Glycogen phosphorylase tetramer from E. coli in complex with AMP

Method: ELECTRON MICROSCOPY D_max: 128.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vfv
deposition_date	2025-06-11
title	Glycogen phosphorylase tetramer from E. coli in complex with AMP
keywords	glycogen metabolism, cryo-EM, gut bacteria, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	38.62 Å
rg_electron	38.12 Å
i0	509700000.00
molecular_weight	183440.0 kDa
excluded_volume	228960 Å³
envelope_volume	287190 Å³
shell_volume	61824 Å³
envelope_diameter	130.4 Å
shell_rg	44.79 Å
envelope_rg	38.10 Å
shape_rg	38.11 Å
total_rg	38.51 Å
total_atoms	12945
n_residues	1592
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	128.3 Å
rg_real	38.63 Å
rg_real_error	1.11 Å
i0_real	5.0970e+08
i0_real_error	9.5130e+06
rg_reciprocal	38.63 Å
i0_reciprocal	509700000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.8 Å
skewness	0.369
kurtosis	-0.372
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	185200000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.841

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Alpha-1,4 glucan phosphorylase
formula_weight	95552.6 kDa
ec_number	2.4.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12945

MGSSHHHHHHENLYFQGMNAPFTYSSPTLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHNTRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPVRL

Source

organism	Escherichia coli BL21(DE3)
ncbi_taxonomy_id	469008
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.14 Å
resolution_method	—
num_particles	134341

fit	/app/data/saxs_computation/vf/9vfv/9vfv.fit
pddf	/app/data/pr_computation/vf/9vfv/9vfv.pr.out
profile	/app/data/saxs_computation/vf/9vfv/9vfv.dat