23 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.9240e+09
I(0) uncertainty (real space) i0_real_error	3.2700e+07
Rg (reciprocal space) rg_reciprocal	48.62 Å
I(0) (reciprocal space) i0_reciprocal	1925000000.0000
Solution quality estimate total_estimate	0.8929
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.3 Å
Skewness Skewness skewness	0.024
Kurtosis Kurtosis kurtosis	-0.600
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	287100000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.897

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Glycogen phosphorylase
Molecular weight formula_weight	93626.6 kDa
EC 编号 ec_number	2.4.1.1
Mutation mutation	N185A/R267E
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25769

MGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHATRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSEVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	4

▶

8. Citations (1)

▶

Unit-cell length a length_a	185.604 Å
Unit-cell length b length_b	185.604 Å
Unit-cell length c length_c	451.242 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	3.450 Å
Low-resolution limit resolution_low	49.450 Å
R factor r_factor	0.1942
R_work r_work	0.1921
R_free r_free	0.2351

fit	/app/data/saxs_computation/v1/9v16/9v16.fit
pddf	/app/data/pr_computation/v1/9v16/9v16.pr.out
profile	/app/data/saxs_computation/v1/9v16/9v16.dat

Crystal structure of E. coli glycogen phosphorylase N185A/R267E mutant 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)