Glycogen phosphorylase from Segatella copri in complex with AMP

Method: ELECTRON MICROSCOPY D_max: 177.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u3a
deposition_date	2025-03-18
title	Glycogen phosphorylase from Segatella copri 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	65.15 Å
rg_electron	64.52 Å
i0	3394740000.00
molecular_weight	495870.0 kDa
excluded_volume	620210 Å³
envelope_volume	961630 Å³
shell_volume	119820 Å³
envelope_diameter	194.2 Å
shell_rg	73.39 Å
envelope_rg	60.67 Å
shape_rg	64.48 Å
total_rg	64.80 Å
total_atoms	34954
n_residues	4255
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	177.6 Å
rg_real	64.75 Å
rg_real_error	1.08 Å
i0_real	3.3950e+09
i0_real_error	6.5450e+07
rg_reciprocal	65.42 Å
i0_reciprocal	3398000000.0000
total_estimate	0.6179
solution_quality	REASONABLE a REASONABLE solution
n_peaks	0
r_peak_primary	— Å
skewness	-0.042
kurtosis	-0.836
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	97370000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.997; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Alpha-glucan family phosphorylase
formula_weight	98795.9 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	34954

MKIKADYANAPQWKETTIKSSLPKELKCLDEIAHNMWWAWNYEGRDLFKSLDPDLYEKCNANPVLLLERLSYDRKEAIVKDKETMAKVKNVYKMFREYMDVKPNAKRPSVAYFCMEYGINQVVKIYSGGLGMLAGDYLKEASDSNVDMCAVGFLYRYGYFKQSLSMDGQQIANYDAQNFNSLPIERVYDENGNPLVVDVPYTNYQVHAYVWQMNVGRIKLYLLDTDNDMNSEFDRPITYSLYGGDWENRLKQEILLGIGGILTLKKLGIKKEIYHCNEGHAALCNLQRLCDYIEEDGLNFNQALELVRASSLYTVHTPVPAGHDYFDEALFGKYMGGYPQRLGISWDEFIGMGRENADDHNERFCLSTFACNTCQEVNGVSKLHGWVSQQMFSNIWKGYFPEENHVGYVTNGVHFPTWTATEWRKLYDTYFDKNFMNDQSNEEIWHAIYKVSDAEIWNTRMTLKKKLVAYIREKFTQTWLKNQGDPARVVSLLERINPNALMIGFCRRFATYKRAHLLFTDLERLSKIVNDPEHPVLFFFSGKAHPADGAGQGLIKKIFEISQRPEFLGKIIFLEDYDMTLARRLVSGVDIWMNTPTRPLEASGTSGEKAEMNGVVNLSVLDGWWVEGYREGAGWALPEKRTYQNQGYQDQLDAATIYNLLENDIIPMYYNKNKEGFSKEWIQVVKNSIATIAPHYTMKRQLDDYYDKFYNKEAARFKKLSANDNALAKEIALWKESVAERWDGIHVVSKDDCMLMAAETGQKIKVQYVIDEQGLNDAVGLELVVLKEQPEDGKQVYAVYPFKMVGHEGNNFTFEAEIEPINAGSFKTGVRMYPKNDKLPHRQDFCYVKWLN

Source

organism	Segatella copri
ncbi_taxonomy_id	165179
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	8

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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	2.98 Å
resolution_method	—
num_particles	188698

fit	/app/data/saxs_computation/u3/9u3a/9u3a.fit
pddf	/app/data/pr_computation/u3/9u3a/9u3a.pr.out
profile	/app/data/saxs_computation/u3/9u3a/9u3a.dat