Glycogen phosphorylase dimer from E. coli in complex with AMP.

Method: ELECTRON MICROSCOPY D_max: 89.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9upe
deposition_date	2025-04-28
title	Glycogen phosphorylase dimer 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	28.90 Å
rg_electron	27.90 Å
i0	138055000.00
molecular_weight	92341.0 kDa
excluded_volume	115300 Å³
envelope_volume	142320 Å³
shell_volume	41074 Å³
envelope_diameter	98.7 Å
shell_rg	36.57 Å
envelope_rg	28.01 Å
shape_rg	27.91 Å
total_rg	28.70 Å
total_atoms	6516
n_residues	802
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	89.6 Å
rg_real	28.77 Å
rg_real_error	0.62 Å
i0_real	1.3810e+08
i0_real_error	2.1450e+06
rg_reciprocal	28.83 Å
i0_reciprocal	138100000.0000
total_estimate	0.9057
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.9 Å
skewness	0.193
kurtosis	-0.486
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	42780000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.994

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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	92142.9 kDa
ec_number	2.4.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6516

TLSVEALKHSIAYKLMFTIGKDPVVANKHEWLNATLFAVRDRLVERWLRSNRAQLSQETRQVYYLSMEFLIGRTLSNAMLSLGIYEDVQGALEAMGLNLEELIDEENDPGLGNGGLGRLAACFLDSLATLGLPGRGYGIRYDYGMFKQNIVNGSQKESPDYWLEYGNPWEFKRHNTRYKVRFGGRIQQEGKKTRWIETEEILGVAYDQIIPGYDTDATNTLRLWSAQASSEINLGKFNQGDYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSSTIQDILSRHYQLHKTYDNLADKIAIHLNDTHPVLSIPEMMRLLIDEHQFSWDDAFEVCCQVFSYTNHTLMSEALETWPVDMLGKILPRHLQIIFEINDYFLKTLQEQYPNDTDLLGRASIIDESNGRRVRMAWLAVVVSHKVNGVSELHSNLMVQSLFADFAKIFPGRFTNVTNGVTPRRWLAVANPSLSAVLDEHLGRNWRTDLSLLNELQQHCDFPMVNHAVHQAKLENKKRLAEYIAQQLNVVVNPKALFDVQIKRIHEYKRQLMNVLHVITRYNRIKADPDAKWVPRVNIFGGKAASAYYMAKHIIHLINDVAKVINNDPQIGDKLKVVFIPNYSVSLAQLIIPAADLSEQISLAGTEASGTSNMKFALNGALTIGTLDGANVEMLDHVGADNIFIFGNTAEEVEELRRQGYKPREYYEKDEELHQVLTQIGSGVFSPEDPGRYRDLVDSLINFGDHYQVLADYRSYVDCQDKVDELYELQEEWTAKAMLNIANMGYFSSDRTIKEYADHIWHIDPV

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	1

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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	3.72 Å
resolution_method	—
num_particles	126140

fit	/app/data/saxs_computation/up/9upe/9upe.fit
pddf	/app/data/pr_computation/up/9upe/9upe.pr.out
profile	/app/data/saxs_computation/up/9upe/9upe.dat